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ARN
Architecture et réactivité de l'ARN
Publications
2024
S. Prabhu, V.N. Pillai, L.Z. Ali, V. Vivet-Boudou, A. Chemeettachal, S. Bernacchi, F. Mustafa, R. Marquet, T.A. Rizvi
MMTV RNA packaging requires an extended long-range interaction for productive Gag binding to packaging signals Article de journal
Dans: PLOS BIOLOGY, vol. 22, p. e3002827, 2024.
Résumé | Liens | BibTeX | Étiquettes: bernacchi, MARQUET, Unité ARN, vivet-boudou
@article{nokey,
title = {MMTV RNA packaging requires an extended long-range interaction for productive Gag binding to packaging signals},
author = {Prabhu S. AND Pillai V.N. AND Ali L.Z. AND Vivet-Boudou V. AND Chemeettachal A. AND Bernacchi S. AND Mustafa F. AND Marquet R. AND Rizvi T.A.},
editor = {PLOS},
url = {https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002827},
doi = {10.1371/journal. pbio.3002827},
year = {2024},
date = {2024-10-04},
urldate = {2024-10-04},
journal = {PLOS BIOLOGY},
volume = {22},
pages = {e3002827},
abstract = {The packaging of genomic RNA (gRNA) into retroviral particles relies on the specific recognition
by the Gag precursor of packaging signals (Psi), which maintain a complex secondary
structure through long-range interactions (LRIs). However, it remains unclear whether the
binding of Gag to Psi alone is enough to promote RNA packaging and what role LRIs play in
this process. Using mouse mammary tumor virus (MMTV), we investigated the effects of
mutations in 4 proposed LRIs on gRNA structure and function. Our findings revealed the
presence of an unsuspected extended LRI, and hSHAPE revealed that maintaining a wildtype–
like Psi structure is crucial for efficient packaging. Surprisingly, filter-binding assays
demonstrated that most mutants, regardless of their packaging capability, exhibited significant
binding to Pr77Gag, suggesting that Gag binding to Psi is insufficient for efficient packaging.
Footprinting experiments indicated that efficient RNA packaging is promoted when
Pr77Gag binds to 2 specific sites within Psi, whereas binding elsewhere in Psi does not lead
to efficient packaging. Taken together, our results suggest that the 3D structure of the Psi/
Pr77Gag complex regulates the assembly of viral particles around gRNA, enabling effective
discrimination against other viral and cellular RNAs that may also bind Gag efficiently},
keywords = {bernacchi, MARQUET, Unité ARN, vivet-boudou},
pubstate = {published},
tppubtype = {article}
}
The packaging of genomic RNA (gRNA) into retroviral particles relies on the specific recognition
by the Gag precursor of packaging signals (Psi), which maintain a complex secondary
structure through long-range interactions (LRIs). However, it remains unclear whether the
binding of Gag to Psi alone is enough to promote RNA packaging and what role LRIs play in
this process. Using mouse mammary tumor virus (MMTV), we investigated the effects of
mutations in 4 proposed LRIs on gRNA structure and function. Our findings revealed the
presence of an unsuspected extended LRI, and hSHAPE revealed that maintaining a wildtype–
like Psi structure is crucial for efficient packaging. Surprisingly, filter-binding assays
demonstrated that most mutants, regardless of their packaging capability, exhibited significant
binding to Pr77Gag, suggesting that Gag binding to Psi is insufficient for efficient packaging.
Footprinting experiments indicated that efficient RNA packaging is promoted when
Pr77Gag binds to 2 specific sites within Psi, whereas binding elsewhere in Psi does not lead
to efficient packaging. Taken together, our results suggest that the 3D structure of the Psi/
Pr77Gag complex regulates the assembly of viral particles around gRNA, enabling effective
discrimination against other viral and cellular RNAs that may also bind Gag efficiently
by the Gag precursor of packaging signals (Psi), which maintain a complex secondary
structure through long-range interactions (LRIs). However, it remains unclear whether the
binding of Gag to Psi alone is enough to promote RNA packaging and what role LRIs play in
this process. Using mouse mammary tumor virus (MMTV), we investigated the effects of
mutations in 4 proposed LRIs on gRNA structure and function. Our findings revealed the
presence of an unsuspected extended LRI, and hSHAPE revealed that maintaining a wildtype–
like Psi structure is crucial for efficient packaging. Surprisingly, filter-binding assays
demonstrated that most mutants, regardless of their packaging capability, exhibited significant
binding to Pr77Gag, suggesting that Gag binding to Psi is insufficient for efficient packaging.
Footprinting experiments indicated that efficient RNA packaging is promoted when
Pr77Gag binds to 2 specific sites within Psi, whereas binding elsewhere in Psi does not lead
to efficient packaging. Taken together, our results suggest that the 3D structure of the Psi/
Pr77Gag complex regulates the assembly of viral particles around gRNA, enabling effective
discrimination against other viral and cellular RNAs that may also bind Gag efficiently
Zoladek J., Kazzi P. El, Caval V., Vivet-Boudou V., Cannac M., Davies E., Rossi S., Bribes I., Rouilly L., Simonin Y., Jouvenet N., Decroly E., Paillart J. -C., Wilson S. J., Nisole S.
A specific domain within the 3' untranslated region of Usutu virus confers resistance to the exonuclease ISG20 Article de journal
Dans: Nature Communications, vol. 15, p. 8528 , 2024.
Résumé | Liens | BibTeX | Étiquettes: PAILLART, Unité ARN, vivet-boudou
@article{nokey,
title = {A specific domain within the 3' untranslated region of Usutu virus confers resistance to the exonuclease ISG20},
author = {J. Zoladek AND P. El Kazzi AND V. Caval AND V. Vivet-Boudou AND M. Cannac AND E. Davies AND S. Rossi AND I. Bribes AND L. Rouilly AND Y. Simonin AND N. Jouvenet AND E. Decroly AND J.-C. Paillart AND S. J. Wilson AND S. Nisole},
editor = {NPG},
doi = {10.1038/s41467-024-52870-w},
year = {2024},
date = {2024-10-02},
urldate = {2024-10-02},
journal = {Nature Communications},
volume = {15},
pages = {8528 },
abstract = {Usutu virus (USUV) and West Nile virus (WNV) are two closely related emergingmosquito-borneflaviviruses. Their natural hosts are wild birds, but they canalso cause severe neurological disorders in humans. Both viruses are efficientlysuppressed by type I interferon (IFN), which interferes with viral replication,dissemination, pathogenesis and transmission. Here, we show that the repli-cation of USUV and WNV are inhibited through a common set of IFN–inducedgenes (ISGs), with the notable exception of ISG20, which USUV is resistant to.Strikingly, USUV was the only virus among all the other tested mosquito-borneflaviviruses that demonstrated resistance to the 3′–5′exonuclease activity ofISG20. Ourfindings highlight that the intrinsic resistance of the USUV genome,irrespective of the presence of cellular or viral proteins or protective post-transcriptional modifications, relies on a uniquesequence present in its3′untranslated region. Importantly,this genomic region alone can conferISG20 resistance to a susceptibleflavivirus, without compromising its infec-tivity, suggesting that it could be acquired by otherflaviviruses. This studyprovides new insights into the strategy employed by emergingflaviviruses toovercome host defense mechanisms.},
keywords = {PAILLART, Unité ARN, vivet-boudou},
pubstate = {published},
tppubtype = {article}
}
Usutu virus (USUV) and West Nile virus (WNV) are two closely related emergingmosquito-borneflaviviruses. Their natural hosts are wild birds, but they canalso cause severe neurological disorders in humans. Both viruses are efficientlysuppressed by type I interferon (IFN), which interferes with viral replication,dissemination, pathogenesis and transmission. Here, we show that the repli-cation of USUV and WNV are inhibited through a common set of IFN–inducedgenes (ISGs), with the notable exception of ISG20, which USUV is resistant to.Strikingly, USUV was the only virus among all the other tested mosquito-borneflaviviruses that demonstrated resistance to the 3′–5′exonuclease activity ofISG20. Ourfindings highlight that the intrinsic resistance of the USUV genome,irrespective of the presence of cellular or viral proteins or protective post-transcriptional modifications, relies on a uniquesequence present in its3′untranslated region. Importantly,this genomic region alone can conferISG20 resistance to a susceptibleflavivirus, without compromising its infec-tivity, suggesting that it could be acquired by otherflaviviruses. This studyprovides new insights into the strategy employed by emergingflaviviruses toovercome host defense mechanisms.
Gomes Marina Vitoria, Landwerlin Pauline, Diebold-Durand Marie-Laure, Shaik Tajith B, Durand Alexandre, Troesch Edouard, Weber Chantal, Brillet Karl, Lemée Marianne Victoria, Decroos Christophe, Dulac Ludivine, Antony Pierre, Watrin Erwan, Ennifar Eric, Golzio Christelle, Romier Christophe
The cohesin ATPase cycle is mediated by specific conformational dynamics and interface plasticity of SMC1A and SMC3 ATPase domains Article de journal
Dans: Cell Rep, vol. 43, no. 9, p. 114656, 2024, ISSN: 2211-1247.
Résumé | Liens | BibTeX | Étiquettes: ENNIFAR, Unité ARN
@article{pmid39240714,
title = {The cohesin ATPase cycle is mediated by specific conformational dynamics and interface plasticity of SMC1A and SMC3 ATPase domains},
author = {Marina Vitoria Gomes and Pauline Landwerlin and Marie-Laure Diebold-Durand and Tajith B Shaik and Alexandre Durand and Edouard Troesch and Chantal Weber and Karl Brillet and Marianne Victoria Lemée and Christophe Decroos and Ludivine Dulac and Pierre Antony and Erwan Watrin and Eric Ennifar and Christelle Golzio and Christophe Romier},
doi = {10.1016/j.celrep.2024.114656},
issn = {2211-1247},
year = {2024},
date = {2024-09-01},
urldate = {2024-09-01},
journal = {Cell Rep},
volume = {43},
number = {9},
pages = {114656},
abstract = {Cohesin is key to eukaryotic genome organization and acts throughout the cell cycle in an ATP-dependent manner. The mechanisms underlying cohesin ATPase activity are poorly understood. Here, we characterize distinct steps of the human cohesin ATPase cycle and show that the SMC1A and SMC3 ATPase domains undergo specific but concerted structural rearrangements along this cycle. Specifically, whereas the proximal coiled coil of the SMC1A ATPase domain remains conformationally stable, that of the SMC3 displays an intrinsic flexibility. The ATP-dependent formation of the heterodimeric SMC1A/SMC3 ATPase module (engaged state) favors this flexibility, which is counteracted by NIPBL and DNA binding (clamped state). Opening of the SMC3/RAD21 interface (open-engaged state) stiffens the SMC3 proximal coiled coil, thus constricting together with that of SMC1A the ATPase module DNA-binding chamber. The plasticity of the ATP-dependent interface between the SMC1A and SMC3 ATPase domains enables these structural rearrangements while keeping the ATP gate shut. VIDEO ABSTRACT.},
keywords = {ENNIFAR, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Cohesin is key to eukaryotic genome organization and acts throughout the cell cycle in an ATP-dependent manner. The mechanisms underlying cohesin ATPase activity are poorly understood. Here, we characterize distinct steps of the human cohesin ATPase cycle and show that the SMC1A and SMC3 ATPase domains undergo specific but concerted structural rearrangements along this cycle. Specifically, whereas the proximal coiled coil of the SMC1A ATPase domain remains conformationally stable, that of the SMC3 displays an intrinsic flexibility. The ATP-dependent formation of the heterodimeric SMC1A/SMC3 ATPase module (engaged state) favors this flexibility, which is counteracted by NIPBL and DNA binding (clamped state). Opening of the SMC3/RAD21 interface (open-engaged state) stiffens the SMC3 proximal coiled coil, thus constricting together with that of SMC1A the ATPase module DNA-binding chamber. The plasticity of the ATP-dependent interface between the SMC1A and SMC3 ATPase domains enables these structural rearrangements while keeping the ATP gate shut. VIDEO ABSTRACT.
Gaucherand Léa, Baldaccini Morgane, Pfeffer Sébastien
Dans: Bioessays, p. e2400173, 2024, ISSN: 1521-1878.
Résumé | Liens | BibTeX | Étiquettes: PFEFFER, Unité ARN
@article{pmid39248656,
title = {Beyond RNAi: How the Dicer protein modulates the antiviral innate immune response in mammalian cells: Mammalian Dicer could regulate the innate immune response in an RNAi-independent manner as a result of losing long dsRNA processive activity},
author = {Léa Gaucherand and Morgane Baldaccini and Sébastien Pfeffer},
doi = {10.1002/bies.202400173},
issn = {1521-1878},
year = {2024},
date = {2024-09-01},
urldate = {2024-09-01},
journal = {Bioessays},
pages = {e2400173},
abstract = {While Dicer plays an important antiviral role through the RNAi pathway in plants and invertebrates, its contribution to antiviral immunity in vertebrates and more specifically mammals is more controversial. The apparent limited RNAi activity in mammalian cells has been attributed to the reduced long dsRNA processive activity of mammalian Dicer, as well as a functional incompatibility between the RNAi and IFN pathways. Why Dicer has lost this antiviral activity in the profit of the IFN pathway is still unclear. We propose that the primary direct antiviral activity of Dicer has been functionally replaced by other sensors in the IFN pathway, leading to its specialization toward microRNA maturation. As a result, Dicer can regulate the innate immune response and prevent basal activation of the IFN pathway in mammals. Here, we discuss this hypothesis, highlighting how the adaptation of the helicase domain of mammalian Dicer may be key to this process.},
keywords = {PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
While Dicer plays an important antiviral role through the RNAi pathway in plants and invertebrates, its contribution to antiviral immunity in vertebrates and more specifically mammals is more controversial. The apparent limited RNAi activity in mammalian cells has been attributed to the reduced long dsRNA processive activity of mammalian Dicer, as well as a functional incompatibility between the RNAi and IFN pathways. Why Dicer has lost this antiviral activity in the profit of the IFN pathway is still unclear. We propose that the primary direct antiviral activity of Dicer has been functionally replaced by other sensors in the IFN pathway, leading to its specialization toward microRNA maturation. As a result, Dicer can regulate the innate immune response and prevent basal activation of the IFN pathway in mammals. Here, we discuss this hypothesis, highlighting how the adaptation of the helicase domain of mammalian Dicer may be key to this process.
Jin Lihao, Gan Dingyi, He Wentao, Wu Na, Xiang Shuchenlu, Wei Yinsheng, Eriani Gilbert, Ji Yanchun, Guan Min-Xin, Wang Meng
Mitochondrial tRNA 14693A>G Mutation, an Article de journal
Dans: Adv Sci (Weinh), p. e2401856, 2024, ISSN: 2198-3844.
Résumé | Liens | BibTeX | Étiquettes: ERIANI, Unité ARN
@article{pmid39264244,
title = {Mitochondrial tRNA 14693A>G Mutation, an },
author = {Lihao Jin and Dingyi Gan and Wentao He and Na Wu and Shuchenlu Xiang and Yinsheng Wei and Gilbert Eriani and Yanchun Ji and Min-Xin Guan and Meng Wang},
doi = {10.1002/advs.202401856},
issn = {2198-3844},
year = {2024},
date = {2024-09-01},
urldate = {2024-09-01},
journal = {Adv Sci (Weinh)},
pages = {e2401856},
abstract = {Leber's hereditary optic neuropathy (LHON), a maternally inherited ocular disease, is predominantly caused by mitochondrial DNA (mtDNA) mutations. Mitochondrial tRNA variants are hypothesized to amplify the pathogenic impact of three primary mutations. However, the exact mechanisms remained unclear. In the present study, the synergistic effect of the tRNA 14693A>G and ND6 14484T>C mutations in three Chinese families affected by LHON is investigated. The m.14693A>G mutation nearly abolishes the pseudouridinylation at position 55 of tRNA, leading to structural abnormalities, decreased stability, aberrant mitochondrial protein synthesis, and increased autophagy. In contrast, the ND6 14484T>C mutation predominantly impairs complex I function, resulting in heightened apoptosis and virtually no induction of mitochondrial autophagy compared to control cell lines. The presence of dual mutations in the same cell lines exhibited a coexistence of both upregulated cellular stress responses to mitochondrial damage, indicating a scenario of autophagy and mutation dysregulation within these dual-mutant cell lines. The data proposes a novel hypothesis that mitochondrial tRNA gene mutations generally lead to increased mitochondrial autophagy, while mutations in genes encoding mitochondrial proteins typically induce apoptosis, shedding light on the intricate interplay between different genetic factors in the manifestation of LHON.},
keywords = {ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Leber's hereditary optic neuropathy (LHON), a maternally inherited ocular disease, is predominantly caused by mitochondrial DNA (mtDNA) mutations. Mitochondrial tRNA variants are hypothesized to amplify the pathogenic impact of three primary mutations. However, the exact mechanisms remained unclear. In the present study, the synergistic effect of the tRNA 14693A>G and ND6 14484T>C mutations in three Chinese families affected by LHON is investigated. The m.14693A>G mutation nearly abolishes the pseudouridinylation at position 55 of tRNA, leading to structural abnormalities, decreased stability, aberrant mitochondrial protein synthesis, and increased autophagy. In contrast, the ND6 14484T>C mutation predominantly impairs complex I function, resulting in heightened apoptosis and virtually no induction of mitochondrial autophagy compared to control cell lines. The presence of dual mutations in the same cell lines exhibited a coexistence of both upregulated cellular stress responses to mitochondrial damage, indicating a scenario of autophagy and mutation dysregulation within these dual-mutant cell lines. The data proposes a novel hypothesis that mitochondrial tRNA gene mutations generally lead to increased mitochondrial autophagy, while mutations in genes encoding mitochondrial proteins typically induce apoptosis, shedding light on the intricate interplay between different genetic factors in the manifestation of LHON.
Bussi Giovanni, Bonomi Massimiliano, Gkeka Paraskevi, Sattler Michael, Al-Hashimi Hashim M, Auffinger Pascal, Duca Maria, Foricher Yann, Incarnato Danny, Jones Alisha N, Kirmizialtin Serdal, Krepl Miroslav, Orozco Modesto, Palermo Giulia, Pasquali Samuela, Salmon Loïc, Schwalbe Harald, Westhof Eric, Zacharias Martin
RNA dynamics from experimental and computational approaches Article de journal
Dans: Structure, vol. 32, no. 9, p. 1281–1287, 2024, ISSN: 1878-4186.
Résumé | Liens | BibTeX | Étiquettes: ENNIFAR, Unité ARN, WESTHOF
@article{pmid39241758,
title = {RNA dynamics from experimental and computational approaches},
author = {Giovanni Bussi and Massimiliano Bonomi and Paraskevi Gkeka and Michael Sattler and Hashim M Al-Hashimi and Pascal Auffinger and Maria Duca and Yann Foricher and Danny Incarnato and Alisha N Jones and Serdal Kirmizialtin and Miroslav Krepl and Modesto Orozco and Giulia Palermo and Samuela Pasquali and Loïc Salmon and Harald Schwalbe and Eric Westhof and Martin Zacharias},
doi = {10.1016/j.str.2024.07.019},
issn = {1878-4186},
year = {2024},
date = {2024-09-01},
urldate = {2024-09-01},
journal = {Structure},
volume = {32},
number = {9},
pages = {1281--1287},
abstract = {Conformational dynamics is crucial for the biological function of RNA molecules and for their potential as therapeutic targets. This meeting report outlines key "take-home" messages that emerged from the presentations and discussions during the CECAM workshop "RNA dynamics from experimental and computational approaches" in Paris, June 26-28, 2023.},
keywords = {ENNIFAR, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Conformational dynamics is crucial for the biological function of RNA molecules and for their potential as therapeutic targets. This meeting report outlines key "take-home" messages that emerged from the presentations and discussions during the CECAM workshop "RNA dynamics from experimental and computational approaches" in Paris, June 26-28, 2023.
Kehrli Janine, Husser Claire, Ryckelynck Michael
Fluorogenic RNA-Based Biosensors of Small Molecules: Current Developments, Uses, and Perspectives Article de journal
Dans: Biosensors (Basel), vol. 14, no. 8, 2024, ISSN: 2079-6374.
Résumé | Liens | BibTeX | Étiquettes: RYCKELYNCK, Unité ARN
@article{pmid39194605,
title = {Fluorogenic RNA-Based Biosensors of Small Molecules: Current Developments, Uses, and Perspectives},
author = {Janine Kehrli and Claire Husser and Michael Ryckelynck},
doi = {10.3390/bios14080376},
issn = {2079-6374},
year = {2024},
date = {2024-08-01},
urldate = {2024-08-01},
journal = {Biosensors (Basel)},
volume = {14},
number = {8},
abstract = {Small molecules are highly relevant targets for detection and quantification. They are also used to diagnose and monitor the progression of disease and infectious processes and track the presence of contaminants. Fluorogenic RNA-based biosensors (FRBs) represent an appealing solution to the problem of detecting these targets. They combine the portability of molecular systems with the sensitivity and multiplexing capacity of fluorescence, as well as the exquisite ligand selectivity of RNA aptamers. In this review, we first present the different sensing and reporting aptamer modules currently available to design an FRB, together with the main methodologies used to discover modules with new specificities. We next introduce and discuss how both modules can be functionally connected prior to exploring the main applications for which FRB have been used. Finally, we conclude by discussing how using alternative nucleotide chemistries may improve FRB properties and further widen their application scope.},
keywords = {RYCKELYNCK, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Small molecules are highly relevant targets for detection and quantification. They are also used to diagnose and monitor the progression of disease and infectious processes and track the presence of contaminants. Fluorogenic RNA-based biosensors (FRBs) represent an appealing solution to the problem of detecting these targets. They combine the portability of molecular systems with the sensitivity and multiplexing capacity of fluorescence, as well as the exquisite ligand selectivity of RNA aptamers. In this review, we first present the different sensing and reporting aptamer modules currently available to design an FRB, together with the main methodologies used to discover modules with new specificities. We next introduce and discuss how both modules can be functionally connected prior to exploring the main applications for which FRB have been used. Finally, we conclude by discussing how using alternative nucleotide chemistries may improve FRB properties and further widen their application scope.
Hoffmann Anne, Lorenz Christian, Fallmann Jörg, Wolff Philippe, Lechner Antony, Betat Heike, Mörl Mario, Stadler Peter F
Temperature-Dependent tRNA Modifications in Bacillales Article de journal
Dans: Int J Mol Sci, vol. 25, no. 16, 2024, ISSN: 1422-0067.
Résumé | Liens | BibTeX | Étiquettes: ARN-MS, Unité ARN
@article{pmid39201508,
title = {Temperature-Dependent tRNA Modifications in Bacillales},
author = {Anne Hoffmann and Christian Lorenz and Jörg Fallmann and Philippe Wolff and Antony Lechner and Heike Betat and Mario Mörl and Peter F Stadler},
doi = {10.3390/ijms25168823},
issn = {1422-0067},
year = {2024},
date = {2024-08-01},
urldate = {2024-08-01},
journal = {Int J Mol Sci},
volume = {25},
number = {16},
abstract = {Transfer RNA (tRNA) modifications are essential for the temperature adaptation of thermophilic and psychrophilic organisms as they control the rigidity and flexibility of transcripts. To further understand how specific tRNA modifications are adjusted to maintain functionality in response to temperature fluctuations, we investigated whether tRNA modifications represent an adaptation of bacteria to different growth temperatures (minimal, optimal, and maximal), focusing on closely related psychrophilic ( and ), mesophilic (), and thermophilic () Bacillales. Utilizing an RNA sequencing approach combined with chemical pre-treatment of tRNA samples, we systematically profiled dihydrouridine (D), 4-thiouridine (sU), 7-methyl-guanosine (mG), and pseudouridine (Ψ) modifications at single-nucleotide resolution. Despite their close relationship, each bacterium exhibited a unique tRNA modification profile. Our findings revealed increased tRNA modifications in the thermophilic bacterium at its optimal growth temperature, particularly showing elevated levels of sU8 and Ψ55 modifications compared to non-thermophilic bacteria, indicating a temperature-dependent regulation that may contribute to thermotolerance. Furthermore, we observed higher levels of D modifications in psychrophilic and mesophilic bacteria, indicating an adaptive strategy for cold environments by enhancing local flexibility in tRNAs. Our method demonstrated high effectiveness in identifying tRNA modifications compared to an established tool, highlighting its potential for precise tRNA profiling studies.},
keywords = {ARN-MS, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Transfer RNA (tRNA) modifications are essential for the temperature adaptation of thermophilic and psychrophilic organisms as they control the rigidity and flexibility of transcripts. To further understand how specific tRNA modifications are adjusted to maintain functionality in response to temperature fluctuations, we investigated whether tRNA modifications represent an adaptation of bacteria to different growth temperatures (minimal, optimal, and maximal), focusing on closely related psychrophilic ( and ), mesophilic (), and thermophilic () Bacillales. Utilizing an RNA sequencing approach combined with chemical pre-treatment of tRNA samples, we systematically profiled dihydrouridine (D), 4-thiouridine (sU), 7-methyl-guanosine (mG), and pseudouridine (Ψ) modifications at single-nucleotide resolution. Despite their close relationship, each bacterium exhibited a unique tRNA modification profile. Our findings revealed increased tRNA modifications in the thermophilic bacterium at its optimal growth temperature, particularly showing elevated levels of sU8 and Ψ55 modifications compared to non-thermophilic bacteria, indicating a temperature-dependent regulation that may contribute to thermotolerance. Furthermore, we observed higher levels of D modifications in psychrophilic and mesophilic bacteria, indicating an adaptive strategy for cold environments by enhancing local flexibility in tRNAs. Our method demonstrated high effectiveness in identifying tRNA modifications compared to an established tool, highlighting its potential for precise tRNA profiling studies.
Pitolli Martina, Cela Marta, Kapps Delphine, Chicher Johana, Despons Laurence, Frugier Magali
Comparative proteomics uncovers low asparagine content in Plasmodium tRip-KO proteins Article de journal
Dans: IUBMB Life, 2024, ISSN: 1521-6551.
Résumé | Liens | BibTeX | Étiquettes: PPSE, RYCKELYNCK, Unité ARN
@article{pmid38963319,
title = {Comparative proteomics uncovers low asparagine content in Plasmodium tRip-KO proteins},
author = {Martina Pitolli and Marta Cela and Delphine Kapps and Johana Chicher and Laurence Despons and Magali Frugier},
doi = {10.1002/iub.2891},
issn = {1521-6551},
year = {2024},
date = {2024-07-01},
urldate = {2024-07-01},
journal = {IUBMB Life},
abstract = {tRNAs are not only essential for decoding the genetic code, but their abundance also has a strong impact on the rate of protein production, folding, and on the stability of the translated messenger RNAs. Plasmodium expresses a unique surface protein called tRip, involved in the import of exogenous tRNAs into the parasite. Comparative proteomic analysis of the blood stage of wild-type and tRip-KO variant of P. berghei parasites revealed that downregulated proteins in the mutant parasite are distinguished by a bias in their asparagine content. Furthermore, the demonstration of the possibility of charging host tRNAs with Plasmodium aminoacyl-tRNA synthetases led us to propose that imported host tRNAs participate in parasite protein synthesis. These results also suggest a novel mechanism of translational control in which import of host tRNAs emerge as regulators of gene expression in the Plasmodium developmental cycle and pathogenesis, by enabling the synthesis of asparagine-rich regulatory proteins that efficiently and selectively control the parasite infectivity.},
keywords = {PPSE, RYCKELYNCK, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
tRNAs are not only essential for decoding the genetic code, but their abundance also has a strong impact on the rate of protein production, folding, and on the stability of the translated messenger RNAs. Plasmodium expresses a unique surface protein called tRip, involved in the import of exogenous tRNAs into the parasite. Comparative proteomic analysis of the blood stage of wild-type and tRip-KO variant of P. berghei parasites revealed that downregulated proteins in the mutant parasite are distinguished by a bias in their asparagine content. Furthermore, the demonstration of the possibility of charging host tRNAs with Plasmodium aminoacyl-tRNA synthetases led us to propose that imported host tRNAs participate in parasite protein synthesis. These results also suggest a novel mechanism of translational control in which import of host tRNAs emerge as regulators of gene expression in the Plasmodium developmental cycle and pathogenesis, by enabling the synthesis of asparagine-rich regulatory proteins that efficiently and selectively control the parasite infectivity.
Silva Elisabete Cruz Da, Gaki Paraskevi, Flieg Fabien, Messmer Melanie, Gucciardi Floriane, Markovska Yevheniia, Reisch Andreas, Fafi-Kremer Samira, Pfeffer Sébastien, Klymchenko Andrey S
Direct Zeptomole Detection of RNA Biomarkers by Ultrabright Fluorescent Nanoparticles on Magnetic Beads Article de journal
Dans: Small, p. e2404167, 2024, ISSN: 1613-6829.
Résumé | Liens | BibTeX | Étiquettes: PFEFFER, Unité ARN
@article{pmid39011971,
title = {Direct Zeptomole Detection of RNA Biomarkers by Ultrabright Fluorescent Nanoparticles on Magnetic Beads},
author = {Elisabete Cruz Da Silva and Paraskevi Gaki and Fabien Flieg and Melanie Messmer and Floriane Gucciardi and Yevheniia Markovska and Andreas Reisch and Samira Fafi-Kremer and Sébastien Pfeffer and Andrey S Klymchenko},
doi = {10.1002/smll.202404167},
issn = {1613-6829},
year = {2024},
date = {2024-07-01},
urldate = {2024-07-01},
journal = {Small},
pages = {e2404167},
abstract = {Nucleic acids are important biomarkers in cancer and viral diseases. However, their ultralow concentration in biological/clinical samples makes direct target detection challenging, because it leads to slow hybridization kinetics with the probe and its insufficient signal-to-noise ratio. Therefore, RNA target detection is done by molecular (target) amplification, notably by RT-PCR, which is a tedious multistep method that includes nucleic acid extraction and reverse transcription. Here, a direct method based on ultrabright dye-loaded polymeric nanoparticles in a sandwich-like hybridization assay with magnetic beads is reported. The ultrabright DNA-functionalized nanoparticle, equivalent to ≈10 000 strongly emissive rhodamine dyes, is hybridized with the magnetic bead to the RNA target, providing the signal amplification for the detection. This concept (magneto-fluorescent sandwich) enables high-throughput detection of DNA and RNA sequences of varied lengths from 48 to 1362 nt with the limit of detection down to 0.3 fm using a plate reader (15 zeptomoles), among the best reported for optical sandwich assays. Moreover, it allows semi-quantitative detection of SARS-CoV-2 viral RNA directly in clinical samples without a dedicated RNA extraction step. The developed technology, combining ultrabright nanoparticles with magnetic beads, addresses fundamental challenges in RNA detection; it is expected to accelerate molecular diagnostics of diseases.},
keywords = {PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Nucleic acids are important biomarkers in cancer and viral diseases. However, their ultralow concentration in biological/clinical samples makes direct target detection challenging, because it leads to slow hybridization kinetics with the probe and its insufficient signal-to-noise ratio. Therefore, RNA target detection is done by molecular (target) amplification, notably by RT-PCR, which is a tedious multistep method that includes nucleic acid extraction and reverse transcription. Here, a direct method based on ultrabright dye-loaded polymeric nanoparticles in a sandwich-like hybridization assay with magnetic beads is reported. The ultrabright DNA-functionalized nanoparticle, equivalent to ≈10 000 strongly emissive rhodamine dyes, is hybridized with the magnetic bead to the RNA target, providing the signal amplification for the detection. This concept (magneto-fluorescent sandwich) enables high-throughput detection of DNA and RNA sequences of varied lengths from 48 to 1362 nt with the limit of detection down to 0.3 fm using a plate reader (15 zeptomoles), among the best reported for optical sandwich assays. Moreover, it allows semi-quantitative detection of SARS-CoV-2 viral RNA directly in clinical samples without a dedicated RNA extraction step. The developed technology, combining ultrabright nanoparticles with magnetic beads, addresses fundamental challenges in RNA detection; it is expected to accelerate molecular diagnostics of diseases.
Mao Xue-Ling, Eriani Gilbert, Zhou Xiao-Long
ADATs: roles in tRNA editing and relevance to disease Article de journal
Dans: Acta Biochim Biophys Sin (Shanghai), 2024, ISSN: 1745-7270.
Résumé | Liens | BibTeX | Étiquettes: ERIANI, Unité ARN
@article{pmid39034823,
title = {ADATs: roles in tRNA editing and relevance to disease},
author = {Xue-Ling Mao and Gilbert Eriani and Xiao-Long Zhou},
doi = {10.3724/abbs.2024125},
issn = {1745-7270},
year = {2024},
date = {2024-07-01},
urldate = {2024-07-01},
journal = {Acta Biochim Biophys Sin (Shanghai)},
abstract = {Transfer RNAs (tRNAs) play central roles in protein biosynthesis. Post-transcriptional RNA modifications affect tRNA function and stability. Among these modifications, RNA editing is a widespread RNA modification in three domains of life. Proteins of the adenosine deaminase acting on tRNA (ADAT) family were discovered more than 20 years ago. They catalyze the deamination of adenosine to inosine (A-to-I) or cytidine to uridine (C-to-U) during tRNA maturation. The most studied example is the TadA- or ADAT2/3-mediated A-to-I conversion of the tRNA wobble position in the anticodon of prokaryotic or eukaryotic tRNAs, respectively. This review provides detailed information on A-to-I and C-to-U editing of tRNAs in different domains of life, presents recent new findings on ADATs for DNA editing, and finally comments on the association of mutations in the gene with intellectual disability.},
keywords = {ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Transfer RNAs (tRNAs) play central roles in protein biosynthesis. Post-transcriptional RNA modifications affect tRNA function and stability. Among these modifications, RNA editing is a widespread RNA modification in three domains of life. Proteins of the adenosine deaminase acting on tRNA (ADAT) family were discovered more than 20 years ago. They catalyze the deamination of adenosine to inosine (A-to-I) or cytidine to uridine (C-to-U) during tRNA maturation. The most studied example is the TadA- or ADAT2/3-mediated A-to-I conversion of the tRNA wobble position in the anticodon of prokaryotic or eukaryotic tRNAs, respectively. This review provides detailed information on A-to-I and C-to-U editing of tRNAs in different domains of life, presents recent new findings on ADATs for DNA editing, and finally comments on the association of mutations in the gene with intellectual disability.
Rios-Delgado Gustavo, McReynolds Aubrey K G, Pagella Emma A, Norambuena Javiera, Briaud Paul, Zheng Vincent, Munneke Matthew J, Kim Jisun, Racine Hugo, Carroll Ronan, Zelzion Ehud, Skaar Eric, Bose Jeffrey L, Parker Dane, Lalaouna David, Boyd Jeffrey M
The small non-coding RNA IsrR regulates TCA cycle activity and virulence Article de journal
Dans: bioRxiv, 2024, ISSN: 2692-8205.
Résumé | Liens | BibTeX | Étiquettes: LALAOUNA, ROMBY, Unité ARN
@article{pmid39005296,
title = {The small non-coding RNA IsrR regulates TCA cycle activity and virulence},
author = {Gustavo Rios-Delgado and Aubrey K G McReynolds and Emma A Pagella and Javiera Norambuena and Paul Briaud and Vincent Zheng and Matthew J Munneke and Jisun Kim and Hugo Racine and Ronan Carroll and Ehud Zelzion and Eric Skaar and Jeffrey L Bose and Dane Parker and David Lalaouna and Jeffrey M Boyd},
doi = {10.1101/2024.07.03.601953},
issn = {2692-8205},
year = {2024},
date = {2024-07-01},
urldate = {2024-07-01},
journal = {bioRxiv},
abstract = { has evolved mechanisms to cope with low iron (Fe) availability in host tissues. uses the ferric uptake transcriptional regulator (Fur) to sense titers of cytosolic Fe. Upon Fe depletion, apo-Fur relieves transcriptional repression of genes utilized for Fe uptake. We demonstrate that an Δ mutant has decreased expression of , which codes for the Fe-dependent enzyme aconitase. Decreased expression prevented the Δ mutant from growing with amino acids as sole carbon and energy sources. Suppressor analysis determined that a mutation in , which produces a regulatory RNA, permitted growth by decreasing transcription. The decreased AcnA activity of the Δ mutant was partially relieved by an Δ mutation. Directed mutation of bases predicted to facilitate the interaction between the transcript and IsrR, decreased the ability of IsrR to control expression and IsrR bound to the transcript . IsrR also bound to the transcripts coding the alternate TCA cycle proteins , , , and . Whole cell metal analyses suggest that IsrR promotes Fe uptake and increases intracellular Fe not ligated by macromolecules. Lastly, we determined that Fur and IsrR promote infection using murine skin and acute pneumonia models.},
keywords = {LALAOUNA, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
has evolved mechanisms to cope with low iron (Fe) availability in host tissues. uses the ferric uptake transcriptional regulator (Fur) to sense titers of cytosolic Fe. Upon Fe depletion, apo-Fur relieves transcriptional repression of genes utilized for Fe uptake. We demonstrate that an Δ mutant has decreased expression of , which codes for the Fe-dependent enzyme aconitase. Decreased expression prevented the Δ mutant from growing with amino acids as sole carbon and energy sources. Suppressor analysis determined that a mutation in , which produces a regulatory RNA, permitted growth by decreasing transcription. The decreased AcnA activity of the Δ mutant was partially relieved by an Δ mutation. Directed mutation of bases predicted to facilitate the interaction between the transcript and IsrR, decreased the ability of IsrR to control expression and IsrR bound to the transcript . IsrR also bound to the transcripts coding the alternate TCA cycle proteins , , , and . Whole cell metal analyses suggest that IsrR promotes Fe uptake and increases intracellular Fe not ligated by macromolecules. Lastly, we determined that Fur and IsrR promote infection using murine skin and acute pneumonia models.
Tajer L., Paillart J. -C., Dib H., Sabatier J. -M., Fajloun Z., Khattar Z. Abi
Molecular Mechanisms of Bacterial Resistance to Antimicrobial Peptides in the Modern Era: An Updated Review Article de journal
Dans: Microorganisms, vol. 12, p. 1259, 2024.
Résumé | Liens | BibTeX | Étiquettes: marquet Paillart, PAILLART, Unité ARN
@article{nokey,
title = {Molecular Mechanisms of Bacterial Resistance to Antimicrobial Peptides in the Modern Era: An Updated Review},
author = {L. Tajer and J.-C. Paillart and H. Dib and J.-M. Sabatier and Z. Fajloun and Z. Abi Khattar},
url = {https://www.mdpi.com/2076-2607/12/7/1259},
doi = {10.3390/ microorganisms12071259},
year = {2024},
date = {2024-06-21},
urldate = {2024-06-21},
journal = {Microorganisms},
volume = {12},
pages = {1259},
abstract = {Antimicrobial resistance (AMR) poses a serious global health concern, resulting in a
significant number of deaths annually due to infections that are resistant to treatment. Amidst
this crisis, antimicrobial peptides (AMPs) have emerged as promising alternatives to conventional
antibiotics (ATBs). These cationic peptides, naturally produced by all kingdoms of life, play a
crucial role in the innate immune system of multicellular organisms and in bacterial interspecies
competition by exhibiting broad-spectrum activity against bacteria, fungi, viruses, and parasites.
AMPs target bacterial pathogens through multiple mechanisms, most importantly by disrupting
their membranes, leading to cell lysis. However, bacterial resistance to host AMPs has emerged
due to a slow co-evolutionary process between microorganisms and their hosts. Alarmingly, the
development of resistance to last-resort AMPs in the treatment of MDR infections, such as colistin, is
attributed to the misuse of this and the high rate of horizontal genetic transfer of the corresponding
resistance genes. AMP-resistant bacteria employ diverse mechanisms, including but not limited to
proteolytic degradation, extracellular trapping and inactivation, active efflux, as well as complex
modifications in bacterial cell wall and membrane structures. This review comprehensively examines
all constitutive and inducible molecular resistance mechanisms to AMPs supported by experimental
evidence described to date in bacterial pathogens. We also explore the specificity of these mechanisms
toward structurally diverse AMPs to broaden and enhance their potential in developing and applying
them as therapeutics for MDR bacteria. Additionally, we provide insights into the significance of
AMP resistance within the context of host–pathogen interactions.},
keywords = {marquet Paillart, PAILLART, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Antimicrobial resistance (AMR) poses a serious global health concern, resulting in a
significant number of deaths annually due to infections that are resistant to treatment. Amidst
this crisis, antimicrobial peptides (AMPs) have emerged as promising alternatives to conventional
antibiotics (ATBs). These cationic peptides, naturally produced by all kingdoms of life, play a
crucial role in the innate immune system of multicellular organisms and in bacterial interspecies
competition by exhibiting broad-spectrum activity against bacteria, fungi, viruses, and parasites.
AMPs target bacterial pathogens through multiple mechanisms, most importantly by disrupting
their membranes, leading to cell lysis. However, bacterial resistance to host AMPs has emerged
due to a slow co-evolutionary process between microorganisms and their hosts. Alarmingly, the
development of resistance to last-resort AMPs in the treatment of MDR infections, such as colistin, is
attributed to the misuse of this and the high rate of horizontal genetic transfer of the corresponding
resistance genes. AMP-resistant bacteria employ diverse mechanisms, including but not limited to
proteolytic degradation, extracellular trapping and inactivation, active efflux, as well as complex
modifications in bacterial cell wall and membrane structures. This review comprehensively examines
all constitutive and inducible molecular resistance mechanisms to AMPs supported by experimental
evidence described to date in bacterial pathogens. We also explore the specificity of these mechanisms
toward structurally diverse AMPs to broaden and enhance their potential in developing and applying
them as therapeutics for MDR bacteria. Additionally, we provide insights into the significance of
AMP resistance within the context of host–pathogen interactions.
significant number of deaths annually due to infections that are resistant to treatment. Amidst
this crisis, antimicrobial peptides (AMPs) have emerged as promising alternatives to conventional
antibiotics (ATBs). These cationic peptides, naturally produced by all kingdoms of life, play a
crucial role in the innate immune system of multicellular organisms and in bacterial interspecies
competition by exhibiting broad-spectrum activity against bacteria, fungi, viruses, and parasites.
AMPs target bacterial pathogens through multiple mechanisms, most importantly by disrupting
their membranes, leading to cell lysis. However, bacterial resistance to host AMPs has emerged
due to a slow co-evolutionary process between microorganisms and their hosts. Alarmingly, the
development of resistance to last-resort AMPs in the treatment of MDR infections, such as colistin, is
attributed to the misuse of this and the high rate of horizontal genetic transfer of the corresponding
resistance genes. AMP-resistant bacteria employ diverse mechanisms, including but not limited to
proteolytic degradation, extracellular trapping and inactivation, active efflux, as well as complex
modifications in bacterial cell wall and membrane structures. This review comprehensively examines
all constitutive and inducible molecular resistance mechanisms to AMPs supported by experimental
evidence described to date in bacterial pathogens. We also explore the specificity of these mechanisms
toward structurally diverse AMPs to broaden and enhance their potential in developing and applying
them as therapeutics for MDR bacteria. Additionally, we provide insights into the significance of
AMP resistance within the context of host–pathogen interactions.
Imbernon Julia Revillo, Weibel Jean‐Marc, Ennifar Eric, Prévost Gilles, Kellenberger Esther
Structural analysis of neomycin B and kanamycin A binding Aminoglycosides Modifying Enzymes (AME) and bacterial ribosomal RNA Article de journal
Dans: Molecular Informatics, 2024, ISSN: 1868-1751.
Résumé | Liens | BibTeX | Étiquettes: ENNIFAR, Unité ARN
@article{RevilloImbernon2024,
title = {Structural analysis of neomycin B and kanamycin A binding Aminoglycosides Modifying Enzymes (AME) and bacterial ribosomal RNA},
author = {Julia Revillo Imbernon and Jean‐Marc Weibel and Eric Ennifar and Gilles Prévost and Esther Kellenberger},
doi = {10.1002/minf.202300339},
issn = {1868-1751},
year = {2024},
date = {2024-06-10},
urldate = {2024-06-10},
journal = {Molecular Informatics},
publisher = {Wiley},
abstract = {<jats:title>Abstract</jats:title><jats:p>Aminoglycosides are crucial antibiotics facing challenges from bacterial resistance. This study addresses the importance of aminoglycoside modifying enzymes in the context of escalating resistance. Drawing upon over two decades of structural data in the Protein Data Bank, we focused on two key antibiotics, neomycin B and kanamycin A, to explore how the aminoglycoside structure is exploited by this family of enzymes. A systematic comparison across diverse enzymes and the RNA A‐site target identified common characteristics in the recognition mode, while assessing the adaptability of neomycin B and kanamycin A in various environments.</jats:p>},
keywords = {ENNIFAR, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
<jats:title>Abstract</jats:title><jats:p>Aminoglycosides are crucial antibiotics facing challenges from bacterial resistance. This study addresses the importance of aminoglycoside modifying enzymes in the context of escalating resistance. Drawing upon over two decades of structural data in the Protein Data Bank, we focused on two key antibiotics, neomycin B and kanamycin A, to explore how the aminoglycoside structure is exploited by this family of enzymes. A systematic comparison across diverse enzymes and the RNA A‐site target identified common characteristics in the recognition mode, while assessing the adaptability of neomycin B and kanamycin A in various environments.</jats:p>
Urzhumtseva Ludmila, Barchet Charles, Klaholz Bruno P, Urzhumtsev Alexandre G
Program : analysing distributions of cryo-EM projections using uniform spherical grids Article de journal
Dans: J Appl Crystallogr, vol. 57, no. Pt 3, p. 865–876, 2024, ISSN: 0021-8898.
Résumé | Liens | BibTeX | Étiquettes: Unité ARN
@article{pmid38846771,
title = {Program : analysing distributions of cryo-EM projections using uniform spherical grids},
author = {Ludmila Urzhumtseva and Charles Barchet and Bruno P Klaholz and Alexandre G Urzhumtsev},
doi = {10.1107/S1600576724002383},
issn = {0021-8898},
year = {2024},
date = {2024-06-01},
urldate = {2024-06-01},
journal = {J Appl Crystallogr},
volume = {57},
number = {Pt 3},
pages = {865--876},
abstract = {Three-dimensional cryo electron microscopy reconstructions are obtained by extracting information from a large number of projections of the object. These projections correspond to different 'views' or 'orientations', directions in which these projections show the reconstructed object. Uneven distribution of these views and the presence of dominating preferred orientations may distort the reconstructed spatial images. This work describes the program (views on uniform grids for cryo electron microscopy), designed to study such distributions. Its algorithms, based on uniform virtual grids on a sphere, allow an easy calculation and accurate quantitative analysis of the frequency distribution of the views. The key computational element is the Lambert azimuthal equal-area projection of a spherical uniform grid onto a disc. This projection keeps the surface area constant and represents the frequency distribution with no visual bias. Since it has multiple tunable parameters, the program is easily adaptable to individual needs, and to the features of a particular project or of the figure to be produced. It can help identify problems related to an uneven distribution of views. Optionally, it can modify the list of projections, distributing the views more uniformly. The program can also be used as a teaching tool.},
keywords = {Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Three-dimensional cryo electron microscopy reconstructions are obtained by extracting information from a large number of projections of the object. These projections correspond to different 'views' or 'orientations', directions in which these projections show the reconstructed object. Uneven distribution of these views and the presence of dominating preferred orientations may distort the reconstructed spatial images. This work describes the program (views on uniform grids for cryo electron microscopy), designed to study such distributions. Its algorithms, based on uniform virtual grids on a sphere, allow an easy calculation and accurate quantitative analysis of the frequency distribution of the views. The key computational element is the Lambert azimuthal equal-area projection of a spherical uniform grid onto a disc. This projection keeps the surface area constant and represents the frequency distribution with no visual bias. Since it has multiple tunable parameters, the program is easily adaptable to individual needs, and to the features of a particular project or of the figure to be produced. It can help identify problems related to an uneven distribution of views. Optionally, it can modify the list of projections, distributing the views more uniformly. The program can also be used as a teaching tool.
Holvec Samuel, Barchet Charles, Lechner Antony, Fréchin Léo, Silva S Nimali T De, Hazemann Isabelle, Wolff Philippe, von Loeffelholz Ottilie, Klaholz Bruno P
The structure of the human 80S ribosome at 1.9 Å resolution reveals the molecular role of chemical modifications and ions in RNA Article de journal
Dans: Nat Struct Mol Biol, 2024, ISSN: 1545-9985.
Résumé | Liens | BibTeX | Étiquettes: ARN-MS, Unité ARN
@article{pmid38844527,
title = {The structure of the human 80S ribosome at 1.9 Å resolution reveals the molecular role of chemical modifications and ions in RNA},
author = {Samuel Holvec and Charles Barchet and Antony Lechner and Léo Fréchin and S Nimali T De Silva and Isabelle Hazemann and Philippe Wolff and Ottilie von Loeffelholz and Bruno P Klaholz},
doi = {10.1038/s41594-024-01274-x},
issn = {1545-9985},
year = {2024},
date = {2024-06-01},
urldate = {2024-06-01},
journal = {Nat Struct Mol Biol},
abstract = {The ribosomal RNA of the human protein synthesis machinery comprises numerous chemical modifications that are introduced during ribosome biogenesis. Here we present the 1.9 Å resolution cryo electron microscopy structure of the 80S human ribosome resolving numerous new ribosomal RNA modifications and functionally important ions such as Zn, K and Mg, including their associated individual water molecules. The 2'-O-methylation, pseudo-uridine and base modifications were confirmed by mass spectrometry, resulting in a complete investigation of the >230 sites, many of which could not be addressed previously. They choreograph key interactions within the RNA and at the interface with proteins, including at the ribosomal subunit interfaces of the fully assembled 80S ribosome. Uridine isomerization turns out to be a key mechanism for U-A base pair stabilization in RNA in general. The structural environment of chemical modifications and ions is primordial for the RNA architecture of the mature human ribosome, hence providing a structural framework to address their role in healthy states and in human diseases.},
keywords = {ARN-MS, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The ribosomal RNA of the human protein synthesis machinery comprises numerous chemical modifications that are introduced during ribosome biogenesis. Here we present the 1.9 Å resolution cryo electron microscopy structure of the 80S human ribosome resolving numerous new ribosomal RNA modifications and functionally important ions such as Zn, K and Mg, including their associated individual water molecules. The 2'-O-methylation, pseudo-uridine and base modifications were confirmed by mass spectrometry, resulting in a complete investigation of the >230 sites, many of which could not be addressed previously. They choreograph key interactions within the RNA and at the interface with proteins, including at the ribosomal subunit interfaces of the fully assembled 80S ribosome. Uridine isomerization turns out to be a key mechanism for U-A base pair stabilization in RNA in general. The structural environment of chemical modifications and ions is primordial for the RNA architecture of the mature human ribosome, hence providing a structural framework to address their role in healthy states and in human diseases.
Han Min-Jin, Luo Chaorui, Hu Hai, Lin Meixing, Lu Kunpeng, Shen Jianghong, Ren Jianyu, Ye Yanzhuo, Westhof Eric, Tong Xiaoling, Dai Fangyin
Multiple independent origins of the female W chromosome in moths and butterflies Article de journal
Dans: Sci Adv, vol. 10, no. 25, p. eadm9851, 2024, ISSN: 2375-2548.
Résumé | Liens | BibTeX | Étiquettes: Unité ARN, WESTHOF
@article{pmid38896616,
title = {Multiple independent origins of the female W chromosome in moths and butterflies},
author = {Min-Jin Han and Chaorui Luo and Hai Hu and Meixing Lin and Kunpeng Lu and Jianghong Shen and Jianyu Ren and Yanzhuo Ye and Eric Westhof and Xiaoling Tong and Fangyin Dai},
doi = {10.1126/sciadv.adm9851},
issn = {2375-2548},
year = {2024},
date = {2024-06-01},
urldate = {2024-06-01},
journal = {Sci Adv},
volume = {10},
number = {25},
pages = {eadm9851},
abstract = {Lepidoptera, the most diverse group of insects, exhibit female heterogamy (Z0 or ZW), which is different from most other insects (male heterogamy, XY). Previous studies suggest a single origin of the Z chromosome. However, the origin of the lepidopteran W chromosome remains poorly understood. Here, we assemble the genome from females down to the chromosome level of a model insect () and identify a W chromosome of approximately 10.1 megabase using a newly developed tool. In addition, we identify 3593 genes that were not previously annotated in the genomes of . Comparisons of 21 lepidopteran species (including 17 ZW and four Z0 systems) and three trichopteran species (Z0 system) reveal that the formation of Ditrysia W involves multiple mechanisms, including previously proposed canonical and noncanonical models, as well as a newly proposed mechanism called single-Z turnover. We conclude that there are multiple independent origins of the W chromosome in the Ditrysia (most moths and all butterflies) of Lepidoptera.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Lepidoptera, the most diverse group of insects, exhibit female heterogamy (Z0 or ZW), which is different from most other insects (male heterogamy, XY). Previous studies suggest a single origin of the Z chromosome. However, the origin of the lepidopteran W chromosome remains poorly understood. Here, we assemble the genome from females down to the chromosome level of a model insect () and identify a W chromosome of approximately 10.1 megabase using a newly developed tool. In addition, we identify 3593 genes that were not previously annotated in the genomes of . Comparisons of 21 lepidopteran species (including 17 ZW and four Z0 systems) and three trichopteran species (Z0 system) reveal that the formation of Ditrysia W involves multiple mechanisms, including previously proposed canonical and noncanonical models, as well as a newly proposed mechanism called single-Z turnover. We conclude that there are multiple independent origins of the W chromosome in the Ditrysia (most moths and all butterflies) of Lepidoptera.
Omar Reine El, Abdellaoui Naoill, Coulibaly Safiatou T, Fontenille Laura, Lanza François, Gachet Christian, Freund Jean-Noel, Negroni Matteo, Kissa Karima, Tavian Manuela
Macrophage depletion overcomes human hematopoietic cell engraftment failure in zebrafish embryo Article de journal
Dans: Cell Death Dis, vol. 15, no. 5, p. 305, 2024, ISSN: 2041-4889.
Résumé | Liens | BibTeX | Étiquettes: NEGRONI, Unité ARN
@article{pmid38693109,
title = {Macrophage depletion overcomes human hematopoietic cell engraftment failure in zebrafish embryo},
author = {Reine El Omar and Naoill Abdellaoui and Safiatou T Coulibaly and Laura Fontenille and François Lanza and Christian Gachet and Jean-Noel Freund and Matteo Negroni and Karima Kissa and Manuela Tavian},
doi = {10.1038/s41419-024-06682-x},
issn = {2041-4889},
year = {2024},
date = {2024-05-01},
urldate = {2024-05-01},
journal = {Cell Death Dis},
volume = {15},
number = {5},
pages = {305},
abstract = {Zebrafish is widely adopted as a grafting model for studying human development and diseases. Current zebrafish xenotransplantations are performed using embryo recipients, as the adaptive immune system, responsible for host versus graft rejection, only reaches maturity at juvenile stage. However, transplanted primary human hematopoietic stem/progenitor cells (HSC) rapidly disappear even in zebrafish embryos, suggesting that another barrier to transplantation exists before the onset of adaptive immunity. Here, using a labelled macrophage zebrafish line, we demonstrated that engraftment of human HSC induces a massive recruitment of macrophages which rapidly phagocyte transplanted cells. Macrophages depletion, by chemical or pharmacological treatments, significantly improved the uptake and survival of transplanted cells, demonstrating the crucial implication of these innate immune cells for the successful engraftment of human cells in zebrafish. Beyond identifying the reasons for human hematopoietic cell engraftment failure, this work images the fate of human cells in real time over several days in macrophage-depleted zebrafish embryos.},
keywords = {NEGRONI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Zebrafish is widely adopted as a grafting model for studying human development and diseases. Current zebrafish xenotransplantations are performed using embryo recipients, as the adaptive immune system, responsible for host versus graft rejection, only reaches maturity at juvenile stage. However, transplanted primary human hematopoietic stem/progenitor cells (HSC) rapidly disappear even in zebrafish embryos, suggesting that another barrier to transplantation exists before the onset of adaptive immunity. Here, using a labelled macrophage zebrafish line, we demonstrated that engraftment of human HSC induces a massive recruitment of macrophages which rapidly phagocyte transplanted cells. Macrophages depletion, by chemical or pharmacological treatments, significantly improved the uptake and survival of transplanted cells, demonstrating the crucial implication of these innate immune cells for the successful engraftment of human cells in zebrafish. Beyond identifying the reasons for human hematopoietic cell engraftment failure, this work images the fate of human cells in real time over several days in macrophage-depleted zebrafish embryos.
Lim Shey-Li, Liu Jinhong, Dupouy Gilles, Singh Gaurav, Baudrey Stéphanie, Yang Lang, Zhong Jia Yi, Chabouté Marie-Edith, Lim Boon Leong
In planta imaging of pyridine nucleotides using second-generation fluorescent protein biosensors Article de journal
Dans: Plant J, 2024, ISSN: 1365-313X.
Résumé | Liens | BibTeX | Étiquettes: RYCKELYNCK, Unité ARN
@article{pmid38761168,
title = {In planta imaging of pyridine nucleotides using second-generation fluorescent protein biosensors},
author = {Shey-Li Lim and Jinhong Liu and Gilles Dupouy and Gaurav Singh and Stéphanie Baudrey and Lang Yang and Jia Yi Zhong and Marie-Edith Chabouté and Boon Leong Lim},
doi = {10.1111/tpj.16796},
issn = {1365-313X},
year = {2024},
date = {2024-05-01},
urldate = {2024-05-01},
journal = {Plant J},
abstract = {Redox changes of pyridine nucleotides in cellular compartments are highly dynamic and their equilibria are under the influence of various reducing and oxidizing reactions. To obtain spatiotemporal data on pyridine nucleotides in living plant cells, typical biochemical approaches require cell destruction. To date, genetically encoded fluorescent biosensors are considered to be the best option to bridge the existing technology gap, as they provide a fast, accurate, and real-time readout. However, the existing pyridine nucleotides genetically encoded fluorescent biosensors are either sensitive to pH change or slow in dissociation rate. Herein, we employed the biosensors which generate readouts that are pH stable for in planta measurement of NADH/NAD ratio and NADPH level. We generated transgenic Arabidopsis lines that express these biosensors in plastid stroma and cytosol of whole plants and pollen tubes under the control of CaMV 35S and LAT52 promoters, respectively. These transgenic biosensor lines allow us to monitor real-time dynamic changes in NADH/NAD ratio and NADPH level in the plastids and cytosol of various plant tissues, including pollen tubes, root hairs, and mesophyll cells, using a variety of fluorescent instruments. We anticipate that these valuable transgenic lines may allow improvements in plant redox biology studies.},
keywords = {RYCKELYNCK, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Redox changes of pyridine nucleotides in cellular compartments are highly dynamic and their equilibria are under the influence of various reducing and oxidizing reactions. To obtain spatiotemporal data on pyridine nucleotides in living plant cells, typical biochemical approaches require cell destruction. To date, genetically encoded fluorescent biosensors are considered to be the best option to bridge the existing technology gap, as they provide a fast, accurate, and real-time readout. However, the existing pyridine nucleotides genetically encoded fluorescent biosensors are either sensitive to pH change or slow in dissociation rate. Herein, we employed the biosensors which generate readouts that are pH stable for in planta measurement of NADH/NAD ratio and NADPH level. We generated transgenic Arabidopsis lines that express these biosensors in plastid stroma and cytosol of whole plants and pollen tubes under the control of CaMV 35S and LAT52 promoters, respectively. These transgenic biosensor lines allow us to monitor real-time dynamic changes in NADH/NAD ratio and NADPH level in the plastids and cytosol of various plant tissues, including pollen tubes, root hairs, and mesophyll cells, using a variety of fluorescent instruments. We anticipate that these valuable transgenic lines may allow improvements in plant redox biology studies.
Niedner-Boblenz A., Monecke T., Hennig J., Klostermann M., Hofweber M., Gerber A. P., Anosova I., Mayer W., Müller M., Heym R., Janowski R., Paillart J. -C., Dormann D., Zarnack K., Sattler M., Niessing D.
Intrinsically disordered RNA-binding motifs cooperate to catalyze RNA folding and drive phase separation Article de journal
Dans: bioRxiv, 2024.
Résumé | Liens | BibTeX | Étiquettes: MARQUET, PAILLART, Unité ARN
@article{A.2024,
title = {Intrinsically disordered RNA-binding motifs cooperate to catalyze RNA folding and drive phase separation},
author = {A. Niedner-Boblenz and T. Monecke and J. Hennig and M. Klostermann and M. Hofweber and A.P. Gerber and I. Anosova and W. Mayer and M. Müller and R. Heym and R. Janowski and J.-C. Paillart and D. Dormann and K. Zarnack and M. Sattler and D. Niessing},
url = {https://www.biorxiv.org/content/10.1101/2024.03.27.586925v2},
doi = {10.1101/2024.03.27.586925},
year = {2024},
date = {2024-03-29},
urldate = {2024-03-29},
journal = {bioRxiv},
abstract = {RNA-binding proteins are essential for gene regulation and the spatial organization of cells. Here, we report that the yeast ribosome biogenesis factor Loc1p is an intrinsically disordered RNA-binding protein with eight repeating positively charged, unstructured nucleic acid binding (PUN) motifs. While a single of these previously undefined motifs stabilizes folded RNAs, multiple copies strongly cooperate to catalyze RNA folding. In the presence of RNA, these multivalent PUN motifs drive phase separation. Proteome-wide searches in pro-and eukaryotes for proteins with similar arrays of PUN motifs reveal a strong enrichment in RNA-mediated processes and DNA remodeling. Thus, PUN motifs are potentially involved in a large variety of RNA-and DNA-related processes by concentrating them in membrane-less organelles. The general function and wide distribution of PUN motifs across species suggests that in an ancient “RNA world” PUN-like motifs may have supported the correct folding of early ribozymes.},
keywords = {MARQUET, PAILLART, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
RNA-binding proteins are essential for gene regulation and the spatial organization of cells. Here, we report that the yeast ribosome biogenesis factor Loc1p is an intrinsically disordered RNA-binding protein with eight repeating positively charged, unstructured nucleic acid binding (PUN) motifs. While a single of these previously undefined motifs stabilizes folded RNAs, multiple copies strongly cooperate to catalyze RNA folding. In the presence of RNA, these multivalent PUN motifs drive phase separation. Proteome-wide searches in pro-and eukaryotes for proteins with similar arrays of PUN motifs reveal a strong enrichment in RNA-mediated processes and DNA remodeling. Thus, PUN motifs are potentially involved in a large variety of RNA-and DNA-related processes by concentrating them in membrane-less organelles. The general function and wide distribution of PUN motifs across species suggests that in an ancient “RNA world” PUN-like motifs may have supported the correct folding of early ribozymes.
Pellequer Jean-Luc, Westhof Eric
Marc van Regenmortel, personal recollections on a forward-thinking editor Article de journal
Dans: J Mol Recognit, p. e3080, 2024, ISSN: 1099-1352.
Résumé | Liens | BibTeX | Étiquettes: Unité ARN, WESTHOF
@article{pmid38439188,
title = {Marc van Regenmortel, personal recollections on a forward-thinking editor},
author = {Jean-Luc Pellequer and Eric Westhof},
doi = {10.1002/jmr.3080},
issn = {1099-1352},
year = {2024},
date = {2024-03-01},
urldate = {2024-03-01},
journal = {J Mol Recognit},
pages = {e3080},
abstract = {Marc van Regenmortel was the Editor-in-Chief of the Journal of Molecular Recognition for the last 25 years. Without attempting to summarize Marc's exceptional career and achievements, we would like to tell the story of the tortuous and contingent path to the unravelling of a key molecular recognition process in antigenicity. Life is indeed full of contingencies and scientific life, full of meetings and random encounters, is prone to contingencies, a key element in discovery and innovation.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Marc van Regenmortel was the Editor-in-Chief of the Journal of Molecular Recognition for the last 25 years. Without attempting to summarize Marc's exceptional career and achievements, we would like to tell the story of the tortuous and contingent path to the unravelling of a key molecular recognition process in antigenicity. Life is indeed full of contingencies and scientific life, full of meetings and random encounters, is prone to contingencies, a key element in discovery and innovation.
Messmer Mélanie, Pierson Louison, Pasquier Charline, Djordjevic Nikola, Chicher Johana, Hammann Philippe, Pfeffer Sébastien, Girardi Erika
DEAD box RNA helicase 5 is a new pro-viral host factor for Sindbis virus infection Article de journal
Dans: Virol J, vol. 21, no. 1, p. 76, 2024, ISSN: 1743-422X.
Résumé | Liens | BibTeX | Étiquettes: PFEFFER, PPSE, Unité ARN
@article{pmid38553727,
title = {DEAD box RNA helicase 5 is a new pro-viral host factor for Sindbis virus infection},
author = {Mélanie Messmer and Louison Pierson and Charline Pasquier and Nikola Djordjevic and Johana Chicher and Philippe Hammann and Sébastien Pfeffer and Erika Girardi},
doi = {10.1186/s12985-024-02349-3},
issn = {1743-422X},
year = {2024},
date = {2024-03-01},
urldate = {2024-03-01},
journal = {Virol J},
volume = {21},
number = {1},
pages = {76},
abstract = {BACKGROUND: RNA helicases are emerging as key factors regulating host-virus interactions. The DEAD-box ATP-dependent RNA helicase DDX5, which plays an important role in many aspects of cellular RNA biology, was also found to either promote or inhibit viral replication upon infection with several RNA viruses. Here, our aim is to examine the impact of DDX5 on Sindbis virus (SINV) infection.nnMETHODS: We analysed the interaction between DDX5 and the viral RNA using imaging and RNA-immunoprecipitation approaches. The interactome of DDX5 in mock- and SINV-infected cells was determined by mass spectrometry. We validated the interaction between DDX17 and the viral capsid by co- immunoprecipitation in the presence or absence of an RNase treatment. We determined the subcellular localization of DDX5, its cofactor DDX17 and the viral capsid protein by co-immunofluorescence. Finally, we investigated the impact of DDX5 depletion and overexpression on SINV infection at the viral protein, RNA and infectious particle accumulation level. The contribution of DDX17 was also tested by knockdown experiments.nnRESULTS: In this study we demonstrate that DDX5 interacts with the SINV RNA during infection. Furthermore, the proteomic analysis of the DDX5 interactome in mock and SINV-infected HCT116 cells identified new cellular and viral partners and confirmed the interaction between DDX5 and DDX17. Both DDX5 and DDX17 re-localize from the nucleus to the cytoplasm upon SINV infection and interact with the viral capsid protein. We also show that DDX5 depletion negatively impacts the viral replication cycle, while its overexpression has a pro-viral effect. Finally, we observed that DDX17 depletion reduces SINV infection, an effect which is even more pronounced in a DDX5-depleted background, suggesting a synergistic pro-viral effect of the DDX5 and DDX17 proteins on SINV.nnCONCLUSIONS: These results not only shed light on DDX5 as a novel and important host factor to the SINV life cycle, but also expand our understanding of the roles played by DDX5 and DDX17 as regulators of viral infections.},
keywords = {PFEFFER, PPSE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
BACKGROUND: RNA helicases are emerging as key factors regulating host-virus interactions. The DEAD-box ATP-dependent RNA helicase DDX5, which plays an important role in many aspects of cellular RNA biology, was also found to either promote or inhibit viral replication upon infection with several RNA viruses. Here, our aim is to examine the impact of DDX5 on Sindbis virus (SINV) infection.nnMETHODS: We analysed the interaction between DDX5 and the viral RNA using imaging and RNA-immunoprecipitation approaches. The interactome of DDX5 in mock- and SINV-infected cells was determined by mass spectrometry. We validated the interaction between DDX17 and the viral capsid by co- immunoprecipitation in the presence or absence of an RNase treatment. We determined the subcellular localization of DDX5, its cofactor DDX17 and the viral capsid protein by co-immunofluorescence. Finally, we investigated the impact of DDX5 depletion and overexpression on SINV infection at the viral protein, RNA and infectious particle accumulation level. The contribution of DDX17 was also tested by knockdown experiments.nnRESULTS: In this study we demonstrate that DDX5 interacts with the SINV RNA during infection. Furthermore, the proteomic analysis of the DDX5 interactome in mock and SINV-infected HCT116 cells identified new cellular and viral partners and confirmed the interaction between DDX5 and DDX17. Both DDX5 and DDX17 re-localize from the nucleus to the cytoplasm upon SINV infection and interact with the viral capsid protein. We also show that DDX5 depletion negatively impacts the viral replication cycle, while its overexpression has a pro-viral effect. Finally, we observed that DDX17 depletion reduces SINV infection, an effect which is even more pronounced in a DDX5-depleted background, suggesting a synergistic pro-viral effect of the DDX5 and DDX17 proteins on SINV.nnCONCLUSIONS: These results not only shed light on DDX5 as a novel and important host factor to the SINV life cycle, but also expand our understanding of the roles played by DDX5 and DDX17 as regulators of viral infections.
D'Agostino Mattia, Simonetti Angelita, Motta Stefano, Wolff Philippe, Romagnoli Alice, Piccinini Astra, Spinozzi Francesco, Marino Daniele Di, Teana Anna La, Ennifar Eric
Crystal structure of archaeal IF5A-DHS complex reveals insights into the hypusination mechanism Article de journal
Dans: Structure, 2024, ISSN: 1878-4186.
Résumé | Liens | BibTeX | Étiquettes: ARN-MS, ENNIFAR, Unité ARN
@article{pmid38582076,
title = {Crystal structure of archaeal IF5A-DHS complex reveals insights into the hypusination mechanism},
author = {Mattia D'Agostino and Angelita Simonetti and Stefano Motta and Philippe Wolff and Alice Romagnoli and Astra Piccinini and Francesco Spinozzi and Daniele Di Marino and Anna La Teana and Eric Ennifar},
doi = {10.1016/j.str.2024.03.008},
issn = {1878-4186},
year = {2024},
date = {2024-03-01},
urldate = {2024-03-01},
journal = {Structure},
abstract = {The translation factor IF5A is highly conserved in Eukarya and Archaea and undergoes a unique post-translational hypusine modification by the deoxyhypusine synthase (DHS) enzyme. DHS transfers the butylamine moiety from spermidine to IF5A using NAD as a cofactor, forming a deoxyhypusine intermediate. IF5A is a key player in protein synthesis, preventing ribosome stalling in proline-rich sequences during translation elongation and facilitating translation elongation and termination. Additionally, human eIF5A participates in various essential cellular processes and contributes to cancer metastasis, with inhibiting hypusination showing anti-proliferative effects. The hypusination pathway of IF5A is therefore an attractive new therapeutic target. We elucidated the 2.0 Å X-ray crystal structure of the archaeal DHS-IF5A complex, revealing hetero-octameric architecture and providing a detailed view of the complex active site including the hypusination loop. This structure, along with biophysical data and molecular dynamics simulations, provides new insights into the catalytic mechanism of the hypusination reaction.},
keywords = {ARN-MS, ENNIFAR, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The translation factor IF5A is highly conserved in Eukarya and Archaea and undergoes a unique post-translational hypusine modification by the deoxyhypusine synthase (DHS) enzyme. DHS transfers the butylamine moiety from spermidine to IF5A using NAD as a cofactor, forming a deoxyhypusine intermediate. IF5A is a key player in protein synthesis, preventing ribosome stalling in proline-rich sequences during translation elongation and facilitating translation elongation and termination. Additionally, human eIF5A participates in various essential cellular processes and contributes to cancer metastasis, with inhibiting hypusination showing anti-proliferative effects. The hypusination pathway of IF5A is therefore an attractive new therapeutic target. We elucidated the 2.0 Å X-ray crystal structure of the archaeal DHS-IF5A complex, revealing hetero-octameric architecture and providing a detailed view of the complex active site including the hypusination loop. This structure, along with biophysical data and molecular dynamics simulations, provides new insights into the catalytic mechanism of the hypusination reaction.
Zhang Jian-Hui, Eriani Gilbert, Zhou Xiao-Long
Pathophysiology of human mitochondrial tRNA metabolism Article de journal
Dans: Trends Endocrinol Metab, 2024, ISSN: 1879-3061.
Résumé | Liens | BibTeX | Étiquettes: ERIANI, Unité ARN
@article{pmid38307811,
title = {Pathophysiology of human mitochondrial tRNA metabolism},
author = {Jian-Hui Zhang and Gilbert Eriani and Xiao-Long Zhou},
doi = {10.1016/j.tem.2024.01.002},
issn = {1879-3061},
year = {2024},
date = {2024-02-01},
urldate = {2024-02-01},
journal = {Trends Endocrinol Metab},
abstract = {Mitochondria play multiple critical roles in cellular activity. In particular, mitochondrial translation is pivotal in the regulation of mitochondrial and cellular homeostasis. In this forum article, we discuss human mitochondrial tRNA metabolism and highlight its tight connection with various mitochondrial diseases caused by mutations in aminoacyl-tRNA synthetases, tRNAs, and tRNA-modifying enzymes.},
keywords = {ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Mitochondria play multiple critical roles in cellular activity. In particular, mitochondrial translation is pivotal in the regulation of mitochondrial and cellular homeostasis. In this forum article, we discuss human mitochondrial tRNA metabolism and highlight its tight connection with various mitochondrial diseases caused by mutations in aminoacyl-tRNA synthetases, tRNAs, and tRNA-modifying enzymes.
Brillet Karl, Janczuk-Richter Marta, Poon Amanda, Laukart-Bradley Joanne, Ennifar Eric, Lebars Isabelle
Characterization of SLA RNA promoter from dengue virus and its interaction with the viral non-structural NS5 protein Article de journal
Dans: Biochimie, vol. 222, p. 87–100, 2024, ISSN: 1638-6183.
Résumé | Liens | BibTeX | Étiquettes: ENNIFAR, Unité ARN
@article{pmid38408720,
title = {Characterization of SLA RNA promoter from dengue virus and its interaction with the viral non-structural NS5 protein},
author = {Karl Brillet and Marta Janczuk-Richter and Amanda Poon and Joanne Laukart-Bradley and Eric Ennifar and Isabelle Lebars},
doi = {10.1016/j.biochi.2024.02.005},
issn = {1638-6183},
year = {2024},
date = {2024-02-01},
urldate = {2024-02-01},
journal = {Biochimie},
volume = {222},
pages = {87--100},
abstract = {The Dengue virus (DENV) is the most significant arthropod-borne viral pathogen in humans with 400 million infections annually. DENV comprises four distinct serotypes (DENV-1 to -4) which complicates vaccine development. Any of the four serotypes can cause clinical illness but with distinctive infection dynamics. Variations in sequences identified within the four genomes induce structural differences in crucial RNA motifs that were suggested to be correlated to the degree of pathogenicity among DENV-1 to -4. In particular, the RNA Stem-loop A (SLA) at the 5'-end of the genome, acts as a key regulator of the viral replication cycle by interacting with the viral NS5 polymerase to initiate the minus-strand viral RNA synthesis and later to methylate and cap the synthesized RNA. The molecular details of this interaction remain not fully described. Here, we report the solution secondary structures of SLA from DENV-1 to -4. Our results highlight that the four SLA exhibit structural and dynamic differences. Secondly, to determine whether SLA RNA contains serotype-specific determinants for the recognition by the viral NS5 protein, we investigated interactions between SLA from DENV -1 to -4 and DENV2 NS5 using combined biophysical approaches. Our results show that NS5 from DENV2 is able to bind SLA from other serotypes, but that other viral or host factors may be necessary to stabilize the complex and promote the catalytically active state of the NS5. By contrast, we show that a serotype-specific binding is driven by specific interactions involving conformational changes within the SLA RNA.},
keywords = {ENNIFAR, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The Dengue virus (DENV) is the most significant arthropod-borne viral pathogen in humans with 400 million infections annually. DENV comprises four distinct serotypes (DENV-1 to -4) which complicates vaccine development. Any of the four serotypes can cause clinical illness but with distinctive infection dynamics. Variations in sequences identified within the four genomes induce structural differences in crucial RNA motifs that were suggested to be correlated to the degree of pathogenicity among DENV-1 to -4. In particular, the RNA Stem-loop A (SLA) at the 5'-end of the genome, acts as a key regulator of the viral replication cycle by interacting with the viral NS5 polymerase to initiate the minus-strand viral RNA synthesis and later to methylate and cap the synthesized RNA. The molecular details of this interaction remain not fully described. Here, we report the solution secondary structures of SLA from DENV-1 to -4. Our results highlight that the four SLA exhibit structural and dynamic differences. Secondly, to determine whether SLA RNA contains serotype-specific determinants for the recognition by the viral NS5 protein, we investigated interactions between SLA from DENV -1 to -4 and DENV2 NS5 using combined biophysical approaches. Our results show that NS5 from DENV2 is able to bind SLA from other serotypes, but that other viral or host factors may be necessary to stabilize the complex and promote the catalytically active state of the NS5. By contrast, we show that a serotype-specific binding is driven by specific interactions involving conformational changes within the SLA RNA.
Soufi G El, Jorio L Di, Gerber Z, Cluzel N, Assche J Van, Delafoy D, Olaso R, Daviaud C, Loustau T, Schwartz C, Trebouet D, Hernalsteens O, Marechal V, Raffestin S, Rousset D, Lint C Van, Deleuze J F, Boni M, and O Rohr, Villain-Gambier M, Wallet C
Highly efficient and sensitive membrane-based concentration process allows quantification, surveillance, and sequencing of viruses in large volumes of wastewater Article de journal
Dans: Water Res, vol. 249, p. 120959, 2024, ISSN: 1879-2448.
Résumé | Liens | BibTeX | Étiquettes: ROHR, Unité ARN
@article{pmid38070350,
title = {Highly efficient and sensitive membrane-based concentration process allows quantification, surveillance, and sequencing of viruses in large volumes of wastewater},
author = {G El Soufi and L Di Jorio and Z Gerber and N Cluzel and J Van Assche and D Delafoy and R Olaso and C Daviaud and T Loustau and C Schwartz and D Trebouet and O Hernalsteens and V Marechal and S Raffestin and D Rousset and C Van Lint and J F Deleuze and M Boni and and O Rohr and M Villain-Gambier and C Wallet},
doi = {10.1016/j.watres.2023.120959},
issn = {1879-2448},
year = {2024},
date = {2024-02-01},
urldate = {2024-02-01},
journal = {Water Res},
volume = {249},
pages = {120959},
abstract = {Wastewater-based epidemiology is experiencing exponential development. Despite undeniable advantages compared to patient-centered approaches (cost, anonymity, survey of large populations without bias, detection of asymptomatic infected peoples…), major technical limitations persist. Among them is the low sensitivity of the current methods used for quantifying and sequencing viral genomes from wastewater. In situations of low viral circulation, during initial stages of viral emergences, or in areas experiencing heavy rains, the extremely low concentrations of viruses in wastewater may fall below the limit of detection of the current methods. The availability during crisis and the cost of the commercial kits, as well as the requirement of expensive materials such as high-speed centrifuge, can also present major blocks to the development of wastewater-based epidemiological survey, specifically in low-income countries. Thereby, highly sensitive, low cost and standardized methods are still needed, to increase the predictability of the viral emergences, to survey low-circulating viruses and to make the results from different labs comparable. Here, we outline and characterize new protocols for concentrating and quantifying SARS-CoV-2 from large volumes (500 mL-1 L) of untreated wastewater. In addition, we report that the methods are applicable for monitoring and sequencing. Our nucleic acid extraction technique (the routine C: 5 mL method) does not require sophisticated equipment such as automatons and is not reliant on commercial kits, making it readily available to a broader range of laboratories for routine epidemiological survey. Furthermore, we demonstrate the efficiency, the repeatability, and the high sensitivity of a new membrane-based concentration method (MBC: 500 mL method) for enveloped (SARS-CoV-2) and non-enveloped (F-specific RNA phages of genogroup II / FRNAPH GGII) viruses. We show that the MBC method allows the quantification and the monitoring of viruses in wastewater with a significantly improved sensitivity compared to the routine C method. In contexts of low viral circulation, we report quantifications of SARS-CoV-2 in wastewater at concentrations as low as 40 genome copies per liter. In highly diluted samples collected in wastewater treatment plants of French Guiana, we confirmed the accuracy of the MBC method compared to the estimations done with the routine C method. Finally, we demonstrate that both the routine C method processing 5 mL and the MBC method processing 500 mL of untreated wastewater are both compatible with SARS-CoV-2 sequencing. We show that the quality of the sequence is correlated with the concentration of the extracted viral genome. Of note, the quality of the sequences obtained with some MBC processed wastewater was improved by dilutions or enzyme substitutions suggesting the presence of specific enzyme inhibitors in some wastewater. To the best of our knowledge, our MBC method is one of the first efficient, sensitive, and repeatable method characterized for SARS-CoV-2 quantification and sequencing from large volumes of wastewater.},
keywords = {ROHR, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Wastewater-based epidemiology is experiencing exponential development. Despite undeniable advantages compared to patient-centered approaches (cost, anonymity, survey of large populations without bias, detection of asymptomatic infected peoples…), major technical limitations persist. Among them is the low sensitivity of the current methods used for quantifying and sequencing viral genomes from wastewater. In situations of low viral circulation, during initial stages of viral emergences, or in areas experiencing heavy rains, the extremely low concentrations of viruses in wastewater may fall below the limit of detection of the current methods. The availability during crisis and the cost of the commercial kits, as well as the requirement of expensive materials such as high-speed centrifuge, can also present major blocks to the development of wastewater-based epidemiological survey, specifically in low-income countries. Thereby, highly sensitive, low cost and standardized methods are still needed, to increase the predictability of the viral emergences, to survey low-circulating viruses and to make the results from different labs comparable. Here, we outline and characterize new protocols for concentrating and quantifying SARS-CoV-2 from large volumes (500 mL-1 L) of untreated wastewater. In addition, we report that the methods are applicable for monitoring and sequencing. Our nucleic acid extraction technique (the routine C: 5 mL method) does not require sophisticated equipment such as automatons and is not reliant on commercial kits, making it readily available to a broader range of laboratories for routine epidemiological survey. Furthermore, we demonstrate the efficiency, the repeatability, and the high sensitivity of a new membrane-based concentration method (MBC: 500 mL method) for enveloped (SARS-CoV-2) and non-enveloped (F-specific RNA phages of genogroup II / FRNAPH GGII) viruses. We show that the MBC method allows the quantification and the monitoring of viruses in wastewater with a significantly improved sensitivity compared to the routine C method. In contexts of low viral circulation, we report quantifications of SARS-CoV-2 in wastewater at concentrations as low as 40 genome copies per liter. In highly diluted samples collected in wastewater treatment plants of French Guiana, we confirmed the accuracy of the MBC method compared to the estimations done with the routine C method. Finally, we demonstrate that both the routine C method processing 5 mL and the MBC method processing 500 mL of untreated wastewater are both compatible with SARS-CoV-2 sequencing. We show that the quality of the sequence is correlated with the concentration of the extracted viral genome. Of note, the quality of the sequences obtained with some MBC processed wastewater was improved by dilutions or enzyme substitutions suggesting the presence of specific enzyme inhibitors in some wastewater. To the best of our knowledge, our MBC method is one of the first efficient, sensitive, and repeatable method characterized for SARS-CoV-2 quantification and sequencing from large volumes of wastewater.
Compain Guillaume, Monsarrat Clément, Blagojevic Julie, Brillet Karl, Dumas Philippe, Hammann Philippe, Kuhn Lauriane, Martiel Isabelle, Engilberge Sylvain, Oliéric Vincent, Wolff Philippe, Burnouf Dominique Y, Wagner Jérôme, Guichard Gilles
Peptide-Based Covalent Inhibitors Bearing Mild Electrophiles to Target a Conserved His Residue of the Bacterial Sliding Clamp Article de journal
Dans: JACS Au, vol. 4, no. 2, p. 432–440, 2024, ISSN: 2691-3704.
Résumé | Liens | BibTeX | Étiquettes: ARN-MS, ENNIFAR, PPSE, Unité ARN
@article{pmid38425897,
title = {Peptide-Based Covalent Inhibitors Bearing Mild Electrophiles to Target a Conserved His Residue of the Bacterial Sliding Clamp},
author = {Guillaume Compain and Clément Monsarrat and Julie Blagojevic and Karl Brillet and Philippe Dumas and Philippe Hammann and Lauriane Kuhn and Isabelle Martiel and Sylvain Engilberge and Vincent Oliéric and Philippe Wolff and Dominique Y Burnouf and Jérôme Wagner and Gilles Guichard},
doi = {10.1021/jacsau.3c00572},
issn = {2691-3704},
year = {2024},
date = {2024-02-01},
urldate = {2024-02-01},
journal = {JACS Au},
volume = {4},
number = {2},
pages = {432--440},
abstract = {Peptide-based covalent inhibitors targeted to nucleophilic protein residues have recently emerged as new modalities to target protein-protein interactions (PPIs) as they may provide some benefits over more classic competitive inhibitors. Covalent inhibitors are generally targeted to cysteine, the most intrinsically reactive amino acid residue, and to lysine, which is more abundant at the surface of proteins but much less frequently to histidine. Herein, we report the structure-guided design of targeted covalent inhibitors (TCIs) able to bind covalently and selectively to the bacterial sliding clamp (SC), by reacting with a well-conserved histidine residue located on the edge of the peptide-binding pocket. SC is an essential component of the bacterial DNA replication machinery, identified as a promising target for the development of new antibacterial compounds. Thermodynamic and kinetic analyses of ligands bearing different mild electrophilic warheads confirmed the higher efficiency of the chloroacetamide compared to Michael acceptors. Two high-resolution X-ray structures of covalent inhibitor-SC adducts were obtained, revealing the canonical orientation of the ligand and details of covalent bond formation with histidine. Proteomic studies were consistent with a selective SC engagement by the chloroacetamide-based TCI. Finally, the TCI of SC was substantially more active than the parent noncovalent inhibitor in an in vitro SC-dependent DNA synthesis assay, validating the potential of the approach to design covalent inhibitors of protein-protein interactions targeted to histidine.},
keywords = {ARN-MS, ENNIFAR, PPSE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Peptide-based covalent inhibitors targeted to nucleophilic protein residues have recently emerged as new modalities to target protein-protein interactions (PPIs) as they may provide some benefits over more classic competitive inhibitors. Covalent inhibitors are generally targeted to cysteine, the most intrinsically reactive amino acid residue, and to lysine, which is more abundant at the surface of proteins but much less frequently to histidine. Herein, we report the structure-guided design of targeted covalent inhibitors (TCIs) able to bind covalently and selectively to the bacterial sliding clamp (SC), by reacting with a well-conserved histidine residue located on the edge of the peptide-binding pocket. SC is an essential component of the bacterial DNA replication machinery, identified as a promising target for the development of new antibacterial compounds. Thermodynamic and kinetic analyses of ligands bearing different mild electrophilic warheads confirmed the higher efficiency of the chloroacetamide compared to Michael acceptors. Two high-resolution X-ray structures of covalent inhibitor-SC adducts were obtained, revealing the canonical orientation of the ligand and details of covalent bond formation with histidine. Proteomic studies were consistent with a selective SC engagement by the chloroacetamide-based TCI. Finally, the TCI of SC was substantially more active than the parent noncovalent inhibitor in an in vitro SC-dependent DNA synthesis assay, validating the potential of the approach to design covalent inhibitors of protein-protein interactions targeted to histidine.
Krishnan A., Ali L. M., Prabhu S. G., Pillai V. N., Chameettachal A., Vivet-Boudou V., Bernacchi S., Mustafa F., Marquet R., Rizvi T. A.
Identification of a putative Gag binding site critical for feline immunodeficiency virus genomic RNA packaging Article de journal
Dans: RNA Journal, vol. 30, p. 68-88, 2024.
Résumé | Liens | BibTeX | Étiquettes: bernacchi, MARQUET, Unité ARN, vivet-boudou
@article{nokey,
title = {Identification of a putative Gag binding site critical for feline immunodeficiency virus genomic RNA packaging},
author = {A. Krishnan and L.M. Ali and S.G. Prabhu and V.N. Pillai and A. Chameettachal and V. Vivet-Boudou and S. Bernacchi and F. Mustafa and R. Marquet and T.A. Rizvi},
editor = {cold spring harbor laboratory press},
url = {https://rnajournal.cshlp.org/content/30/1/68.long},
doi = {10.1261/rna.079840.123},
year = {2024},
date = {2024-01-10},
urldate = {2024-01-10},
journal = {RNA Journal},
volume = {30},
pages = {68-88},
abstract = {The retroviral Gag precursor plays a central role in the selection and packaging of viral genomic RNA (gRNA) by binding to
virus-specific packaging signal(s) (psi or ψ). Previously, we mapped the feline immunodeficiency virus (FIV) ψ to two discontinuous
regions within the 5′ end of the gRNA that assumes a higher order structure harboring several structural motifs. To
better define the region and structural elements important for gRNA packaging, we methodically investigated these FIV ψ
sequences using genetic, biochemical, and structure–function relationship approaches. Our mutational analysis revealed
that the unpaired U85CUG88 stretch within FIV ψ is crucial for gRNA encapsidation into nascent virions. High-throughput
selective 2′ hydroxyl acylation analyzed by primer extension (hSHAPE) performed on wild type (WT) and mutant FIV ψ sequences,
with substitutions in the U85CUG88 stretch, revealed that these mutations had limited structural impact and maintained
nucleotides 80–92 unpaired, as in the WT structure. Since these mutations dramatically affected packaging, our
data suggest that the single-stranded U85CUG88 sequence is important during FIV RNA packaging. Filter-binding assays
performed using purified FIV Pr50Gag on WT and mutant U85CUG88 ψ RNAs led to reduced levels of Pr50Gag binding to
mutant U85CUG88 ψ RNAs, indicating that the U85CUG88 stretch is crucial for ψ RNA–Pr50Gag interactions. Delineating
sequences important for FIV gRNA encapsidation should enhance our understanding of both gRNA packaging and virion
assembly, making them potential targets for novel retroviral therapeutic interventions, as well as the development of
FIV-based vectors for human gene therapy.},
keywords = {bernacchi, MARQUET, Unité ARN, vivet-boudou},
pubstate = {published},
tppubtype = {article}
}
The retroviral Gag precursor plays a central role in the selection and packaging of viral genomic RNA (gRNA) by binding to
virus-specific packaging signal(s) (psi or ψ). Previously, we mapped the feline immunodeficiency virus (FIV) ψ to two discontinuous
regions within the 5′ end of the gRNA that assumes a higher order structure harboring several structural motifs. To
better define the region and structural elements important for gRNA packaging, we methodically investigated these FIV ψ
sequences using genetic, biochemical, and structure–function relationship approaches. Our mutational analysis revealed
that the unpaired U85CUG88 stretch within FIV ψ is crucial for gRNA encapsidation into nascent virions. High-throughput
selective 2′ hydroxyl acylation analyzed by primer extension (hSHAPE) performed on wild type (WT) and mutant FIV ψ sequences,
with substitutions in the U85CUG88 stretch, revealed that these mutations had limited structural impact and maintained
nucleotides 80–92 unpaired, as in the WT structure. Since these mutations dramatically affected packaging, our
data suggest that the single-stranded U85CUG88 sequence is important during FIV RNA packaging. Filter-binding assays
performed using purified FIV Pr50Gag on WT and mutant U85CUG88 ψ RNAs led to reduced levels of Pr50Gag binding to
mutant U85CUG88 ψ RNAs, indicating that the U85CUG88 stretch is crucial for ψ RNA–Pr50Gag interactions. Delineating
sequences important for FIV gRNA encapsidation should enhance our understanding of both gRNA packaging and virion
assembly, making them potential targets for novel retroviral therapeutic interventions, as well as the development of
FIV-based vectors for human gene therapy.
virus-specific packaging signal(s) (psi or ψ). Previously, we mapped the feline immunodeficiency virus (FIV) ψ to two discontinuous
regions within the 5′ end of the gRNA that assumes a higher order structure harboring several structural motifs. To
better define the region and structural elements important for gRNA packaging, we methodically investigated these FIV ψ
sequences using genetic, biochemical, and structure–function relationship approaches. Our mutational analysis revealed
that the unpaired U85CUG88 stretch within FIV ψ is crucial for gRNA encapsidation into nascent virions. High-throughput
selective 2′ hydroxyl acylation analyzed by primer extension (hSHAPE) performed on wild type (WT) and mutant FIV ψ sequences,
with substitutions in the U85CUG88 stretch, revealed that these mutations had limited structural impact and maintained
nucleotides 80–92 unpaired, as in the WT structure. Since these mutations dramatically affected packaging, our
data suggest that the single-stranded U85CUG88 sequence is important during FIV RNA packaging. Filter-binding assays
performed using purified FIV Pr50Gag on WT and mutant U85CUG88 ψ RNAs led to reduced levels of Pr50Gag binding to
mutant U85CUG88 ψ RNAs, indicating that the U85CUG88 stretch is crucial for ψ RNA–Pr50Gag interactions. Delineating
sequences important for FIV gRNA encapsidation should enhance our understanding of both gRNA packaging and virion
assembly, making them potential targets for novel retroviral therapeutic interventions, as well as the development of
FIV-based vectors for human gene therapy.
Lechner Antony, Wolff Philippe
In-Gel Cyanoethylation for Pseudouridines Mass Spectrometry Detection of Bacterial Regulatory RNA Chapitre d'ouvrage
Dans: Véronique Arluison, Claudio Valverde (Ed.): vol. 2741, p. 273–287, Véronique Arluison, Claudio Valverde, 2024, ISSN: 1940-6029.
Résumé | Liens | BibTeX | Étiquettes: ARN-MS, Unité ARN
@inbook{pmid38217659,
title = {In-Gel Cyanoethylation for Pseudouridines Mass Spectrometry Detection of Bacterial Regulatory RNA},
author = {Antony Lechner and Philippe Wolff},
editor = {Véronique Arluison, Claudio Valverde},
doi = {10.1007/978-1-0716-3565-0_15},
issn = {1940-6029},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {Methods Mol Biol},
volume = {2741},
pages = {273--287},
publisher = {Véronique Arluison, Claudio Valverde},
series = {Bacterial Regulatory RNA, Methods and Protocols},
abstract = {Regulatory RNAs, as well as many RNA families, contain chemically modified nucleotides, including pseudouridines (ψ). To map nucleotide modifications, approaches based on enzymatic digestion of RNA followed by nano liquid chromatography-tandem mass spectrometry (nanoLC-MS/MS) analysis were implemented several years ago. However, detection of ψ by mass spectrometry (MS) is challenging as ψ exhibits the same mass as uridine. Thus, a chemical labeling strategy using acrylonitrile was developed to detect this mass-silent modification. Acrylonitrile reacts specifically to ψ to form 1-cyanoethylpseudouridine (Ceψ), resulting in a mass shift of ψ detectable by MS. Here, a protocol detailing the steps from the purification of RNA by polyacrylamide gel electrophoresis, including in-gel labeling of ψ, to MS data interpretation to map ψ and other modifications is proposed. To demonstrate its efficiency, the protocol was applied to bacterial regulatory RNAs from E. coli: 6S RNA and transfer-messenger RNA (tmRNA, also known as 10Sa RNA). Moreover, ribonuclease P (RNase P) was also mapped using this approach. This method enabled the detection of several ψ at single nucleotide resolution.},
keywords = {ARN-MS, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Regulatory RNAs, as well as many RNA families, contain chemically modified nucleotides, including pseudouridines (ψ). To map nucleotide modifications, approaches based on enzymatic digestion of RNA followed by nano liquid chromatography-tandem mass spectrometry (nanoLC-MS/MS) analysis were implemented several years ago. However, detection of ψ by mass spectrometry (MS) is challenging as ψ exhibits the same mass as uridine. Thus, a chemical labeling strategy using acrylonitrile was developed to detect this mass-silent modification. Acrylonitrile reacts specifically to ψ to form 1-cyanoethylpseudouridine (Ceψ), resulting in a mass shift of ψ detectable by MS. Here, a protocol detailing the steps from the purification of RNA by polyacrylamide gel electrophoresis, including in-gel labeling of ψ, to MS data interpretation to map ψ and other modifications is proposed. To demonstrate its efficiency, the protocol was applied to bacterial regulatory RNAs from E. coli: 6S RNA and transfer-messenger RNA (tmRNA, also known as 10Sa RNA). Moreover, ribonuclease P (RNase P) was also mapped using this approach. This method enabled the detection of several ψ at single nucleotide resolution.
Kohl Maximilian P, Chane-Woon-Ming Béatrice, Bahena-Ceron Roberto, Jaramillo-Ponce Jose, Antoine Laura, Herrgott Lucas, Romby Pascale, Marzi Stefano
Ribosome Profiling Methods Adapted to the Study of RNA-Dependent Translation Regulation in Staphylococcus aureus Chapitre d'ouvrage
Dans: Claudio ValverdeVéronique Arluison Véronique Arluison, Claudio Valverde (Ed.): vol. 2741, p. 73–100, Véronique Arluison, Claudio Valverde, Springer, 2024, ISSN: 1940-6029.
Résumé | Liens | BibTeX | Étiquettes: MARZI, ROMBY, Unité ARN
@inbook{pmid38217649,
title = {Ribosome Profiling Methods Adapted to the Study of RNA-Dependent Translation Regulation in Staphylococcus aureus},
author = {Maximilian P Kohl and Béatrice Chane-Woon-Ming and Roberto Bahena-Ceron and Jose Jaramillo-Ponce and Laura Antoine and Lucas Herrgott and Pascale Romby and Stefano Marzi},
editor = {Véronique Arluison, Claudio ValverdeVéronique Arluison, Claudio Valverde},
doi = {10.1007/978-1-0716-3565-0_5},
issn = {1940-6029},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {Methods Mol Biol},
volume = {2741},
pages = {73--100},
publisher = {Véronique Arluison, Claudio Valverde},
edition = {Springer},
series = {Bacterial Regulatory RNA, Methods and Protocols},
abstract = {Noncoding RNAs, including regulatory RNAs (sRNAs), are instrumental in regulating gene expression in pathogenic bacteria, allowing them to adapt to various stresses encountered in their host environments. Staphylococcus aureus is a well-studied model for RNA-mediated regulation of virulence and pathogenicity, with sRNAs playing significant roles in shaping S. aureus interactions with human and animal hosts. By modulating the translation and/or stability of target mRNAs, sRNAs regulate the synthesis of virulence factors and regulatory proteins required for pathogenesis. Moreover, perturbation of the levels of RNA modifications in two other classes of noncoding RNAs, rRNAs, and tRNAs, has been proposed to contribute to stress adaptation. However, the study of how these various factors affect translation regulation has often been restricted to specific genes, using in vivo reporters and/or in vitro translation systems. Genome-wide sequencing approaches offer novel perspectives for studying RNA-dependent regulation. In particular, ribosome profiling methods provide a powerful resource for characterizing the overall landscape of translational regulation, contributing to a better understanding of S. aureus physiopathology. Here, we describe protocols that we have adapted to perform ribosome profiling in S. aureus.},
keywords = {MARZI, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Noncoding RNAs, including regulatory RNAs (sRNAs), are instrumental in regulating gene expression in pathogenic bacteria, allowing them to adapt to various stresses encountered in their host environments. Staphylococcus aureus is a well-studied model for RNA-mediated regulation of virulence and pathogenicity, with sRNAs playing significant roles in shaping S. aureus interactions with human and animal hosts. By modulating the translation and/or stability of target mRNAs, sRNAs regulate the synthesis of virulence factors and regulatory proteins required for pathogenesis. Moreover, perturbation of the levels of RNA modifications in two other classes of noncoding RNAs, rRNAs, and tRNAs, has been proposed to contribute to stress adaptation. However, the study of how these various factors affect translation regulation has often been restricted to specific genes, using in vivo reporters and/or in vitro translation systems. Genome-wide sequencing approaches offer novel perspectives for studying RNA-dependent regulation. In particular, ribosome profiling methods provide a powerful resource for characterizing the overall landscape of translational regulation, contributing to a better understanding of S. aureus physiopathology. Here, we describe protocols that we have adapted to perform ribosome profiling in S. aureus.
Baldaccini Morgane, Gaucherand Léa, Chane-Woon-Ming Béatrice, Messmer Mélanie, Gucciardi Floriane, Pfeffer Sébastien
The helicase domain of human Dicer prevents RNAi-independent activation of antiviral and inflammatory pathways Article de journal
Dans: EMBO J, 2024, ISSN: 1460-2075.
Résumé | Liens | BibTeX | Étiquettes: PFEFFER, Unité ARN
@article{pmid38287188,
title = {The helicase domain of human Dicer prevents RNAi-independent activation of antiviral and inflammatory pathways},
author = {Morgane Baldaccini and Léa Gaucherand and Béatrice Chane-Woon-Ming and Mélanie Messmer and Floriane Gucciardi and Sébastien Pfeffer},
doi = {10.1038/s44318-024-00035-2},
issn = {1460-2075},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {EMBO J},
abstract = {In mammalian somatic cells, the relative contribution of RNAi and the type I interferon response during viral infection is unclear. The apparent inefficiency of antiviral RNAi might be due to self-limiting properties and mitigating co-factors of the key enzyme Dicer. In particular, the helicase domain of human Dicer appears to be an important restriction factor of its activity. Here, we study the involvement of several helicase-truncated mutants of human Dicer in the antiviral response. All deletion mutants display a PKR-dependent antiviral phenotype against certain viruses, and one of them, Dicer N1, acts in a completely RNAi-independent manner. Transcriptomic analyses show that many genes from the interferon and inflammatory response pathways are upregulated in Dicer N1 expressing cells. We show that some of these genes are controlled by NF-kB and that blocking this pathway abrogates the antiviral phenotype of Dicer N1. Our findings highlight the crosstalk between Dicer, PKR, and the NF-kB pathway, and suggest that human Dicer may have repurposed its helicase domain to prevent basal activation of antiviral and inflammatory pathways.},
keywords = {PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
In mammalian somatic cells, the relative contribution of RNAi and the type I interferon response during viral infection is unclear. The apparent inefficiency of antiviral RNAi might be due to self-limiting properties and mitigating co-factors of the key enzyme Dicer. In particular, the helicase domain of human Dicer appears to be an important restriction factor of its activity. Here, we study the involvement of several helicase-truncated mutants of human Dicer in the antiviral response. All deletion mutants display a PKR-dependent antiviral phenotype against certain viruses, and one of them, Dicer N1, acts in a completely RNAi-independent manner. Transcriptomic analyses show that many genes from the interferon and inflammatory response pathways are upregulated in Dicer N1 expressing cells. We show that some of these genes are controlled by NF-kB and that blocking this pathway abrogates the antiviral phenotype of Dicer N1. Our findings highlight the crosstalk between Dicer, PKR, and the NF-kB pathway, and suggest that human Dicer may have repurposed its helicase domain to prevent basal activation of antiviral and inflammatory pathways.
Nerantzaki Maria, Husser Claire, Ryckelynck Michael, Lutz Jean-François
Exchanging and Releasing Information in Synthetic Digital Polymers Using a Strand-Displacement Strategy Article de journal
Dans: J Am Chem Soc, 2024, ISSN: 1520-5126.
Résumé | Liens | BibTeX | Étiquettes: RYCKELYNCK, Unité ARN
@article{pmid38286022,
title = {Exchanging and Releasing Information in Synthetic Digital Polymers Using a Strand-Displacement Strategy},
author = {Maria Nerantzaki and Claire Husser and Michael Ryckelynck and Jean-François Lutz},
doi = {10.1021/jacs.3c13953},
issn = {1520-5126},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {J Am Chem Soc},
abstract = {Toehold-mediated strand displacement (TMSD) was tested as a tool to edit information in synthetic digital polymers. Uniform DNA-polymer biohybrid macromolecules were first synthesized by automated phosphoramidite chemistry and characterized by HPLC, mass spectrometry, and polyacrylamide gel electrophoresis (PAGE). These precursors were diblock structures containing a synthetic poly(phosphodiester) (PPDE) segment covalently attached to a single-stranded DNA sequence. Three types of biohybrids were prepared herein: a substrate containing an accessible toehold as well as input and output macromolecules. The substrate and the input macromolecules contained noncoded PPDE homopolymers, whereas the output macromolecule contained a digitally encoded segment. After hybridization of the substrate with the output, incubation in the presence of the input led to efficient TMSD and the release of the digital segment. TMSD can therefore be used to erase or rewrite information in self-assembled biohybrid superstructures. Furthermore, it was found in this work that the conjugation of DNA single strands to synthetic segments of chosen lengths greatly facilitates the characterization and PAGE visualization of the TMSD process.},
keywords = {RYCKELYNCK, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Toehold-mediated strand displacement (TMSD) was tested as a tool to edit information in synthetic digital polymers. Uniform DNA-polymer biohybrid macromolecules were first synthesized by automated phosphoramidite chemistry and characterized by HPLC, mass spectrometry, and polyacrylamide gel electrophoresis (PAGE). These precursors were diblock structures containing a synthetic poly(phosphodiester) (PPDE) segment covalently attached to a single-stranded DNA sequence. Three types of biohybrids were prepared herein: a substrate containing an accessible toehold as well as input and output macromolecules. The substrate and the input macromolecules contained noncoded PPDE homopolymers, whereas the output macromolecule contained a digitally encoded segment. After hybridization of the substrate with the output, incubation in the presence of the input led to efficient TMSD and the release of the digital segment. TMSD can therefore be used to erase or rewrite information in self-assembled biohybrid superstructures. Furthermore, it was found in this work that the conjugation of DNA single strands to synthetic segments of chosen lengths greatly facilitates the characterization and PAGE visualization of the TMSD process.
Quignon E., Ferhadian D., Hache A., Vivet-Boudou V., Isel C., Printz-Schweigert A., Donchet A., Crépin T., Marquet R.
Structural Impact of the Interaction of the Influenza A Virus Nucleoprotein with Genomic RNA Segments Article de journal
Dans: Viruses, vol. 16, no. 3, p. 421, 2024, ISBN: 10.3390/v16030421.
Résumé | Liens | BibTeX | Étiquettes: MARQUET, MARQUET influenza A virus NP nucleoprotein vRNA RNA structure RNA chaperon chemical probing, Unité ARN
@article{nokey,
title = {Structural Impact of the Interaction of the Influenza A Virus Nucleoprotein with Genomic RNA Segments},
author = {E. Quignon and D. Ferhadian and A. Hache and V. Vivet-Boudou and C. Isel and A. Printz-Schweigert and A. Donchet and T. Crépin and R. Marquet},
url = {https://www.mdpi.com/1999-4915/16/3/421},
isbn = {10.3390/v16030421},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {Viruses},
volume = {16},
number = {3},
pages = {421},
abstract = {Influenza A viruses (IAVs) possess a segmented genome consisting of eight viral RNAs (vRNAs) associated with multiple copies of viral nucleoprotein (NP) and a viral polymerase complex. Despite the crucial role of RNA structure in IAV replication, the impact of NP binding on vRNA structure is not well understood. In this study, we employed SHAPE chemical probing to compare the structure of NS and M vRNAs of WSN IAV in various states: before the addition of NP, in complex with NP, and after the removal of NP. Comparison of the RNA structures before the addition of NP and after its removal reveals that NP, while introducing limited changes, remodels local structures in both vRNAs and long-range interactions in the NS vRNA, suggesting a potentially biologically relevant RNA chaperone activity. In contrast, NP significantly alters the structure of vRNAs in vRNA/NP complexes, though incorporating experimental data into RNA secondary structure prediction proved challenging. Finally, our results suggest that NP not only binds single-stranded RNA but also helices with interruptions, such as bulges or small internal loops, with a preference for G-poor and C/U-rich regions.},
keywords = {MARQUET, MARQUET influenza A virus NP nucleoprotein vRNA RNA structure RNA chaperon chemical probing, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Influenza A viruses (IAVs) possess a segmented genome consisting of eight viral RNAs (vRNAs) associated with multiple copies of viral nucleoprotein (NP) and a viral polymerase complex. Despite the crucial role of RNA structure in IAV replication, the impact of NP binding on vRNA structure is not well understood. In this study, we employed SHAPE chemical probing to compare the structure of NS and M vRNAs of WSN IAV in various states: before the addition of NP, in complex with NP, and after the removal of NP. Comparison of the RNA structures before the addition of NP and after its removal reveals that NP, while introducing limited changes, remodels local structures in both vRNAs and long-range interactions in the NS vRNA, suggesting a potentially biologically relevant RNA chaperone activity. In contrast, NP significantly alters the structure of vRNAs in vRNA/NP complexes, though incorporating experimental data into RNA secondary structure prediction proved challenging. Finally, our results suggest that NP not only binds single-stranded RNA but also helices with interruptions, such as bulges or small internal loops, with a preference for G-poor and C/U-rich regions.
Hayek Hassan, Gross Lauriane, Alghoul Fatima, Martin Franck, Eriani Gilbert, Allmang Christine
Immunoprecipitation Methods to Isolate Messenger Ribonucleoprotein Complexes (mRNP) Chapitre d'ouvrage
Dans: vol. 3234, p. 1–15, M. Cristina Vega, Francisco J. Fernández, Springer, 2024, ISSN: 0065-2598.
Résumé | Liens | BibTeX | Étiquettes: ERIANI, MARTIN, PPSE, Unité ARN
@inbook{pmid38507196,
title = {Immunoprecipitation Methods to Isolate Messenger Ribonucleoprotein Complexes (mRNP)},
author = {Hassan Hayek and Lauriane Gross and Fatima Alghoul and Franck Martin and Gilbert Eriani and Christine Allmang},
doi = {10.1007/978-3-031-52193-5_1},
issn = {0065-2598},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {Adv Exp Med Biol},
volume = {3234},
pages = {1--15},
publisher = {M. Cristina Vega, Francisco J. Fernández},
edition = {Springer},
series = {Advanced Technologies for Protein Complex Production and Characterization},
abstract = {Throughout their life cycle, messenger RNAs (mRNAs) associate with proteins to form ribonucleoproteins (mRNPs). Each mRNA is part of multiple successive mRNP complexes that participate in their biogenesis, cellular localization, translation and decay. The dynamic composition of mRNP complexes and their structural remodelling play crucial roles in the control of gene expression. Studying the endogenous composition of different mRNP complexes is a major challenge. In this chapter, we describe the variety of protein-centric immunoprecipitation methods available for the identification of mRNP complexes and the requirements for their experimental settings.},
keywords = {ERIANI, MARTIN, PPSE, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Throughout their life cycle, messenger RNAs (mRNAs) associate with proteins to form ribonucleoproteins (mRNPs). Each mRNA is part of multiple successive mRNP complexes that participate in their biogenesis, cellular localization, translation and decay. The dynamic composition of mRNP complexes and their structural remodelling play crucial roles in the control of gene expression. Studying the endogenous composition of different mRNP complexes is a major challenge. In this chapter, we describe the variety of protein-centric immunoprecipitation methods available for the identification of mRNP complexes and the requirements for their experimental settings.
Janvier Aurélie, Hayek Hassan, Alghoul Fatima, Gross Lauriane, Allmang Christine, Martin Franck, Eriani Gilbert
Purification of In Vivo or In Vitro-Assembled RNA-Protein Complexes by RNA Centric Methods Chapitre d'ouvrage
Dans: vol. 3234, p. 17–29, M. Cristina Vega, Francisco J. Fernández, Springer, 2024, ISSN: 0065-2598.
Résumé | Liens | BibTeX | Étiquettes: ERIANI, MARTIN, Unité ARN
@inbook{pmid38507197,
title = {Purification of In Vivo or In Vitro-Assembled RNA-Protein Complexes by RNA Centric Methods},
author = {Aurélie Janvier and Hassan Hayek and Fatima Alghoul and Lauriane Gross and Christine Allmang and Franck Martin and Gilbert Eriani},
doi = {10.1007/978-3-031-52193-5_2},
issn = {0065-2598},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {Adv Exp Med Biol},
volume = {3234},
pages = {17--29},
publisher = {M. Cristina Vega, Francisco J. Fernández},
edition = {Springer},
series = {Advanced Technologies for Protein Complex Production and Characterization},
abstract = {Throughout their entire life cycle, RNAs are associated with RNA-binding proteins (RBPs), forming ribonucleoprotein (RNP) complexes with highly dynamic compositions and very diverse functions in RNA metabolism, including splicing, translational regulation, ribosome assembly. Many RNPs remain poorly characterized due to the challenges inherent in their purification and subsequent biochemical characterization. Therefore, developing methods to isolate specific RNA-protein complexes is an important initial step toward understanding their function. Many elegant methodologies have been developed to isolate RNPs. This chapter describes different approaches and methods devised for RNA-specific purification of a target RNP. We focused on general methods for selecting RNPs that target a given RNA under conditions favourable for the copurification of associated factors including RNAs and protein components of the RNP.},
keywords = {ERIANI, MARTIN, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Throughout their entire life cycle, RNAs are associated with RNA-binding proteins (RBPs), forming ribonucleoprotein (RNP) complexes with highly dynamic compositions and very diverse functions in RNA metabolism, including splicing, translational regulation, ribosome assembly. Many RNPs remain poorly characterized due to the challenges inherent in their purification and subsequent biochemical characterization. Therefore, developing methods to isolate specific RNA-protein complexes is an important initial step toward understanding their function. Many elegant methodologies have been developed to isolate RNPs. This chapter describes different approaches and methods devised for RNA-specific purification of a target RNP. We focused on general methods for selecting RNPs that target a given RNA under conditions favourable for the copurification of associated factors including RNAs and protein components of the RNP.
Khodr Radi, Husser Claire, Ryckelynck Michael
Direct fluoride monitoring using a fluorogenic RNA-based biosensor Chapitre d'ouvrage
Dans: Stockbridge, Randy B. (Ed.): vol. 696, p. 85–107, Randy B. Stockbridge, 2024, ISSN: 1557-7988.
Résumé | Liens | BibTeX | Étiquettes: RYCKELYNCK, Unité ARN
@inbook{pmid38658090,
title = {Direct fluoride monitoring using a fluorogenic RNA-based biosensor},
author = {Radi Khodr and Claire Husser and Michael Ryckelynck},
editor = {Randy B. Stockbridge},
doi = {10.1016/bs.mie.2023.12.019},
issn = {1557-7988},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {Methods Enzymol},
volume = {696},
pages = {85--107},
publisher = {Randy B. Stockbridge},
abstract = {Fluorinated compounds, whether naturally occurring or from anthropogenic origin, have been extensively exploited in the last century. Degradation of these compounds by physical or biochemical processes is expected to result in the release of fluoride. Several fluoride detection mechanisms have been previously described. However, most of these methods are not compatible with high- and ultrahigh-throughput screening technologies, lack the ability to real-time monitor the increase of fluoride concentration in solution, or rely on costly reagents (such as cell-free expression systems). Our group recently developed "FluorMango" as the first completely RNA-based and direct fluoride-specific fluorogenic biosensor. To do so, we merged and engineered the Mango-III light-up RNA aptamer and the fluoride-specific aptamer derived from a riboswitch, crcB. In this chapter, we explain how this RNA-based biosensor can be produced in large scale before providing examples of how it can be used to quantitatively detect (end-point measurement) or monitor in real-time fluoride release in complex biological systems by translating it into measurable fluorescent signal.},
keywords = {RYCKELYNCK, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Fluorinated compounds, whether naturally occurring or from anthropogenic origin, have been extensively exploited in the last century. Degradation of these compounds by physical or biochemical processes is expected to result in the release of fluoride. Several fluoride detection mechanisms have been previously described. However, most of these methods are not compatible with high- and ultrahigh-throughput screening technologies, lack the ability to real-time monitor the increase of fluoride concentration in solution, or rely on costly reagents (such as cell-free expression systems). Our group recently developed "FluorMango" as the first completely RNA-based and direct fluoride-specific fluorogenic biosensor. To do so, we merged and engineered the Mango-III light-up RNA aptamer and the fluoride-specific aptamer derived from a riboswitch, crcB. In this chapter, we explain how this RNA-based biosensor can be produced in large scale before providing examples of how it can be used to quantitatively detect (end-point measurement) or monitor in real-time fluoride release in complex biological systems by translating it into measurable fluorescent signal.
2023
Skerniskyte Jurate, Mulet Céline, André Antonin C, Anderson Mark C, Injarabian Louise, Buck Achim, Prade Verena M, Sansonetti Philippe J, Reibel-Foisset Sophie, Walch Axel K, Lebel Michel, Lykkesfeldt Jens, Marteyn Benoit S
Ascorbate deficiency increases progression of shigellosis in guinea pigs and mice infection models Article de journal
Dans: Gut Microbes, vol. 15, no. 2, p. 2271597, 2023, ISSN: 1949-0984.
Résumé | Liens | BibTeX | Étiquettes: MARTEYN, Unité ARN
@article{pmid37876025,
title = {Ascorbate deficiency increases progression of shigellosis in guinea pigs and mice infection models},
author = {Jurate Skerniskyte and Céline Mulet and Antonin C André and Mark C Anderson and Louise Injarabian and Achim Buck and Verena M Prade and Philippe J Sansonetti and Sophie Reibel-Foisset and Axel K Walch and Michel Lebel and Jens Lykkesfeldt and Benoit S Marteyn},
doi = {10.1080/19490976.2023.2271597},
issn = {1949-0984},
year = {2023},
date = {2023-12-01},
urldate = {2023-12-01},
journal = {Gut Microbes},
volume = {15},
number = {2},
pages = {2271597},
abstract = { spp. are the causative agents of bacterial dysentery and shigellosis, mainly in children living in developing countries. The study of entire life cycle and the evaluation of vaccine candidates' protective efficacy have been hampered by the lack of a suitable animal model of infection. None of the studies evaluated so far (rabbit, guinea pig, mouse) allowed the recapitulation of full shigellosis symptoms upon oral challenge. Historical reports have suggested that dysentery and scurvy are both metabolic diseases associated with ascorbate deficiency. Mammals, which are susceptible to infection (humans, non-human primates and guinea pigs) are among the few species unable to synthesize ascorbate. We optimized a low-ascorbate diet to induce moderate ascorbate deficiency, but not scurvy, in guinea pigs to investigate whether poor vitamin C status increases the progression of shigellosis. Moderate ascorbate deficiency increased shigellosis symptom severity during an extended period of time (up to 48 h) in all strains tested (, 5a, and 2a). At late time points, an important influx of neutrophils was observed both within the disrupted colonic mucosa and in the luminal compartment, although was able to disseminate deep into the organ to reach the sub-mucosal layer and the bloodstream. Moreover, we found that ascorbate deficiency also increased penetration into the colon epithelium layer in a Gulo mouse infection model. The use of these new rodent models of shigellosis opens new doors for the study of both infection strategies and immune responses to infection.},
keywords = {MARTEYN, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
spp. are the causative agents of bacterial dysentery and shigellosis, mainly in children living in developing countries. The study of entire life cycle and the evaluation of vaccine candidates' protective efficacy have been hampered by the lack of a suitable animal model of infection. None of the studies evaluated so far (rabbit, guinea pig, mouse) allowed the recapitulation of full shigellosis symptoms upon oral challenge. Historical reports have suggested that dysentery and scurvy are both metabolic diseases associated with ascorbate deficiency. Mammals, which are susceptible to infection (humans, non-human primates and guinea pigs) are among the few species unable to synthesize ascorbate. We optimized a low-ascorbate diet to induce moderate ascorbate deficiency, but not scurvy, in guinea pigs to investigate whether poor vitamin C status increases the progression of shigellosis. Moderate ascorbate deficiency increased shigellosis symptom severity during an extended period of time (up to 48 h) in all strains tested (, 5a, and 2a). At late time points, an important influx of neutrophils was observed both within the disrupted colonic mucosa and in the luminal compartment, although was able to disseminate deep into the organ to reach the sub-mucosal layer and the bloodstream. Moreover, we found that ascorbate deficiency also increased penetration into the colon epithelium layer in a Gulo mouse infection model. The use of these new rodent models of shigellosis opens new doors for the study of both infection strategies and immune responses to infection.
Kompatscher Maria, Bartosik Karolina, Erharter Kevin, Plangger Raphael, Juen Fabian Sebastian, Kreutz Christoph, Micura Ronald, Westhof Eric, Erlacher Matthias D
Contribution of tRNA sequence and modifications to the decoding preferences of E. coli and M. mycoides tRNAGlyUCC for synonymous glycine codons Article de journal
Dans: Nucleic Acids Res, 2023, ISSN: 1362-4962.
Résumé | Liens | BibTeX | Étiquettes: Unité ARN, WESTHOF
@article{pmid38050960,
title = {Contribution of tRNA sequence and modifications to the decoding preferences of E. coli and M. mycoides tRNAGlyUCC for synonymous glycine codons},
author = {Maria Kompatscher and Karolina Bartosik and Kevin Erharter and Raphael Plangger and Fabian Sebastian Juen and Christoph Kreutz and Ronald Micura and Eric Westhof and Matthias D Erlacher},
doi = {10.1093/nar/gkad1136},
issn = {1362-4962},
year = {2023},
date = {2023-12-01},
urldate = {2023-12-01},
journal = {Nucleic Acids Res},
abstract = {tRNA superwobbling, used by certain bacteria and organelles, is an intriguing decoding concept in which a single tRNA isoacceptor is used to decode all synonymous codons of a four-fold degenerate codon box. While Escherichia coli relies on three tRNAGly isoacceptors to decode the four glycine codons (GGN), Mycoplasma mycoides requires only a single tRNAGly. Both organisms express tRNAGly with the anticodon UCC, which are remarkably similar in sequence but different in their decoding ability. By systematically introducing mutations and altering the number and type of tRNA modifications using chemically synthesized tRNAs, we elucidated the contribution of individual nucleotides and chemical groups to decoding by the E. coli and M. mycoides tRNAGly. The tRNA sequence was identified as the key factor for superwobbling, revealing the T-arm sequence as a novel pivotal element. In addition, the presence of tRNA modifications, although not essential for providing superwobbling, was shown to delicately fine-tune and balance the decoding of synonymous codons. This emphasizes that the tRNA sequence and its modifications together form an intricate system of high complexity that is indispensable for accurate and efficient decoding.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
tRNA superwobbling, used by certain bacteria and organelles, is an intriguing decoding concept in which a single tRNA isoacceptor is used to decode all synonymous codons of a four-fold degenerate codon box. While Escherichia coli relies on three tRNAGly isoacceptors to decode the four glycine codons (GGN), Mycoplasma mycoides requires only a single tRNAGly. Both organisms express tRNAGly with the anticodon UCC, which are remarkably similar in sequence but different in their decoding ability. By systematically introducing mutations and altering the number and type of tRNA modifications using chemically synthesized tRNAs, we elucidated the contribution of individual nucleotides and chemical groups to decoding by the E. coli and M. mycoides tRNAGly. The tRNA sequence was identified as the key factor for superwobbling, revealing the T-arm sequence as a novel pivotal element. In addition, the presence of tRNA modifications, although not essential for providing superwobbling, was shown to delicately fine-tune and balance the decoding of synonymous codons. This emphasizes that the tRNA sequence and its modifications together form an intricate system of high complexity that is indispensable for accurate and efficient decoding.
Bahena-Ceron Roberto, Teixeira Chloe, Ponce Jose R Jaramillo, Wolff Philippe, Couzon Florence, François Pauline, Klaholz Bruno, Vandenesch François, Romby Pascale, Moreau Karen, Marzi Stefano
RlmQ: A Newly Discovered rRNA Modification Enzyme Bridging RNA Modification and Virulence Traits in Article de journal
Dans: RNA, vol. 30, no. 3, p. 200-212, 2023, ISSN: 1469-9001.
Résumé | Liens | BibTeX | Étiquettes: ARN-MS, ROMBY, Unité ARN
@article{pmid38164596,
title = {RlmQ: A Newly Discovered rRNA Modification Enzyme Bridging RNA Modification and Virulence Traits in },
author = {Roberto Bahena-Ceron and Chloe Teixeira and Jose R Jaramillo Ponce and Philippe Wolff and Florence Couzon and Pauline François and Bruno Klaholz and François Vandenesch and Pascale Romby and Karen Moreau and Stefano Marzi},
doi = {10.1261/rna.079850.123},
issn = {1469-9001},
year = {2023},
date = {2023-12-01},
urldate = {2023-12-01},
journal = {RNA},
volume = {30},
number = {3},
pages = {200-212},
abstract = {rRNA modifications play crucial roles in fine-tuning the delicate balance between translation speed and accuracy, yet the underlying mechanisms remain elusive. Comparative analyses of the ribosomal RNA modifications in taxonomically distant bacteria could help define their general, as well as species-specific, roles. In this study, we identified a new methyltransferase, RlmQ, in responsible for the Gram-positive specific mG2601, which is not modified in (G2574). We also demonstrate the absence of methylation on C1989, equivalent to C1962, which is methylated at position 5 by the Gram-negative specific RlmI methyltransferase, a paralogue of RlmQ. Both modifications ( mG2601 and mC1962) are situated within the same tRNA accommodation corridor, hinting at a potential shared function in translation. Inactivation of Q causes the loss of methylation at G2601 and significantly impacts growth, cytotoxicity, and biofilm formation. These findings unravel the intricate connections between rRNA modifications, translation, and virulence in pathogenic Gram-positive bacteria.},
keywords = {ARN-MS, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
rRNA modifications play crucial roles in fine-tuning the delicate balance between translation speed and accuracy, yet the underlying mechanisms remain elusive. Comparative analyses of the ribosomal RNA modifications in taxonomically distant bacteria could help define their general, as well as species-specific, roles. In this study, we identified a new methyltransferase, RlmQ, in responsible for the Gram-positive specific mG2601, which is not modified in (G2574). We also demonstrate the absence of methylation on C1989, equivalent to C1962, which is methylated at position 5 by the Gram-negative specific RlmI methyltransferase, a paralogue of RlmQ. Both modifications ( mG2601 and mC1962) are situated within the same tRNA accommodation corridor, hinting at a potential shared function in translation. Inactivation of Q causes the loss of methylation at G2601 and significantly impacts growth, cytotoxicity, and biofilm formation. These findings unravel the intricate connections between rRNA modifications, translation, and virulence in pathogenic Gram-positive bacteria.
Ponce José R Jaramillo, Frugier Magali
Plasmodium, the Apicomplexa Outlier When It Comes to Protein Synthesis Article de journal
Dans: Biomolecules, vol. 14, no. 1, p. 46, 2023, ISSN: 2218-273X.
Résumé | Liens | BibTeX | Étiquettes: FRUGIER, Unité ARN
@article{pmid38254646,
title = {Plasmodium, the Apicomplexa Outlier When It Comes to Protein Synthesis},
author = {José R Jaramillo Ponce and Magali Frugier},
doi = {10.3390/biom14010046},
issn = {2218-273X},
year = {2023},
date = {2023-12-01},
urldate = {2023-12-01},
journal = {Biomolecules},
volume = {14},
number = {1},
pages = {46},
abstract = {Plasmodium is an obligate intracellular parasite that has numerous interactions with different hosts during its elaborate life cycle. This is also the case for the other parasites belonging to the same phylum Apicomplexa. In this study, we bioinformatically identified the components of the multi-synthetase complexes (MSCs) of several Apicomplexa parasites and modelled their assembly using AlphaFold2. It appears that none of these MSCs resemble the two MSCs that we have identified and characterized in Plasmodium. Indeed, tRip, the central protein involved in the association of the two Plasmodium MSCs is different from its homologues, suggesting also that the tRip-dependent import of exogenous tRNAs is not conserved in other apicomplexan parasites. Based on this observation, we searched for obvious differences that could explain the singularity of Plasmodium protein synthesis by comparing tRNA genes and amino acid usage in the different genomes. We noted a contradiction between the large number of asparagine residues used in Plasmodium proteomes and the single gene encoding the tRNA that inserts them into proteins. This observation remains true for all the Plasmodia strains studied, even those that do not contain long asparagine homorepeats. },
keywords = {FRUGIER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Plasmodium is an obligate intracellular parasite that has numerous interactions with different hosts during its elaborate life cycle. This is also the case for the other parasites belonging to the same phylum Apicomplexa. In this study, we bioinformatically identified the components of the multi-synthetase complexes (MSCs) of several Apicomplexa parasites and modelled their assembly using AlphaFold2. It appears that none of these MSCs resemble the two MSCs that we have identified and characterized in Plasmodium. Indeed, tRip, the central protein involved in the association of the two Plasmodium MSCs is different from its homologues, suggesting also that the tRip-dependent import of exogenous tRNAs is not conserved in other apicomplexan parasites. Based on this observation, we searched for obvious differences that could explain the singularity of Plasmodium protein synthesis by comparing tRNA genes and amino acid usage in the different genomes. We noted a contradiction between the large number of asparagine residues used in Plasmodium proteomes and the single gene encoding the tRNA that inserts them into proteins. This observation remains true for all the Plasmodia strains studied, even those that do not contain long asparagine homorepeats.
Lu Kunpeng, Pan Yifei, Shen Jianghong, Yang Lin, Zhan Chengyu, Liang Shubo, Tai Shuaishuai, Wan Linrong, Li Tian, Cheng Tingcai, Ma Bi, Pan Guoqing, He Ningjia, Lu Cheng, Westhof Eric, Xiang Zhonghuai, Han Min-Jin, Tong Xiaoling, Dai Fangyin
SilkMeta: a comprehensive platform for sharing and exploiting pan-genomic and multi-omic silkworm data Article de journal
Dans: Nucleic Acids Res, vol. 52, iss. D1, p. D1024-D1032, 2023, ISSN: 1362-4962.
Résumé | Liens | BibTeX | Étiquettes: Unité ARN, WESTHOF
@article{pmid37941143,
title = {SilkMeta: a comprehensive platform for sharing and exploiting pan-genomic and multi-omic silkworm data},
author = {Kunpeng Lu and Yifei Pan and Jianghong Shen and Lin Yang and Chengyu Zhan and Shubo Liang and Shuaishuai Tai and Linrong Wan and Tian Li and Tingcai Cheng and Bi Ma and Guoqing Pan and Ningjia He and Cheng Lu and Eric Westhof and Zhonghuai Xiang and Min-Jin Han and Xiaoling Tong and Fangyin Dai},
doi = {10.1093/nar/gkad956},
issn = {1362-4962},
year = {2023},
date = {2023-11-01},
urldate = {2023-11-01},
journal = {Nucleic Acids Res},
volume = {52},
issue = {D1},
pages = {D1024-D1032},
abstract = {The silkworm Bombyx mori is a domesticated insect that serves as an animal model for research and agriculture. The silkworm super-pan-genome dataset, which we published last year, is a unique resource for the study of global genomic diversity and phenotype-genotype association. Here we present SilkMeta (http://silkmeta.org.cn), a comprehensive database covering the available silkworm pan-genome and multi-omics data. The database contains 1082 short-read genomes, 546 long-read assembled genomes, 1168 transcriptomes, 294 phenotype characterizations (phenome), tens of millions of variations (variome), 7253 long non-coding RNAs (lncRNAs), 18 717 full length transcripts and a set of population statistics. We have compiled publications on functional genomics research and genetic stock deciphering (mutant map). A range of bioinformatics tools is also provided for data visualization and retrieval. The large batch of omics data and tools were integrated in twelve functional modules that provide useful strategies and data for comparative and functional genomics research. The interactive bioinformatics platform SilkMeta will benefit not only the silkworm but also the insect biology communities.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
The silkworm Bombyx mori is a domesticated insect that serves as an animal model for research and agriculture. The silkworm super-pan-genome dataset, which we published last year, is a unique resource for the study of global genomic diversity and phenotype-genotype association. Here we present SilkMeta (http://silkmeta.org.cn), a comprehensive database covering the available silkworm pan-genome and multi-omics data. The database contains 1082 short-read genomes, 546 long-read assembled genomes, 1168 transcriptomes, 294 phenotype characterizations (phenome), tens of millions of variations (variome), 7253 long non-coding RNAs (lncRNAs), 18 717 full length transcripts and a set of population statistics. We have compiled publications on functional genomics research and genetic stock deciphering (mutant map). A range of bioinformatics tools is also provided for data visualization and retrieval. The large batch of omics data and tools were integrated in twelve functional modules that provide useful strategies and data for comparative and functional genomics research. The interactive bioinformatics platform SilkMeta will benefit not only the silkworm but also the insect biology communities.
Arrivé Mathilde, Bruggeman Mathieu, Skaltsogiannis Vasileios, Coudray Léna, Quan Yi-Fat, Schelcher Cédric, Cognat Valérie, Hammann Philippe, Chicher Johana, Wolff Philippe, Gobert Anthony, Giegé Philippe
A tRNA-modifying enzyme facilitates RNase P activity in Arabidopsis nuclei Article de journal
Dans: Nat Plants, vol. 9, iss. 12, p. 2031-2041, 2023, ISSN: 2055-0278.
Résumé | Liens | BibTeX | Étiquettes: ARN-MS, PPSE, Unité ARN
@article{pmid37945696,
title = {A tRNA-modifying enzyme facilitates RNase P activity in Arabidopsis nuclei},
author = {Mathilde Arrivé and Mathieu Bruggeman and Vasileios Skaltsogiannis and Léna Coudray and Yi-Fat Quan and Cédric Schelcher and Valérie Cognat and Philippe Hammann and Johana Chicher and Philippe Wolff and Anthony Gobert and Philippe Giegé},
doi = {10.1038/s41477-023-01564-0},
issn = {2055-0278},
year = {2023},
date = {2023-11-01},
urldate = {2023-11-01},
journal = {Nat Plants},
volume = {9},
issue = {12},
pages = {2031-2041},
abstract = {RNase P is the essential activity that performs the 5' maturation of transfer RNA (tRNA) precursors. Beyond the ancestral form of RNase P containing a ribozyme, protein-only RNase P enzymes termed PRORP were identified in eukaryotes. In human mitochondria, PRORP forms a complex with two protein partners to become functional. In plants, although PRORP enzymes are active alone, we investigate their interaction network to identify potential tRNA maturation complexes. Here we investigate functional interactions involving the Arabidopsis nuclear RNase P PRORP2. We show, using an immuno-affinity strategy, that PRORP2 occurs in a complex with the tRNA methyl transferases TRM1A and TRM1B in vivo. Beyond RNase P, these enzymes can also interact with RNase Z. We show that TRM1A/TRM1B localize in the nucleus and find that their double knockout mutation results in a severe macroscopic phenotype. Using a combination of immuno-detections, mass spectrometry and a transcriptome-wide tRNA sequencing approach, we observe that TRM1A/TRM1B are responsible for the mG26 modification of 70% of cytosolic tRNAs in vivo. We use the transcriptome wide tRNAseq approach as well as RNA blot hybridizations to show that RNase P activity is impaired in TRM1A/TRM1B mutants for specific tRNAs, in particular, tRNAs containing a mG modification at position 26 that are strongly downregulated in TRM1A/TRM1B mutants. Altogether, results indicate that the mG-adding enzymes TRM1A/TRM1B functionally cooperate with nuclear RNase P in vivo for the early steps of cytosolic tRNA biogenesis.},
keywords = {ARN-MS, PPSE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
RNase P is the essential activity that performs the 5' maturation of transfer RNA (tRNA) precursors. Beyond the ancestral form of RNase P containing a ribozyme, protein-only RNase P enzymes termed PRORP were identified in eukaryotes. In human mitochondria, PRORP forms a complex with two protein partners to become functional. In plants, although PRORP enzymes are active alone, we investigate their interaction network to identify potential tRNA maturation complexes. Here we investigate functional interactions involving the Arabidopsis nuclear RNase P PRORP2. We show, using an immuno-affinity strategy, that PRORP2 occurs in a complex with the tRNA methyl transferases TRM1A and TRM1B in vivo. Beyond RNase P, these enzymes can also interact with RNase Z. We show that TRM1A/TRM1B localize in the nucleus and find that their double knockout mutation results in a severe macroscopic phenotype. Using a combination of immuno-detections, mass spectrometry and a transcriptome-wide tRNA sequencing approach, we observe that TRM1A/TRM1B are responsible for the mG26 modification of 70% of cytosolic tRNAs in vivo. We use the transcriptome wide tRNAseq approach as well as RNA blot hybridizations to show that RNase P activity is impaired in TRM1A/TRM1B mutants for specific tRNAs, in particular, tRNAs containing a mG modification at position 26 that are strongly downregulated in TRM1A/TRM1B mutants. Altogether, results indicate that the mG-adding enzymes TRM1A/TRM1B functionally cooperate with nuclear RNase P in vivo for the early steps of cytosolic tRNA biogenesis.
Silva P Malaka De, Bennett Rebecca J, Kuhn Lauriane, Ngondo Patryk, Debande Lorine, Njamkepo Elisabeth, Ho Brian, Weill François-Xavier, Marteyn Benoît S, Jenkins Claire, Baker Kate S
Escherichia coli killing by epidemiologically successful sublineages of Shigella sonnei is mediated by colicins Article de journal
Dans: EBioMedicine, vol. 97, p. 104822, 2023, ISSN: 2352-3964.
Résumé | Liens | BibTeX | Étiquettes: MARTEYN, PPSE, Unité ARN
@article{pmid37806286,
title = {Escherichia coli killing by epidemiologically successful sublineages of Shigella sonnei is mediated by colicins},
author = {P Malaka De Silva and Rebecca J Bennett and Lauriane Kuhn and Patryk Ngondo and Lorine Debande and Elisabeth Njamkepo and Brian Ho and François-Xavier Weill and Benoît S Marteyn and Claire Jenkins and Kate S Baker},
doi = {10.1016/j.ebiom.2023.104822},
issn = {2352-3964},
year = {2023},
date = {2023-10-01},
urldate = {2023-10-01},
journal = {EBioMedicine},
volume = {97},
pages = {104822},
abstract = {BACKGROUND: Shigella sp. are enteric pathogens which causes >125 million cases of shigellosis annually. S. sonnei accounts for about a quarter of those cases and is increasingly prevalent in industrialising nations. Being an enteric pathogen, S. sonnei benefits from outcompeting gut commensals such as Escherichia coli to establish itself and cause disease. There are numerous mechanisms that bacterial pathogens use to outcompete its rivals including molecules called colicins. A Type 6 Secretion System (T6SS) was recently described as contributing to E. coli killing in S. sonnei.nnMETHODS: We used Bulk Phenotyping of Epidemiological Replicates (BPER) which combined bacterial Genome Wide Association Studies (bGWAS) and high throughput phenotyping on a collection of S. sonnei surveillance isolates to identify the genetic features associated with E. coli killing and explore their relationship with epidemiological behaviour. We further explored the presence of colicins and T6SS components in the isolates using genomics, laboratory experimentation, and proteomics.nnFINDINGS: Our bGWAS analysis returned known and novel colicin and colicin related genes as significantly associated with E. coli killing. In silico analyses identified key colicin clusters responsible for the killing phenotype associated with epidemiologically successful sub-lineages. The killing phenotype was not associated with the presence of a T6SS. Laboratory analyses confirmed the presence of the key colicin clusters and that killing was contact-independent.nnINTERPRETATION: Colicins are responsible for E. coli killing by S. sonnei, not a T6SS. This phenotype contributes to shaping the observed epidemiology of S. sonnei and may contribute to its increasing prevalence globally. BPER is an epidemiologically relevant approach to phenotypic testing that enables the rapid identification of genetic drivers of phenotypic changes, and assessment of their relevance to epidemiology in natural settings.nnFUNDING: Biotechnology and Biological Sciences Research Council, Biotechnology and Biological Sciences Research Council Doctoral Training Partnership studentship, Wellcome Trust, Medical Research Council (UK), French National Research Agency.},
keywords = {MARTEYN, PPSE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
BACKGROUND: Shigella sp. are enteric pathogens which causes >125 million cases of shigellosis annually. S. sonnei accounts for about a quarter of those cases and is increasingly prevalent in industrialising nations. Being an enteric pathogen, S. sonnei benefits from outcompeting gut commensals such as Escherichia coli to establish itself and cause disease. There are numerous mechanisms that bacterial pathogens use to outcompete its rivals including molecules called colicins. A Type 6 Secretion System (T6SS) was recently described as contributing to E. coli killing in S. sonnei.nnMETHODS: We used Bulk Phenotyping of Epidemiological Replicates (BPER) which combined bacterial Genome Wide Association Studies (bGWAS) and high throughput phenotyping on a collection of S. sonnei surveillance isolates to identify the genetic features associated with E. coli killing and explore their relationship with epidemiological behaviour. We further explored the presence of colicins and T6SS components in the isolates using genomics, laboratory experimentation, and proteomics.nnFINDINGS: Our bGWAS analysis returned known and novel colicin and colicin related genes as significantly associated with E. coli killing. In silico analyses identified key colicin clusters responsible for the killing phenotype associated with epidemiologically successful sub-lineages. The killing phenotype was not associated with the presence of a T6SS. Laboratory analyses confirmed the presence of the key colicin clusters and that killing was contact-independent.nnINTERPRETATION: Colicins are responsible for E. coli killing by S. sonnei, not a T6SS. This phenotype contributes to shaping the observed epidemiology of S. sonnei and may contribute to its increasing prevalence globally. BPER is an epidemiologically relevant approach to phenotypic testing that enables the rapid identification of genetic drivers of phenotypic changes, and assessment of their relevance to epidemiology in natural settings.nnFUNDING: Biotechnology and Biological Sciences Research Council, Biotechnology and Biological Sciences Research Council Doctoral Training Partnership studentship, Wellcome Trust, Medical Research Council (UK), French National Research Agency.
Das Rhiju, Kretsch Rachael C, Simpkin Adam J, Mulvaney Thomas, Pham Phillip, Rangan Ramya, Bu Fan, Keegan Ronan M, Topf Maya, Rigden Daniel J, Miao Zhichao, Westhof Eric
Assessment of three-dimensional RNA structure prediction in CASP15 Article de journal
Dans: Proteins, vol. 91, iss. 12, p. 1747-1770, 2023, ISSN: 1097-0134.
Résumé | Liens | BibTeX | Étiquettes: Unité ARN, WESTHOF
@article{pmid37876231,
title = {Assessment of three-dimensional RNA structure prediction in CASP15},
author = {Rhiju Das and Rachael C Kretsch and Adam J Simpkin and Thomas Mulvaney and Phillip Pham and Ramya Rangan and Fan Bu and Ronan M Keegan and Maya Topf and Daniel J Rigden and Zhichao Miao and Eric Westhof},
doi = {10.1002/prot.26602},
issn = {1097-0134},
year = {2023},
date = {2023-10-01},
urldate = {2023-10-01},
journal = {Proteins},
volume = {91},
issue = {12},
pages = {1747-1770},
abstract = {The prediction of RNA three-dimensional structures remains an unsolved problem. Here, we report assessments of RNA structure predictions in CASP15, the first CASP exercise that involved RNA structure modeling. Forty-two predictor groups submitted models for at least one of twelve RNA-containing targets. These models were evaluated by the RNA-Puzzles organizers and, separately, by a CASP-recruited team using metrics (GDT, lDDT) and approaches (Z-score rankings) initially developed for assessment of proteins and generalized here for RNA assessment. The two assessments independently ranked the same predictor groups as first (AIchemy_RNA2), second (Chen), and third (RNAPolis and GeneSilico, tied); predictions from deep learning approaches were significantly worse than these top ranked groups, which did not use deep learning. Further analyses based on direct comparison of predicted models to cryogenic electron microscopy (cryo-EM) maps and x-ray diffraction data support these rankings. With the exception of two RNA-protein complexes, models submitted by CASP15 groups correctly predicted the global fold of the RNA targets. Comparisons of CASP15 submissions to designed RNA nanostructures as well as molecular replacement trials highlight the potential utility of current RNA modeling approaches for RNA nanotechnology and structural biology, respectively. Nevertheless, challenges remain in modeling fine details such as noncanonical pairs, in ranking among submitted models, and in prediction of multiple structures resolved by cryo-EM or crystallography.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
The prediction of RNA three-dimensional structures remains an unsolved problem. Here, we report assessments of RNA structure predictions in CASP15, the first CASP exercise that involved RNA structure modeling. Forty-two predictor groups submitted models for at least one of twelve RNA-containing targets. These models were evaluated by the RNA-Puzzles organizers and, separately, by a CASP-recruited team using metrics (GDT, lDDT) and approaches (Z-score rankings) initially developed for assessment of proteins and generalized here for RNA assessment. The two assessments independently ranked the same predictor groups as first (AIchemy_RNA2), second (Chen), and third (RNAPolis and GeneSilico, tied); predictions from deep learning approaches were significantly worse than these top ranked groups, which did not use deep learning. Further analyses based on direct comparison of predicted models to cryogenic electron microscopy (cryo-EM) maps and x-ray diffraction data support these rankings. With the exception of two RNA-protein complexes, models submitted by CASP15 groups correctly predicted the global fold of the RNA targets. Comparisons of CASP15 submissions to designed RNA nanostructures as well as molecular replacement trials highlight the potential utility of current RNA modeling approaches for RNA nanotechnology and structural biology, respectively. Nevertheless, challenges remain in modeling fine details such as noncanonical pairs, in ranking among submitted models, and in prediction of multiple structures resolved by cryo-EM or crystallography.
Labaronne E., Decimo D., Bertrand L., Guiguettaz L., Sohier T. J. M., Cluet D., Vivet-Boudou V., Dahoui C., François P., Hatin I., Lambotte O., Samri A., Autran B., Etienne L., Goujon C., Paillart J. -C., Namy O., Ramirez B. C., Ohlmann T., Morris A., Ricci E. P.
Dans: (bioRxiv), 2023.
Liens | BibTeX | Étiquettes: PAILLART, Unité ARN
@article{nokey,
title = {Extensive uORF translation from HIV-1 transcripts elicits specific T cell immune responses in infected individuals and conditions DDX3 dependency for expression of main ORFs},
author = {E. Labaronne and D. Decimo and L. Bertrand and L. Guiguettaz and T.J.M. Sohier and D. Cluet and V. Vivet-Boudou and C. Dahoui and P. François and I. Hatin and O. Lambotte and A. Samri and B. Autran and L. Etienne and C. Goujon and J.-C. Paillart and O. Namy and B.C. Ramirez and T. Ohlmann and A. Morris and E.P. Ricci},
doi = {10.1101/2022.04.29.489990},
year = {2023},
date = {2023-09-20},
urldate = {2023-09-20},
journal = {(bioRxiv)},
keywords = {PAILLART, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Zheng Wen-Qiang, Zhang Jian-Hui, Li Zi-Han, Liu Xiuxiu, Zhang Yong, Huang Shuo, Li Jinsong, Zhou Bin, Eriani Gilbert, Wang En-Duo, Zhou Xiao-Long
Mammalian mitochondrial translation infidelity leads to oxidative stress-induced cell cycle arrest and cardiomyopathy Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 120, no. 37, p. e2309714120, 2023, ISSN: 1091-6490.
Résumé | Liens | BibTeX | Étiquettes: ERIANI, Unité ARN
@article{pmid37669377,
title = {Mammalian mitochondrial translation infidelity leads to oxidative stress-induced cell cycle arrest and cardiomyopathy},
author = {Wen-Qiang Zheng and Jian-Hui Zhang and Zi-Han Li and Xiuxiu Liu and Yong Zhang and Shuo Huang and Jinsong Li and Bin Zhou and Gilbert Eriani and En-Duo Wang and Xiao-Long Zhou},
doi = {10.1073/pnas.2309714120},
issn = {1091-6490},
year = {2023},
date = {2023-09-01},
urldate = {2023-09-01},
journal = {Proc Natl Acad Sci U S A},
volume = {120},
number = {37},
pages = {e2309714120},
abstract = {Proofreading (editing) of mischarged tRNAs by cytoplasmic aminoacyl-tRNA synthetases (aaRSs), whose impairment causes neurodegeneration and cardiac diseases, is of high significance for protein homeostasis. However, whether mitochondrial translation needs fidelity and the significance of editing by mitochondrial aaRSs have been unclear. Here, we show that mammalian cells critically depended on the editing of mitochondrial threonyl-tRNA synthetase (mtThrRS, encoded by ), disruption of which accumulated Ser-tRNA and generated a large abundance of Thr-to-Ser misincorporated peptides in vivo. Such infidelity impaired mitochondrial translation and oxidative phosphorylation, causing oxidative stress and cell cycle arrest in the G0/G1 phase. Notably, reactive oxygen species (ROS) scavenging by N-acetylcysteine attenuated this abnormal cell proliferation. A mouse model of heart-specific defective mtThrRS editing was established. Increased ROS levels, blocked cardiomyocyte proliferation, contractile dysfunction, dilated cardiomyopathy, and cardiac fibrosis were observed. Our results elucidate that mitochondria critically require a high level of translational accuracy at Thr codons and highlight the cellular dysfunctions and imbalance in tissue homeostasis caused by mitochondrial mistranslation.},
keywords = {ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Proofreading (editing) of mischarged tRNAs by cytoplasmic aminoacyl-tRNA synthetases (aaRSs), whose impairment causes neurodegeneration and cardiac diseases, is of high significance for protein homeostasis. However, whether mitochondrial translation needs fidelity and the significance of editing by mitochondrial aaRSs have been unclear. Here, we show that mammalian cells critically depended on the editing of mitochondrial threonyl-tRNA synthetase (mtThrRS, encoded by ), disruption of which accumulated Ser-tRNA and generated a large abundance of Thr-to-Ser misincorporated peptides in vivo. Such infidelity impaired mitochondrial translation and oxidative phosphorylation, causing oxidative stress and cell cycle arrest in the G0/G1 phase. Notably, reactive oxygen species (ROS) scavenging by N-acetylcysteine attenuated this abnormal cell proliferation. A mouse model of heart-specific defective mtThrRS editing was established. Increased ROS levels, blocked cardiomyocyte proliferation, contractile dysfunction, dilated cardiomyopathy, and cardiac fibrosis were observed. Our results elucidate that mitochondria critically require a high level of translational accuracy at Thr codons and highlight the cellular dysfunctions and imbalance in tissue homeostasis caused by mitochondrial mistranslation.
Dufossez Robin, Krafft Marie-Pierre, Ursuegui Sylvain, Mosser Michel, Mouftakhir Safae, Pernod Ketty, Chaubet Guilhem, Ryckelynck Michael, Wagner Alain
Microfluidic Droplet Stabilization via SPAAC Promoted Antibody Conjugation at the Water/Oil Interface Article de journal
Dans: ACS Appl Mater Interfaces, vol. 15, iss. 38, p. 45498-45505, 2023, ISSN: 1944-8252.
Résumé | Liens | BibTeX | Étiquettes: RYCKELYNCK, Unité ARN
@article{pmid37704020,
title = {Microfluidic Droplet Stabilization via SPAAC Promoted Antibody Conjugation at the Water/Oil Interface},
author = {Robin Dufossez and Marie-Pierre Krafft and Sylvain Ursuegui and Michel Mosser and Safae Mouftakhir and Ketty Pernod and Guilhem Chaubet and Michael Ryckelynck and Alain Wagner},
doi = {10.1021/acsami.3c10655},
issn = {1944-8252},
year = {2023},
date = {2023-09-01},
urldate = {2023-09-01},
journal = {ACS Appl Mater Interfaces},
volume = {15},
issue = {38},
pages = {45498-45505},
abstract = {Droplet-based microfluidics is leading the development of miniaturized, rapid, and sensitive version of enzyme-linked immunosorbent assays (ELISAs), a central method for protein detection. These assays involve the use of a functionalized surface able to selectively capture the desired analyte. Using the droplet's oil water interface as a capture surface requires designing custom-perfluorinated fluorosurfactants bearing azide-containing polar groups, which spontaneously react when forming the droplet with strain-alkyne-functionalized antibodies solubilized in the aqueous phase. In this article, we present our research on the influence of the structure of surfactant's hydrophilic heads on the efficiency of SPAAC functionalization and on the effect of this antibody grafting process on droplet stability. We have shown that while short linkers lead to high grafting efficiency, long linkers lead to high stability, and that an intermediate size is required to balance both parameters. In the described family of surfactants, the optimal structure proved to be a PEG linker connecting a polar di-azide head and a per-fluoropolyether tail (Krytox). We also found that grafting an increasing amount of antibody, thus increasing interface coverage, increases droplet stability. It thus appears that such a bi-partite system with a reactive fluoro-surfactant in the oil phase and reactive antibody counterpart in the aqueous phase gives access in situ to novel surfactant construct providing unexplored interface structures and droplet functionality.},
keywords = {RYCKELYNCK, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Droplet-based microfluidics is leading the development of miniaturized, rapid, and sensitive version of enzyme-linked immunosorbent assays (ELISAs), a central method for protein detection. These assays involve the use of a functionalized surface able to selectively capture the desired analyte. Using the droplet's oil water interface as a capture surface requires designing custom-perfluorinated fluorosurfactants bearing azide-containing polar groups, which spontaneously react when forming the droplet with strain-alkyne-functionalized antibodies solubilized in the aqueous phase. In this article, we present our research on the influence of the structure of surfactant's hydrophilic heads on the efficiency of SPAAC functionalization and on the effect of this antibody grafting process on droplet stability. We have shown that while short linkers lead to high grafting efficiency, long linkers lead to high stability, and that an intermediate size is required to balance both parameters. In the described family of surfactants, the optimal structure proved to be a PEG linker connecting a polar di-azide head and a per-fluoropolyether tail (Krytox). We also found that grafting an increasing amount of antibody, thus increasing interface coverage, increases droplet stability. It thus appears that such a bi-partite system with a reactive fluoro-surfactant in the oil phase and reactive antibody counterpart in the aqueous phase gives access in situ to novel surfactant construct providing unexplored interface structures and droplet functionality.
Tidu Antonin, Martin Franck
The interplay between cis- and trans-acting factors drives selective mRNA translation initiation in eukaryotes Article de journal
Dans: Biochimie, vol. 217, p. 20-30, 2023, ISSN: 1638-6183.
Résumé | Liens | BibTeX | Étiquettes: MARTIN, Unité ARN
@article{pmid37741547,
title = {The interplay between cis- and trans-acting factors drives selective mRNA translation initiation in eukaryotes},
author = {Antonin Tidu and Franck Martin},
doi = {10.1016/j.biochi.2023.09.017},
issn = {1638-6183},
year = {2023},
date = {2023-09-01},
urldate = {2023-09-01},
journal = {Biochimie},
volume = {217},
pages = {20-30},
abstract = {Translation initiation consists in the assembly of the small and large ribosomal subunits on the start codon. This important step directly modulates the general proteome in living cells. Recently, genome wide studies revealed unexpected translation initiation events from unsuspected novel open reading frames resulting in the synthesis of a so-called 'dark proteome'. Indeed, the identification of the start codon by the translation machinery is a critical step that defines the translational landscape of the cell. Therefore, translation initiation is a highly regulated process in all organisms. In this review, we focus on the various cis- and trans-acting factors that rule the regulation of translation initiation in eukaryotes. Recent discoveries have shown that the guidance of the translation machinery for the choice of the start codon require sophisticated molecular mechanisms. In particular, the 5'UTR and the coding sequences contain cis-acting elements that trigger the use of AUG codons but also non-AUG codons to initiate protein synthesis. The use of these alternative start codons is also largely influenced by numerous trans-acting elements that drive selective mRNA translation in response to environmental changes.},
keywords = {MARTIN, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Translation initiation consists in the assembly of the small and large ribosomal subunits on the start codon. This important step directly modulates the general proteome in living cells. Recently, genome wide studies revealed unexpected translation initiation events from unsuspected novel open reading frames resulting in the synthesis of a so-called 'dark proteome'. Indeed, the identification of the start codon by the translation machinery is a critical step that defines the translational landscape of the cell. Therefore, translation initiation is a highly regulated process in all organisms. In this review, we focus on the various cis- and trans-acting factors that rule the regulation of translation initiation in eukaryotes. Recent discoveries have shown that the guidance of the translation machinery for the choice of the start codon require sophisticated molecular mechanisms. In particular, the 5'UTR and the coding sequences contain cis-acting elements that trigger the use of AUG codons but also non-AUG codons to initiate protein synthesis. The use of these alternative start codons is also largely influenced by numerous trans-acting elements that drive selective mRNA translation in response to environmental changes.
- <