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2023
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 Journal Article
In: Proc Natl Acad Sci U S A, vol. 120, no. 37, pp. e2309714120, 2023, ISSN: 1091-6490.
Abstract | Links | BibTeX | Tags: 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.
Tardivat Yann, Sosnowski Piotr, Tidu Antonin, Westhof Eric, Eriani Gilbert, Martin Franck
SARS-CoV-2 NSP1 induces mRNA cleavages on the ribosome Journal Article
In: Nucleic Acids Res, 2023, ISSN: 1362-4962.
Abstract | Links | BibTeX | Tags: ERIANI, MARTIN, Unité ARN
@article{pmid37503833b,
title = {SARS-CoV-2 NSP1 induces mRNA cleavages on the ribosome},
author = {Yann Tardivat and Piotr Sosnowski and Antonin Tidu and Eric Westhof and Gilbert Eriani and Franck Martin},
doi = {10.1093/nar/gkad627},
issn = {1362-4962},
year = {2023},
date = {2023-07-01},
urldate = {2023-07-01},
journal = {Nucleic Acids Res},
abstract = {In severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the non-structural protein NSP1 inhibits translation of host mRNAs by binding to the mRNA entry channel of the ribosome and, together with the 5'-untranslated region (UTR) of the viral mRNAs, allows the evasion of that inhibition. Here, we show that NSP1 mediates endonucleolytic cleavages of both host and viral mRNAs in the 5'UTR, but with different cleavage patterns. The first pattern is observed in host mRNAs with cleavages interspersed regularly and close to the 5' cap (6-11 nt downstream of the cap). Those cleavage positions depend more on the position relative to the 5' cap than on the sequence itself. The second cleavage pattern occurs at high NSP1 concentrations and only in SARS-CoV-2 RNAs, with the cleavages clustered at positions 45, 46 and 49. Both patterns of cleavage occur with the mRNA and NSP1 bound to the ribosome, with the SL1 hairpin at the 5' end sufficient to protect from NSP1-mediated degradation at low NSP1 concentrations. We show further that the N-terminal domain of NSP1 is necessary and sufficient for efficient cleavage. We suggest that in the ribosome-bound NSP1 protein the catalytic residues of the N-terminal domain are unmasked by the remodelling of the α1- and α2-helices of the C-terminal domain.},
keywords = {ERIANI, MARTIN, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
In severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the non-structural protein NSP1 inhibits translation of host mRNAs by binding to the mRNA entry channel of the ribosome and, together with the 5'-untranslated region (UTR) of the viral mRNAs, allows the evasion of that inhibition. Here, we show that NSP1 mediates endonucleolytic cleavages of both host and viral mRNAs in the 5'UTR, but with different cleavage patterns. The first pattern is observed in host mRNAs with cleavages interspersed regularly and close to the 5' cap (6-11 nt downstream of the cap). Those cleavage positions depend more on the position relative to the 5' cap than on the sequence itself. The second cleavage pattern occurs at high NSP1 concentrations and only in SARS-CoV-2 RNAs, with the cleavages clustered at positions 45, 46 and 49. Both patterns of cleavage occur with the mRNA and NSP1 bound to the ribosome, with the SL1 hairpin at the 5' end sufficient to protect from NSP1-mediated degradation at low NSP1 concentrations. We show further that the N-terminal domain of NSP1 is necessary and sufficient for efficient cleavage. We suggest that in the ribosome-bound NSP1 protein the catalytic residues of the N-terminal domain are unmasked by the remodelling of the α1- and α2-helices of the C-terminal domain.
Giegé Richard, Eriani Gilbert
The tRNA identity landscape for aminoacylation and beyond Journal Article
In: Nucleic Acids Res, vol. 51, no. 4, pp. 1528–1570, 2023, ISSN: 1362-4962.
Abstract | Links | BibTeX | Tags: ERIANI, GIEGE, Unité ARN
@article{pmid36744444,
title = {The tRNA identity landscape for aminoacylation and beyond},
author = {Richard Giegé and Gilbert Eriani},
doi = {10.1093/nar/gkad007},
issn = {1362-4962},
year = {2023},
date = {2023-02-01},
urldate = {2023-02-01},
journal = {Nucleic Acids Res},
volume = {51},
number = {4},
pages = {1528--1570},
abstract = {tRNAs are key partners in ribosome-dependent protein synthesis. This process is highly dependent on the fidelity of tRNA aminoacylation by aminoacyl-tRNA synthetases and relies primarily on sets of identities within tRNA molecules composed of determinants and antideterminants preventing mischarging by non-cognate synthetases. Such identity sets were discovered in the tRNAs of a few model organisms, and their properties were generalized as universal identity rules. Since then, the panel of identity elements governing the accuracy of tRNA aminoacylation has expanded considerably, but the increasing number of reported functional idiosyncrasies has led to some confusion. In parallel, the description of other processes involving tRNAs, often well beyond aminoacylation, has progressed considerably, greatly expanding their interactome and uncovering multiple novel identities on the same tRNA molecule. This review highlights key findings on the mechanistics and evolution of tRNA and tRNA-like identities. In addition, new methods and their results for searching sets of multiple identities on a single tRNA are discussed. Taken together, this knowledge shows that a comprehensive understanding of the functional role of individual and collective nucleotide identity sets in tRNA molecules is needed for medical, biotechnological and other applications.},
keywords = {ERIANI, GIEGE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
tRNAs are key partners in ribosome-dependent protein synthesis. This process is highly dependent on the fidelity of tRNA aminoacylation by aminoacyl-tRNA synthetases and relies primarily on sets of identities within tRNA molecules composed of determinants and antideterminants preventing mischarging by non-cognate synthetases. Such identity sets were discovered in the tRNAs of a few model organisms, and their properties were generalized as universal identity rules. Since then, the panel of identity elements governing the accuracy of tRNA aminoacylation has expanded considerably, but the increasing number of reported functional idiosyncrasies has led to some confusion. In parallel, the description of other processes involving tRNAs, often well beyond aminoacylation, has progressed considerably, greatly expanding their interactome and uncovering multiple novel identities on the same tRNA molecule. This review highlights key findings on the mechanistics and evolution of tRNA and tRNA-like identities. In addition, new methods and their results for searching sets of multiple identities on a single tRNA are discussed. Taken together, this knowledge shows that a comprehensive understanding of the functional role of individual and collective nucleotide identity sets in tRNA molecules is needed for medical, biotechnological and other applications.
2022
Xu Rui, Lou Yanyan, Tidu Antonin, Bulet Philippe, Heinekamp Thorsten, Martin Franck, Brakhage Axel, Li Zi, Liégeois Samuel, Ferrandon Dominique
The Toll pathway mediates Drosophila resilience to Aspergillus mycotoxins through specific Bomanins Journal Article
In: EMBO Rep, pp. e56036, 2022, ISSN: 1469-3178.
Abstract | Links | BibTeX | Tags: ERIANI, ferrandon, M3i, MARTIN, Unité ARN
@article{pmid36322050,
title = {The Toll pathway mediates Drosophila resilience to Aspergillus mycotoxins through specific Bomanins},
author = {Rui Xu and Yanyan Lou and Antonin Tidu and Philippe Bulet and Thorsten Heinekamp and Franck Martin and Axel Brakhage and Zi Li and Samuel Liégeois and Dominique Ferrandon},
url = {https://pubmed.ncbi.nlm.nih.gov/36322050/},
doi = {10.15252/embr.202256036},
issn = {1469-3178},
year = {2022},
date = {2022-11-01},
urldate = {2022-11-01},
journal = {EMBO Rep},
pages = {e56036},
abstract = {Host defense against infections encompasses both resistance, which targets microorganisms for neutralization or elimination, and resilience/disease tolerance, which allows the host to withstand/tolerate pathogens and repair damages. In Drosophila, the Toll signaling pathway is thought to mediate resistance against fungal infections by regulating the secretion of antimicrobial peptides, potentially including Bomanins. We find that Aspergillus fumigatus kills Drosophila Toll pathway mutants without invasion because its dissemination is blocked by melanization, suggesting a role for Toll in host defense distinct from resistance. We report that mutants affecting the Toll pathway or the 55C Bomanin locus are susceptible to the injection of two Aspergillus mycotoxins, restrictocin and verruculogen. The vulnerability of 55C deletion mutants to these mycotoxins is rescued by the overexpression of Bomanins specific to each challenge. Mechanistically, flies in which BomS6 is expressed in the nervous system exhibit an enhanced recovery from the tremors induced by injected verruculogen and display improved survival. Thus, innate immunity also protects the host against the action of microbial toxins through secreted peptides and thereby increases its resilience to infection.},
keywords = {ERIANI, ferrandon, M3i, MARTIN, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Host defense against infections encompasses both resistance, which targets microorganisms for neutralization or elimination, and resilience/disease tolerance, which allows the host to withstand/tolerate pathogens and repair damages. In Drosophila, the Toll signaling pathway is thought to mediate resistance against fungal infections by regulating the secretion of antimicrobial peptides, potentially including Bomanins. We find that Aspergillus fumigatus kills Drosophila Toll pathway mutants without invasion because its dissemination is blocked by melanization, suggesting a role for Toll in host defense distinct from resistance. We report that mutants affecting the Toll pathway or the 55C Bomanin locus are susceptible to the injection of two Aspergillus mycotoxins, restrictocin and verruculogen. The vulnerability of 55C deletion mutants to these mycotoxins is rescued by the overexpression of Bomanins specific to each challenge. Mechanistically, flies in which BomS6 is expressed in the nervous system exhibit an enhanced recovery from the tremors induced by injected verruculogen and display improved survival. Thus, innate immunity also protects the host against the action of microbial toxins through secreted peptides and thereby increases its resilience to infection.
Hayek Hassan, Eriani Gilbert, Allmang Christine
eIF3 Interacts with Selenoprotein mRNAs Journal Article
In: Biomolecules, vol. 12, no. 9, 2022, ISSN: 2218-273X.
Abstract | Links | BibTeX | Tags: ERIANI, Unité ARN
@article{pmid36139107,
title = {eIF3 Interacts with Selenoprotein mRNAs},
author = {Hassan Hayek and Gilbert Eriani and Christine Allmang},
doi = {10.3390/biom12091268},
issn = {2218-273X},
year = {2022},
date = {2022-09-01},
urldate = {2022-09-01},
journal = {Biomolecules},
volume = {12},
number = {9},
abstract = {The synthesis of selenoproteins requires the co-translational recoding of an in-frame UGASec codon. Interactions between the Selenocysteine Insertion Sequence (SECIS) and the SECIS binding protein 2 (SBP2) in the 3'untranslated region (3'UTR) of selenoprotein mRNAs enable the recruitment of the selenocysteine insertion machinery. Several selenoprotein mRNAs undergo unusual cap hypermethylation and are not recognized by the translation initiation factor 4E (eIF4E) but nevertheless translated. The human eukaryotic translation initiation factor 3 (eIF3), composed of 13 subunits (a-m), can selectively recruit several cellular mRNAs and plays roles in specialized translation initiation. Here, we analyzed the ability of eIF3 to interact with selenoprotein mRNAs. By combining ribonucleoprotein immunoprecipitation (RNP IP) in vivo and in vitro with cross-linking experiments, we found interactions between eIF3 and a subgroup of selenoprotein mRNAs. We showed that eIF3 preferentially interacts with hypermethylated capped selenoprotein mRNAs rather than mG-capped mRNAs. We identified direct contacts between GPx1 mRNA and eIF3 c, d, and e subunits and showed the existence of common interaction patterns for all hypermethylated capped selenoprotein mRNAs. Differential interactions of eIF3 with selenoprotein mRNAs may trigger specific translation pathways independent of eIF4E. eIF3 could represent a new player in the translation regulation and hierarchy of selenoprotein expression.},
keywords = {ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The synthesis of selenoproteins requires the co-translational recoding of an in-frame UGASec codon. Interactions between the Selenocysteine Insertion Sequence (SECIS) and the SECIS binding protein 2 (SBP2) in the 3'untranslated region (3'UTR) of selenoprotein mRNAs enable the recruitment of the selenocysteine insertion machinery. Several selenoprotein mRNAs undergo unusual cap hypermethylation and are not recognized by the translation initiation factor 4E (eIF4E) but nevertheless translated. The human eukaryotic translation initiation factor 3 (eIF3), composed of 13 subunits (a-m), can selectively recruit several cellular mRNAs and plays roles in specialized translation initiation. Here, we analyzed the ability of eIF3 to interact with selenoprotein mRNAs. By combining ribonucleoprotein immunoprecipitation (RNP IP) in vivo and in vitro with cross-linking experiments, we found interactions between eIF3 and a subgroup of selenoprotein mRNAs. We showed that eIF3 preferentially interacts with hypermethylated capped selenoprotein mRNAs rather than mG-capped mRNAs. We identified direct contacts between GPx1 mRNA and eIF3 c, d, and e subunits and showed the existence of common interaction patterns for all hypermethylated capped selenoprotein mRNAs. Differential interactions of eIF3 with selenoprotein mRNAs may trigger specific translation pathways independent of eIF4E. eIF3 could represent a new player in the translation regulation and hierarchy of selenoprotein expression.
Costa P. J. Da, Hamdane M., Buee L., Martin F.
Tau mRNA Metabolism in Neurodegenerative Diseases: A Tangle Journey Journal Article
In: Biomedicines, vol. 10, no. 2, pp. 241, 2022.
Abstract | Links | BibTeX | Tags: ERIANI, mRNA metabolism, Neurodegenerative Diseases, tau protein, Translation, Unité ARN
@article{nokey,
title = {Tau mRNA Metabolism in Neurodegenerative Diseases: A Tangle Journey},
author = {P. J. Da Costa and M. Hamdane and L. Buee and F. Martin},
url = {https://www.mdpi.com/2227-9059/10/2/241/htm},
doi = {10.3390/biomedicines10020241},
year = {2022},
date = {2022-01-01},
journal = {Biomedicines},
volume = {10},
number = {2},
pages = {241},
abstract = {Tau proteins are known to be mainly involved in regulation of microtubule dynamics. Besides this function, which is critical for axonal transport and signal transduction, tau proteins also have other roles in neurons. Moreover, tau proteins are turned into aggregates and consequently trigger many neurodegenerative diseases termed tauopathies, of which Alzheimerﾒs disease (AD) is the figurehead. Such pathological aggregation processes are critical for the onset of these diseases. Among the various causes of tau protein pathogenicity, abnormal tau mRNA metabolism, expression and dysregulation of tau post-translational modifications are critical steps. Moreover, the relevance of tau function to general mRNA metabolism has been highlighted recently in tauopathies. In this review, we mainly focus on how mRNA metabolism impacts the onset and development of tauopathies. Thus, we intend to portray how mRNA metabolism of, or mediated by, tau is associated with neurodegenerative diseases.},
keywords = {ERIANI, mRNA metabolism, Neurodegenerative Diseases, tau protein, Translation, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Tau proteins are known to be mainly involved in regulation of microtubule dynamics. Besides this function, which is critical for axonal transport and signal transduction, tau proteins also have other roles in neurons. Moreover, tau proteins are turned into aggregates and consequently trigger many neurodegenerative diseases termed tauopathies, of which Alzheimerﾒs disease (AD) is the figurehead. Such pathological aggregation processes are critical for the onset of these diseases. Among the various causes of tau protein pathogenicity, abnormal tau mRNA metabolism, expression and dysregulation of tau post-translational modifications are critical steps. Moreover, the relevance of tau function to general mRNA metabolism has been highlighted recently in tauopathies. In this review, we mainly focus on how mRNA metabolism impacts the onset and development of tauopathies. Thus, we intend to portray how mRNA metabolism of, or mediated by, tau is associated with neurodegenerative diseases.
Sosnowski P, Tidu A, Eriani G, Westhof E, Martin F
Correlated sequence signatures are present within the genomic 5'UTR RNA and NSP1 protein in coronaviruses Journal Article
In: Rna, vol. 28, iss. 5, pp. 729-741, 2022, ISBN: 35236777, (1469-9001 (Electronic) 1355-8382 (Linking) Journal Article).
Abstract | Links | BibTeX | Tags: ERIANI, MARTIN, Unité ARN, WESTHOF
@article{nokey,
title = {Correlated sequence signatures are present within the genomic 5'UTR RNA and NSP1 protein in coronaviruses},
author = {P Sosnowski and A Tidu and G Eriani and E Westhof and F Martin},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35236777},
doi = {10.1261/rna.078972.121},
isbn = {35236777},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Rna},
volume = {28},
issue = {5},
pages = {729-741},
abstract = {The 5'UTR part of coronavirus genomes plays key roles in the viral replication cycle and the translation of the viral mRNAs. The first 75-80 nucleotides, also called the leader sequence, are identical for the genomic mRNA and for the subgenomic mRNAs. Recently, it was shown that cooperative actions of a 5'UTR segment and the non-structural protein NSP1 are essential for both the inhibition of host mRNAs and for specific translation of viral mRNAs. Here, sequence analyses of both the 5'UTR RNA segment and the NSP1 protein have been done for several coronaviruses with special attention to the betacoronaviruses. The conclusions are (i) precise specific molecular signatures can be found in both the RNA and the NSP1 protein; (ii) both types of signatures strongly correlate between each other. Indeed, definite sequence motifs in the RNA correlate with sequence motifs in the protein indicating a co-evolution of 5'UTR with NSP1 in betacoronaviruses. Experimental mutational data on 5'UTR and NSP1 from SARS-CoV-2 using cell-free translation extracts support those conclusions and show that the N-terminal half of the NSP1 protein contains conserved key residues that are essential for evasion to the inhibitory effect of NSP1 on translation.},
note = {1469-9001 (Electronic)
1355-8382 (Linking)
Journal Article},
keywords = {ERIANI, MARTIN, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
The 5'UTR part of coronavirus genomes plays key roles in the viral replication cycle and the translation of the viral mRNAs. The first 75-80 nucleotides, also called the leader sequence, are identical for the genomic mRNA and for the subgenomic mRNAs. Recently, it was shown that cooperative actions of a 5'UTR segment and the non-structural protein NSP1 are essential for both the inhibition of host mRNAs and for specific translation of viral mRNAs. Here, sequence analyses of both the 5'UTR RNA segment and the NSP1 protein have been done for several coronaviruses with special attention to the betacoronaviruses. The conclusions are (i) precise specific molecular signatures can be found in both the RNA and the NSP1 protein; (ii) both types of signatures strongly correlate between each other. Indeed, definite sequence motifs in the RNA correlate with sequence motifs in the protein indicating a co-evolution of 5'UTR with NSP1 in betacoronaviruses. Experimental mutational data on 5'UTR and NSP1 from SARS-CoV-2 using cell-free translation extracts support those conclusions and show that the N-terminal half of the NSP1 protein contains conserved key residues that are essential for evasion to the inhibitory effect of NSP1 on translation.
Eriani G., Martin F.
Viral and cellular translation during SARS-CoV-2 infection Journal Article
In: FEBS Open Bio, vol. 12, iss. 9, pp. 1584-1601, 2022, ISBN: 35429230, (2211-5463 (Electronic) 2211-5463 (Linking) Journal Article Review).
Abstract | Links | BibTeX | Tags: ERIANI, Unité ARN
@article{nokey,
title = {Viral and cellular translation during SARS-CoV-2 infection},
author = {G. Eriani and F. Martin},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35429230},
doi = {10.1002/2211-5463.13413},
isbn = {35429230},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {FEBS Open Bio},
volume = {12},
issue = {9},
pages = {1584-1601},
abstract = {SARS-CoV-2 is a betacoronavirus that emerged in China in December 2019 and which is the causative agent of the Covid-19 pandemic. This enveloped virus contains a large positive-sense single-stranded RNA genome. In this review, we summarize the current knowledge on the molecular mechanisms for the translation of both viral transcripts and cellular messenger RNAs. Non-structural proteins are encoded by the genomic RNA and are produced in the early steps of infection. In contrast, the structural proteins are produced from subgenomic RNAs that are translated in the late phase of the infectious program. Non-structural protein 1 (NSP1) is a key molecule that regulates both viral and cellular translation. In addition, NSP1 interferes with multiple steps of the interferon I pathway and thereby blocks host antiviral responses. Therefore, NSP1 is a drug target of choice for the development of antiviral therapies.},
note = {2211-5463 (Electronic)
2211-5463 (Linking)
Journal Article
Review},
keywords = {ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
SARS-CoV-2 is a betacoronavirus that emerged in China in December 2019 and which is the causative agent of the Covid-19 pandemic. This enveloped virus contains a large positive-sense single-stranded RNA genome. In this review, we summarize the current knowledge on the molecular mechanisms for the translation of both viral transcripts and cellular messenger RNAs. Non-structural proteins are encoded by the genomic RNA and are produced in the early steps of infection. In contrast, the structural proteins are produced from subgenomic RNAs that are translated in the late phase of the infectious program. Non-structural protein 1 (NSP1) is a key molecule that regulates both viral and cellular translation. In addition, NSP1 interferes with multiple steps of the interferon I pathway and thereby blocks host antiviral responses. Therefore, NSP1 is a drug target of choice for the development of antiviral therapies.
2021
Li G, Eriani G, Wang E D, Zhou X L
Distinct pathogenic mechanisms of various RARS1 mutations in Pelizaeus-Merzbacher-like disease Journal Article
In: Sci China Life Sci, vol. 64, no. 10, pp. 1645-1660, 2021, ISBN: 33515434, (1869-1889 (Electronic) 1674-7305 (Linking) Journal Article).
Abstract | Links | BibTeX | Tags: aminoacyl-tRNA synthetase (aaRS), central nervous system (CNS), ERIANI, Protein Biosynthesis, translation initiation, tRNA, Unité ARN
@article{,
title = {Distinct pathogenic mechanisms of various RARS1 mutations in Pelizaeus-Merzbacher-like disease},
author = {G Li and G Eriani and E D Wang and X L Zhou},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33515434},
doi = {10.1007/s11427-020-1838-2},
isbn = {33515434},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Sci China Life Sci},
volume = {64},
number = {10},
pages = {1645-1660},
abstract = {Mutations of the genes encoding aminoacyl-tRNA synthetases are highly associated with various central nervous system disorders. Recurrent mutations, including c.5A>G, p.D2G; c.1367C>T, p.S456L; c.1535G>A, p.R512Q and c.1846_1847del, p. Y616Lfs*6 of RARS1 gene, which encodes two forms of human cytoplasmic arginyl-tRNA synthetase (hArgRS), are linked to Pelizaeus-Merzbacher-like disease (PMLD) with unclear pathogenesis. Among these mutations, c.5A>G is the most extensively reported mutation, leading to a p.D2G mutation in the N-terminal extension of the long-form hArgRS. Here, we showed the detrimental effects of R512Q substitution and DeltaC mutations on the structure and function of hArgRS, while the most frequent mutation c.5A>G, p.D2G acted in a different manner without impairing hArgRS activity. The nucleotide substitution c.5A>G reduced translation of hArgRS mRNA, and an upstream open reading frame contributed to the suppressed translation of the downstream main ORF. Taken together, our results elucidated distinct pathogenic mechanisms of various RARS1 mutations in PMLD.},
note = {1869-1889 (Electronic)
1674-7305 (Linking)
Journal Article},
keywords = {aminoacyl-tRNA synthetase (aaRS), central nervous system (CNS), ERIANI, Protein Biosynthesis, translation initiation, tRNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Mutations of the genes encoding aminoacyl-tRNA synthetases are highly associated with various central nervous system disorders. Recurrent mutations, including c.5A>G, p.D2G; c.1367C>T, p.S456L; c.1535G>A, p.R512Q and c.1846_1847del, p. Y616Lfs*6 of RARS1 gene, which encodes two forms of human cytoplasmic arginyl-tRNA synthetase (hArgRS), are linked to Pelizaeus-Merzbacher-like disease (PMLD) with unclear pathogenesis. Among these mutations, c.5A>G is the most extensively reported mutation, leading to a p.D2G mutation in the N-terminal extension of the long-form hArgRS. Here, we showed the detrimental effects of R512Q substitution and DeltaC mutations on the structure and function of hArgRS, while the most frequent mutation c.5A>G, p.D2G acted in a different manner without impairing hArgRS activity. The nucleotide substitution c.5A>G reduced translation of hArgRS mRNA, and an upstream open reading frame contributed to the suppressed translation of the downstream main ORF. Taken together, our results elucidated distinct pathogenic mechanisms of various RARS1 mutations in PMLD.
Hayek H, Gross L, Janvier A, Schaeffer L, Martin F, Eriani G, Allmang C
eIF3 interacts with histone H4 messenger RNA to regulate its translation Journal Article
In: J Biol Chem, vol. 296, pp. 100578, 2021, ISBN: 33766559, (1083-351X (Electronic) 0021-9258 (Linking) Journal Article).
Abstract | Links | BibTeX | Tags: ERIANI, eukaryotic initiation factor, histone mRNA, protein synthesis, RNA protein interaction, RNA structure, translation initiation, translation regulation
@article{Hayek2021,
title = {eIF3 interacts with histone H4 messenger RNA to regulate its translation},
author = {H Hayek and L Gross and A Janvier and L Schaeffer and F Martin and G Eriani and C Allmang},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33766559},
doi = {10.1016/j.jbc.2021.100578},
isbn = {33766559},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {J Biol Chem},
volume = {296},
pages = {100578},
abstract = {In eukaryotes, various alternative translation initiation mechanisms have been unveiled for the translation of specific mRNAs. Some do not conform to the conventional scanning-initiation model. Translation initiation of histone H4 mRNA combines both canonical (cap-dependent) and viral initiation strategies (no-scanning, internal recruitment of initiation factors). Specific H4 mRNA structures tether the translation machinery directly onto the initiation codon and allow massive production of histone H4 during the S phase of the cell cycle. The human eukaryotic translation initiation factor 3 (eIF3), composed of 13 subunits (a-m), was shown to selectively recruit and control the expression of several cellular mRNAs. Whether eIF3 mediates H4 mRNA translation remains to be elucidated. Here, we report that eIF3 binds to a stem-loop structure (eIF3-BS) located in the coding region of H4 mRNA. Combining cross-linking and ribonucleoprotein immunoprecipitation experiments in vivo and in vitro, we also found that eIF3 binds to H1, H2A, H2B and H3 histone mRNAs. We identified direct contacts between eIF3c, d, e, g subunits and histone mRNAs but observed distinct interaction patterns to each histone mRNA. Our results show that eIF3 depletion in vivo reduces histone mRNA binding and modulates histone neosynthesis, suggesting that synthesis of histones is sensitive to the levels of eIF3. Thus, we provide evidence that eIF3 acts as a regulator of histone translation.},
note = {1083-351X (Electronic)
0021-9258 (Linking)
Journal Article},
keywords = {ERIANI, eukaryotic initiation factor, histone mRNA, protein synthesis, RNA protein interaction, RNA structure, translation initiation, translation regulation},
pubstate = {published},
tppubtype = {article}
}
In eukaryotes, various alternative translation initiation mechanisms have been unveiled for the translation of specific mRNAs. Some do not conform to the conventional scanning-initiation model. Translation initiation of histone H4 mRNA combines both canonical (cap-dependent) and viral initiation strategies (no-scanning, internal recruitment of initiation factors). Specific H4 mRNA structures tether the translation machinery directly onto the initiation codon and allow massive production of histone H4 during the S phase of the cell cycle. The human eukaryotic translation initiation factor 3 (eIF3), composed of 13 subunits (a-m), was shown to selectively recruit and control the expression of several cellular mRNAs. Whether eIF3 mediates H4 mRNA translation remains to be elucidated. Here, we report that eIF3 binds to a stem-loop structure (eIF3-BS) located in the coding region of H4 mRNA. Combining cross-linking and ribonucleoprotein immunoprecipitation experiments in vivo and in vitro, we also found that eIF3 binds to H1, H2A, H2B and H3 histone mRNAs. We identified direct contacts between eIF3c, d, e, g subunits and histone mRNAs but observed distinct interaction patterns to each histone mRNA. Our results show that eIF3 depletion in vivo reduces histone mRNA binding and modulates histone neosynthesis, suggesting that synthesis of histones is sensitive to the levels of eIF3. Thus, we provide evidence that eIF3 acts as a regulator of histone translation.
Alghoul F, Eriani G, Martin F
RNA Secondary Structure Study by Chemical Probing Methods Using DMS and CMCT Book Chapter
In: Rederstorff, M (Ed.): Methods Mol Biol, vol. 2300, pp. 241-250, Springer Protocols, Humana Press, New York, NY, 2021, ISBN: 978-1-0716-1385-6/ISSN, (1940-6029 (Electronic) 1064-3745 (Linking) Journal Article).
Abstract | Links | BibTeX | Tags: Capillary electrophoresis, chemical probing, CMCT, DMS, ERIANI, Primer extension, QuSHAPE, RNA secondary structure, Unité ARN
@inbook{Alghoul2021,
title = {RNA Secondary Structure Study by Chemical Probing Methods Using DMS and CMCT},
author = {F Alghoul and G Eriani and F Martin},
editor = {M Rederstorff},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33792883},
doi = {10.1007/978-1-0716-1386-3_18},
isbn = {978-1-0716-1385-6/ISSN},
year = {2021},
date = {2021-01-01},
booktitle = {Methods Mol Biol},
volume = {2300},
pages = {241-250},
publisher = {Springer Protocols, Humana Press},
address = {New York, NY},
series = {Methods in Molecular Biology},
abstract = {RNA folds into secondary structures that can serve in understanding various RNA functions (Weeks KM. Curr Opin Struct Biol 20(3):295-304, 2010). Chemical probing is a method that enables the characterization of RNA secondary structures using chemical reagents that specifically modify RNA nucleotides that are located in single-stranded areas. In our protocol, we used Dimethyl Sulfate (DMS) and Cyclohexyl-3-(2-Morpholinoethyl) Carbodiimide metho-p-Toluene sulfonate (CMCT) that are both base-specific modifying reagents (Behm-Ansmant I, et al. J Nucleic Acids 2011:408053, 2011). These modifications are mapped by primer extension arrests using 5' fluorescently labeled primers. In this protocol, we show a comprehensive method to identify RNA secondary structures in vitro using fluorescently labeled oligos. To demonstrate the efficiency of the method, we give an example of a structure we have designed which corresponds to a part of the 5'-UTR regulatory element called Translation Inhibitory Element (TIE) from Hox a3 mRNA (Xue S, et al. Nature 517(7532):33-38, 2015).},
note = {1940-6029 (Electronic)
1064-3745 (Linking)
Journal Article},
keywords = {Capillary electrophoresis, chemical probing, CMCT, DMS, ERIANI, Primer extension, QuSHAPE, RNA secondary structure, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
RNA folds into secondary structures that can serve in understanding various RNA functions (Weeks KM. Curr Opin Struct Biol 20(3):295-304, 2010). Chemical probing is a method that enables the characterization of RNA secondary structures using chemical reagents that specifically modify RNA nucleotides that are located in single-stranded areas. In our protocol, we used Dimethyl Sulfate (DMS) and Cyclohexyl-3-(2-Morpholinoethyl) Carbodiimide metho-p-Toluene sulfonate (CMCT) that are both base-specific modifying reagents (Behm-Ansmant I, et al. J Nucleic Acids 2011:408053, 2011). These modifications are mapped by primer extension arrests using 5' fluorescently labeled primers. In this protocol, we show a comprehensive method to identify RNA secondary structures in vitro using fluorescently labeled oligos. To demonstrate the efficiency of the method, we give an example of a structure we have designed which corresponds to a part of the 5'-UTR regulatory element called Translation Inhibitory Element (TIE) from Hox a3 mRNA (Xue S, et al. Nature 517(7532):33-38, 2015).
Alghoul F, Laure S, Eriani G, Martin F
Translation inhibitory elements from Hoxa3 and Hoxa11 mRNAs use uORFs for translation inhibition Journal Article
In: Elife, vol. 10, 2021, ISBN: 34076576, (2050-084X (Electronic) 2050-084X (Linking) Journal Article).
Abstract | Links | BibTeX | Tags: ERIANI, Unité ARN
@article{Alghoul2021b,
title = {Translation inhibitory elements from Hoxa3 and Hoxa11 mRNAs use uORFs for translation inhibition},
author = {F Alghoul and S Laure and G Eriani and F Martin},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34076576},
doi = {10.7554/eLife.66369},
isbn = {34076576},
year = {2021},
date = {2021-01-01},
journal = {Elife},
volume = {10},
abstract = {During embryogenesis, Hox mRNA translation is tightly regulated by a sophisticated molecular mechanism that combines two RNA regulons located in their 5'UTR. First, an internal ribosome entry site (IRES) enables cap-independent translation. The second regulon is a translation inhibitory element or TIE, which ensures concomitant cap-dependent translation inhibition. In this study, we deciphered the molecular mechanisms of mouse Hoxa3 and Hoxa11 TIEs. Both TIEs possess an upstream open reading frame (uORF) that is critical to inhibit cap-dependent translation. However, the molecular mechanisms used are different. In Hoxa3 TIE, we identify an uORF which inhibits cap-dependent translation and we show the requirement of the non-canonical initiation factor eIF2D for this process. The mode of action of Hoxa11 TIE is different, it also contains an uORF but it is a minimal uORF formed by an uAUG followed immediately by a stop codon, namely a 'start-stop'. The 'start-stop' sequence is species-specific and in mice, is located upstream of a highly stable stem loop structure which stalls the 80S ribosome and thereby inhibits cap-dependent translation of Hoxa11 main ORF.},
note = {2050-084X (Electronic)
2050-084X (Linking)
Journal Article},
keywords = {ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
During embryogenesis, Hox mRNA translation is tightly regulated by a sophisticated molecular mechanism that combines two RNA regulons located in their 5'UTR. First, an internal ribosome entry site (IRES) enables cap-independent translation. The second regulon is a translation inhibitory element or TIE, which ensures concomitant cap-dependent translation inhibition. In this study, we deciphered the molecular mechanisms of mouse Hoxa3 and Hoxa11 TIEs. Both TIEs possess an upstream open reading frame (uORF) that is critical to inhibit cap-dependent translation. However, the molecular mechanisms used are different. In Hoxa3 TIE, we identify an uORF which inhibits cap-dependent translation and we show the requirement of the non-canonical initiation factor eIF2D for this process. The mode of action of Hoxa11 TIE is different, it also contains an uORF but it is a minimal uORF formed by an uAUG followed immediately by a stop codon, namely a 'start-stop'. The 'start-stop' sequence is species-specific and in mice, is located upstream of a highly stable stem loop structure which stalls the 80S ribosome and thereby inhibits cap-dependent translation of Hoxa11 main ORF.
2020
Tidu A, Janvier A, Schaeffer L, Sosnowski P, Kuhn L, Hammann P, Westhof E, Eriani G, Martin F
The viral protein NSP1 acts as a ribosome gatekeeper for shutting down host translation and fostering SARS-CoV-2 translation Journal Article
In: RNA, vol. 27, no. 3, pp. 253-264, 2020.
Abstract | Links | BibTeX | Tags: ERIANI, PPSE, Unité ARN
@article{A.2020,
title = {The viral protein NSP1 acts as a ribosome gatekeeper for shutting down host translation and fostering SARS-CoV-2 translation},
author = {A Tidu and A Janvier and L Schaeffer and P Sosnowski and L Kuhn and P Hammann and E Westhof and G Eriani and F Martin
},
url = {https://rnajournal.cshlp.org/content/early/2020/12/02/rna.078121.120},
doi = {10.1261/rna.078121.120 },
year = {2020},
date = {2020-12-02},
journal = {RNA},
volume = {27},
number = {3},
pages = {253-264},
abstract = {SARS-CoV-2 coronavirus is responsible for Covid-19 pandemic. In the early phase of infection, the single-strand positive RNA genome is translated into non-structural proteins (NSP). One of the first proteins produced during viral infection, NSP1, binds to the host ribosome and blocks the mRNA entry channel. This triggers translation inhibition of cellular translation. In spite of the presence of NSP1 on the ribosome, viral translation proceeds however. The molecular mechanism of the so-called viral evasion to NSP1 inhibition remains elusive. Here, we confirm that viral translation is maintained in the presence of NSP1. The evasion to NSP1-inhibition is mediated by the cis-acting RNA hairpin SL1 in the 5'UTR of SARS-CoV-2. NSP1-evasion can be transferred on a reporter transcript by SL1 transplantation. The apical part of SL1 is only required for viral translation. We show that NSP1 remains bound on the ribosome during viral translation. We suggest that the interaction between NSP1 and SL1 frees the mRNA accommodation channel while maintaining NSP1 bound to the ribosome. Thus, NSP1 acts as a ribosome gatekeeper, shutting down host translation or fostering SARS-CoV-2 translation depending on the presence of the SL1 5'UTR hairpin. SL1 is also present and necessary for translation of sub-genomic RNAs in the late phase of the infectious program. Consequently, therapeutic strategies targeting SL1 should affect viral translation at early and late stages of infection. Therefore, SL1 might be seen as a genuine 'Achille heel' of the virus. },
keywords = {ERIANI, PPSE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
SARS-CoV-2 coronavirus is responsible for Covid-19 pandemic. In the early phase of infection, the single-strand positive RNA genome is translated into non-structural proteins (NSP). One of the first proteins produced during viral infection, NSP1, binds to the host ribosome and blocks the mRNA entry channel. This triggers translation inhibition of cellular translation. In spite of the presence of NSP1 on the ribosome, viral translation proceeds however. The molecular mechanism of the so-called viral evasion to NSP1 inhibition remains elusive. Here, we confirm that viral translation is maintained in the presence of NSP1. The evasion to NSP1-inhibition is mediated by the cis-acting RNA hairpin SL1 in the 5'UTR of SARS-CoV-2. NSP1-evasion can be transferred on a reporter transcript by SL1 transplantation. The apical part of SL1 is only required for viral translation. We show that NSP1 remains bound on the ribosome during viral translation. We suggest that the interaction between NSP1 and SL1 frees the mRNA accommodation channel while maintaining NSP1 bound to the ribosome. Thus, NSP1 acts as a ribosome gatekeeper, shutting down host translation or fostering SARS-CoV-2 translation depending on the presence of the SL1 5'UTR hairpin. SL1 is also present and necessary for translation of sub-genomic RNAs in the late phase of the infectious program. Consequently, therapeutic strategies targeting SL1 should affect viral translation at early and late stages of infection. Therefore, SL1 might be seen as a genuine 'Achille heel' of the virus.
Despons L, Martin F
How Many Messenger RNAs Can Be Translated by the START Mechanism? Journal Article
In: International Journal of Molecular Sciences, vol. 21, no. 21, pp. 8373, 2020.
Abstract | Links | BibTeX | Tags: ERIANI, LESCURE, mRNA, Ribosome, secondary structures, START, translation initiation, Unité ARN
@article{Despons2020,
title = {How Many Messenger RNAs Can Be Translated by the START Mechanism? },
author = {L Despons and F Martin
},
url = {https://pubmed.ncbi.nlm.nih.gov/33171614/},
doi = {10.3390/ijms21218373 },
year = {2020},
date = {2020-11-01},
journal = {International Journal of Molecular Sciences},
volume = {21},
number = {21},
pages = {8373},
abstract = {Translation initiation is a key step in the protein synthesis stage of the gene expression pathway of all living cells. In this important process, ribosomes have to accurately find the AUG start codon in order to ensure the integrity of the proteome. "Structure Assisted RNA Translation", or "START", has been proposed to use stable secondary structures located in the coding sequence to augment start site selection by steric hindrance of the progression of pre-initiation complex on messenger RNA. This implies that such structures have to be located downstream and at on optimal distance from the AUG start codon (i.e., downstream nucleotide +16). In order to assess the importance of the START mechanism in the overall mRNA translation process, we developed a bioinformatic tool to screen coding sequences for such stable structures in a 50 nucleotide-long window spanning the nucleotides from +16 to +65. We screened eight bacterial genomes and six eukaryotic genomes. We found stable structures in 0.6-2.5% of eukaryotic coding sequences. Among these, approximately half of them were structures predicted to form G-quadruplex structures. In humans, we selected 747 structures. In bacteria, the coding sequences from Gram-positive bacteria contained 2.6-4.2% stable structures, whereas the structures were less abundant in Gram-negative bacteria (0.2-2.7%). In contrast to eukaryotes, putative G-quadruplex structures are very rare in the coding sequence of bacteria. Altogether, our study reveals that the START mechanism seems to be an ancient strategy to facilitate the start codon recognition that is used in different kingdoms of life. },
keywords = {ERIANI, LESCURE, mRNA, Ribosome, secondary structures, START, translation initiation, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Translation initiation is a key step in the protein synthesis stage of the gene expression pathway of all living cells. In this important process, ribosomes have to accurately find the AUG start codon in order to ensure the integrity of the proteome. "Structure Assisted RNA Translation", or "START", has been proposed to use stable secondary structures located in the coding sequence to augment start site selection by steric hindrance of the progression of pre-initiation complex on messenger RNA. This implies that such structures have to be located downstream and at on optimal distance from the AUG start codon (i.e., downstream nucleotide +16). In order to assess the importance of the START mechanism in the overall mRNA translation process, we developed a bioinformatic tool to screen coding sequences for such stable structures in a 50 nucleotide-long window spanning the nucleotides from +16 to +65. We screened eight bacterial genomes and six eukaryotic genomes. We found stable structures in 0.6-2.5% of eukaryotic coding sequences. Among these, approximately half of them were structures predicted to form G-quadruplex structures. In humans, we selected 747 structures. In bacteria, the coding sequences from Gram-positive bacteria contained 2.6-4.2% stable structures, whereas the structures were less abundant in Gram-negative bacteria (0.2-2.7%). In contrast to eukaryotes, putative G-quadruplex structures are very rare in the coding sequence of bacteria. Altogether, our study reveals that the START mechanism seems to be an ancient strategy to facilitate the start codon recognition that is used in different kingdoms of life.
Pernod K, Schaeffer L, Chicher J, Hok E, Rick C, Geslain R, Eriani G, Westhof E, Ryckelynck M, Martin F
In: Nucleic Acids Res, vol. 48, no. 11, pp. 6170-6183, 2020, ISBN: 32266934.
Abstract | Links | BibTeX | Tags: ERIANI, PPSE, RYCKELYNCK, Unité ARN, WESTHOF
@article{,
title = {The Nature of the Purine at Position 34 in tRNAs of 4-codon Boxes Is Correlated With Nucleotides at Positions 32 and 38 to Maintain Decoding Fidelity},
author = {K Pernod and L Schaeffer and J Chicher and E Hok and C Rick and R Geslain and G Eriani and E Westhof and M Ryckelynck and F Martin},
url = {https://www.ncbi.nlm.nih.gov/pubmed/32266934?dopt=Abstract},
doi = {10.1093/nar/gkaa221},
isbn = {32266934},
year = {2020},
date = {2020-01-01},
journal = {Nucleic Acids Res},
volume = {48},
number = {11},
pages = {6170-6183},
abstract = {Translation fidelity relies essentially on the ability of ribosomes to accurately recognize triplet interactions between codons on mRNAs and anticodons of tRNAs. To determine the codon-anticodon pairs that are efficiently accepted by the eukaryotic ribosome, we took advantage of the IRES from the intergenic region (IGR) of the Cricket Paralysis Virus. It contains an essential pseudoknot PKI that structurally and functionally mimics a codon-anticodon helix. We screened the entire set of 4096 possible combinations using ultrahigh-throughput screenings combining coupled transcription/translation and droplet-based microfluidics. Only 97 combinations are efficiently accepted and accommodated for translocation and further elongation: 38 combinations involve cognate recognition with Watson-Crick pairs and 59 involve near-cognate recognition pairs with at least one mismatch. More than half of the near-cognate combinations (36/59) contain a G at the first position of the anticodon (numbered 34 of tRNA). G34-containing tRNAs decoding 4-codon boxes are almost absent from eukaryotic genomes in contrast to bacterial genomes. We reconstructed these missing tRNAs and could demonstrate that these tRNAs are toxic to cells due to their miscoding capacity in eukaryotic translation systems. We also show that the nature of the purine at position 34 is correlated with the nucleotides present at 32 and 38.},
keywords = {ERIANI, PPSE, RYCKELYNCK, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Translation fidelity relies essentially on the ability of ribosomes to accurately recognize triplet interactions between codons on mRNAs and anticodons of tRNAs. To determine the codon-anticodon pairs that are efficiently accepted by the eukaryotic ribosome, we took advantage of the IRES from the intergenic region (IGR) of the Cricket Paralysis Virus. It contains an essential pseudoknot PKI that structurally and functionally mimics a codon-anticodon helix. We screened the entire set of 4096 possible combinations using ultrahigh-throughput screenings combining coupled transcription/translation and droplet-based microfluidics. Only 97 combinations are efficiently accepted and accommodated for translocation and further elongation: 38 combinations involve cognate recognition with Watson-Crick pairs and 59 involve near-cognate recognition pairs with at least one mismatch. More than half of the near-cognate combinations (36/59) contain a G at the first position of the anticodon (numbered 34 of tRNA). G34-containing tRNAs decoding 4-codon boxes are almost absent from eukaryotic genomes in contrast to bacterial genomes. We reconstructed these missing tRNAs and could demonstrate that these tRNAs are toxic to cells due to their miscoding capacity in eukaryotic translation systems. We also show that the nature of the purine at position 34 is correlated with the nucleotides present at 32 and 38.
Miao Z, Tidu A, Eriani G, Martin F
Secondary structure of the SARS-CoV-2 5'-UTR Journal Article
In: RNA Biol, vol. 18, no. 4, pp. 447-456, 2020, ISBN: 32965173.
Abstract | Links | BibTeX | Tags: 5ʹ-UTR SARS-CoV-2 probing secondary structure, ERIANI, Unité ARN
@article{,
title = {Secondary structure of the SARS-CoV-2 5'-UTR},
author = {Z Miao and A Tidu and G Eriani and F Martin},
url = {https://pubmed.ncbi.nlm.nih.gov/32965173/},
doi = {10.1080/15476286.2020.1814556},
isbn = {32965173},
year = {2020},
date = {2020-01-01},
journal = {RNA Biol},
volume = {18},
number = {4},
pages = {447-456},
abstract = {The SARS-CoV-2, a positive-sense single-stranded RNA Coronavirus, is a global threat to human health. Thus, understanding its life cycle mechanistically would be important to facilitate the design of antiviral drugs. A key aspect of viral progression is the synthesis of viral proteins by the ribosome of the human host. In Coronaviruses, this process is regulated by the viral 5' and 3' untranslated regions (UTRs), but the precise regulatory mechanism has not yet been well understood. In particular, the 5'-UTR of the viral genome is most likely involved in translation initiation of viral proteins. Here, we performed inline probing and RNase V1 probing to establish a model of the secondary structure of SARS-CoV-2 5'-UTR. We found that the 5'-UTR contains stable structures including a very stable four-way junction close to the AUG start codon. Sequence alignment analysis of SARS-CoV-2 variants 5'-UTRs revealed a highly conserved structure with few co-variations that confirmed our secondary structure model based on probing experiments.},
keywords = {5ʹ-UTR SARS-CoV-2 probing secondary structure, ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The SARS-CoV-2, a positive-sense single-stranded RNA Coronavirus, is a global threat to human health. Thus, understanding its life cycle mechanistically would be important to facilitate the design of antiviral drugs. A key aspect of viral progression is the synthesis of viral proteins by the ribosome of the human host. In Coronaviruses, this process is regulated by the viral 5' and 3' untranslated regions (UTRs), but the precise regulatory mechanism has not yet been well understood. In particular, the 5'-UTR of the viral genome is most likely involved in translation initiation of viral proteins. Here, we performed inline probing and RNase V1 probing to establish a model of the secondary structure of SARS-CoV-2 5'-UTR. We found that the 5'-UTR contains stable structures including a very stable four-way junction close to the AUG start codon. Sequence alignment analysis of SARS-CoV-2 variants 5'-UTRs revealed a highly conserved structure with few co-variations that confirmed our secondary structure model based on probing experiments.
2019
Jackson C B, Huemer M, Bolognini R, Martin F, Szinnai G, Donner B C, Richter U, Battersby B J, Nuoffer J M, Suomalainen A, Schaller A
In: Hum Mol Genet, vol. 28, no. 4, pp. 639-649, 2019, ISBN: 30358850.
Abstract | Links | BibTeX | Tags: ERIANI, Unité ARN
@article{,
title = {A variant in MRPS14 (uS14m) causes perinatal hypertrophic cardiomyopathy with neonatal lactic acidosis, growth retardation, dysmorphic features and neurological involvement},
author = {C B Jackson and M Huemer and R Bolognini and F Martin and G Szinnai and B C Donner and U Richter and B J Battersby and J M Nuoffer and A Suomalainen and A Schaller},
url = {https://www.ncbi.nlm.nih.gov/pubmed/30358850},
doi = {10.1093/hmg/ddy374},
isbn = {30358850},
year = {2019},
date = {2019-01-01},
journal = {Hum Mol Genet},
volume = {28},
number = {4},
pages = {639-649},
abstract = {Dysfunction of mitochondrial translation is increasingly an important molecular cause of human disease, but structural defects of mitochondrial ribosomal subunits are rare. We used next-generation sequencing to identify a homozygous variant in the mitochondrial small ribosomal protein 14 (MRPS14, uS14m) in a patient manifesting with perinatal hypertrophic cardiomyopathy, growth retardation, muscle hypotonia, elevated lactate, dysmorphy and mental retardation. In skeletal muscle and fibroblasts from the patient there was biochemical deficiency in complex IV of the respiratory chain. In fibroblasts mitochondrial translation was impaired and ectopic expression of a wild type MRPS14 cDNA functionally complemented this defect. Surprisingly, the mutant uS14m was stable and did not affect assembly of the small ribosomal subunit. Instead, structural modeling of the uS14m mutation predicted a disruption to the ribosomal mRNA channel. Collectively, our data demonstrates pathogenic mutations in MRPS14 can manifest as a perinatal-onset mitochondrial hypertrophic cardiomyopathy with a novel molecular pathogenic mechanism that impairs the function of mitochondrial ribosomes during translation elongation or mitochondrial mRNA recruitment rather than assembly.},
keywords = {ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Dysfunction of mitochondrial translation is increasingly an important molecular cause of human disease, but structural defects of mitochondrial ribosomal subunits are rare. We used next-generation sequencing to identify a homozygous variant in the mitochondrial small ribosomal protein 14 (MRPS14, uS14m) in a patient manifesting with perinatal hypertrophic cardiomyopathy, growth retardation, muscle hypotonia, elevated lactate, dysmorphy and mental retardation. In skeletal muscle and fibroblasts from the patient there was biochemical deficiency in complex IV of the respiratory chain. In fibroblasts mitochondrial translation was impaired and ectopic expression of a wild type MRPS14 cDNA functionally complemented this defect. Surprisingly, the mutant uS14m was stable and did not affect assembly of the small ribosomal subunit. Instead, structural modeling of the uS14m mutation predicted a disruption to the ribosomal mRNA channel. Collectively, our data demonstrates pathogenic mutations in MRPS14 can manifest as a perinatal-onset mitochondrial hypertrophic cardiomyopathy with a novel molecular pathogenic mechanism that impairs the function of mitochondrial ribosomes during translation elongation or mitochondrial mRNA recruitment rather than assembly.
Janvier A, Despons L, Schaeffer L, Tidu A, Martin F, Eriani G
A tRNA-mimic Strategy to Explore the Role of G34 of tRNAGly in Translation and Codon Frameshifting Journal Article
In: Int J Mol Sci, vol. 20, no. 16, pp. 3911, 2019, ISBN: 31405256.
Abstract | Links | BibTeX | Tags: ERIANI, IRES element frameshifting genetic code glycine codon tRNA translation, LESCURE, Unité ARN
@article{,
title = {A tRNA-mimic Strategy to Explore the Role of G34 of tRNA^{Gly} in Translation and Codon Frameshifting},
author = {A Janvier and L Despons and L Schaeffer and A Tidu and F Martin and G Eriani},
url = {https://www.ncbi.nlm.nih.gov/pubmed/31405256?dopt=Abstract},
doi = {10.3390/ijms20163911},
isbn = {31405256},
year = {2019},
date = {2019-01-01},
journal = {Int J Mol Sci},
volume = {20},
number = {16},
pages = {3911},
abstract = {Decoding of the 61 sense codons of the genetic code requires a variable number of tRNAs that establish codon-anticodon interactions. Thanks to the wobble base pairing at the third codon position, less than 61 different tRNA isoacceptors are needed to decode the whole set of codons. On the tRNA, a subtle distribution of nucleoside modifications shapes the anticodon loop structure and participates to accurate decoding and reading frame maintenance. Interestingly, although the 61 anticodons should exist in tRNAs, a strict absence of some tRNAs decoders is found in several codon families. For instance, in Eukaryotes, G34-containing tRNAs translating 3-, 4- and 6-codon boxes are absent. This includes tRNA specific for Ala, Arg, Ile, Leu, Pro, Ser, Thr, and Val. tRNAGly is the only exception for which in the three kingdoms, a G34-containing tRNA exists to decode C3 and U3-ending codons. To understand why G34-tRNAGly exists, we analysed at the genome wide level the codon distribution in codon +1 relative to the four GGN Gly codons. When considering codon GGU, a bias was found towards an unusual high usage of codons starting with a G whatever the amino acid at +1 codon. It is expected that GGU codons are decoded by G34-containing tRNAGly, decoding also GGC codons. Translation studies revealed that the presence of a G at the first position of the downstream codon reduces the +1 frameshift by stabilizing the G34U3 wobble interaction. This result partially explains why G34-containing tRNAGly exists in Eukaryotes whereas all the other G34-containing tRNAs for multiple codon boxes are absent.},
keywords = {ERIANI, IRES element frameshifting genetic code glycine codon tRNA translation, LESCURE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Decoding of the 61 sense codons of the genetic code requires a variable number of tRNAs that establish codon-anticodon interactions. Thanks to the wobble base pairing at the third codon position, less than 61 different tRNA isoacceptors are needed to decode the whole set of codons. On the tRNA, a subtle distribution of nucleoside modifications shapes the anticodon loop structure and participates to accurate decoding and reading frame maintenance. Interestingly, although the 61 anticodons should exist in tRNAs, a strict absence of some tRNAs decoders is found in several codon families. For instance, in Eukaryotes, G34-containing tRNAs translating 3-, 4- and 6-codon boxes are absent. This includes tRNA specific for Ala, Arg, Ile, Leu, Pro, Ser, Thr, and Val. tRNAGly is the only exception for which in the three kingdoms, a G34-containing tRNA exists to decode C3 and U3-ending codons. To understand why G34-tRNAGly exists, we analysed at the genome wide level the codon distribution in codon +1 relative to the four GGN Gly codons. When considering codon GGU, a bias was found towards an unusual high usage of codons starting with a G whatever the amino acid at +1 codon. It is expected that GGU codons are decoded by G34-containing tRNAGly, decoding also GGC codons. Translation studies revealed that the presence of a G at the first position of the downstream codon reduces the +1 frameshift by stabilizing the G34U3 wobble interaction. This result partially explains why G34-containing tRNAGly exists in Eukaryotes whereas all the other G34-containing tRNAs for multiple codon boxes are absent.
2018
Tabet R, Schaeffer L, Freyermuth F, Jambeau M, Workman M, Lee C Z, Lin C C, Jiang J, Jansen-West K, Abou-Hamdan H, Désaubry L, Gendron T, Petrucelli L, Martin F, Lagier-Tourenne C
CUG initiation and frameshifting enable production of dipeptide repeat proteins from ALS/FTD C9ORF72 transcript Journal Article
In: Nat Commun, vol. 9, no. 1, pp. 152, 2018, ISBN: 29323119.
Abstract | Links | BibTeX | Tags: ERIANI, Unité ARN
@article{,
title = {CUG initiation and frameshifting enable production of dipeptide repeat proteins from ALS/FTD C9ORF72 transcript},
author = {R Tabet and L Schaeffer and F Freyermuth and M Jambeau and M Workman and C Z Lee and C C Lin and J Jiang and K Jansen-West and H Abou-Hamdan and L Désaubry and T Gendron and L Petrucelli and F Martin and C Lagier-Tourenne},
url = {https://www.ncbi.nlm.nih.gov/pubmed/29323119?dopt=Abstract},
doi = {10.1038/s41467-017-02643-5},
isbn = {29323119},
year = {2018},
date = {2018-01-01},
journal = {Nat Commun},
volume = {9},
number = {1},
pages = {152},
abstract = {Expansion of G4C2 repeats in the C9ORF72 gene is the most prevalent inherited form of amyotrophic lateral sclerosis and frontotemporal dementia. Expanded transcripts undergo repeat-associated non-AUG (RAN) translation producing dipeptide repeat proteins from all reading frames. We determined cis-factors and trans-factors influencing translation of the human C9ORF72 transcripts. G4C2 translation operates through a 5'-3' cap-dependent scanning mechanism, requiring a CUG codon located upstream of the repeats and an initiator Met-tRNAMeti. Production of poly-GA, poly-GP, and poly-GR proteins from the three frames is influenced by mutation of the same CUG start codon supporting a frameshifting mechanism. RAN translation is also regulated by an upstream open reading frame (uORF) present in mis-spliced C9ORF72 transcripts. Inhibitors of the pre-initiation ribosomal complex and RNA antisense oligonucleotides selectively targeting the 5'-flanking G4C2 sequence block ribosomal scanning and prevent translation. Finally, we identified an unexpected affinity of expanded transcripts for the ribosomal subunits independently from translation.},
keywords = {ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Expansion of G4C2 repeats in the C9ORF72 gene is the most prevalent inherited form of amyotrophic lateral sclerosis and frontotemporal dementia. Expanded transcripts undergo repeat-associated non-AUG (RAN) translation producing dipeptide repeat proteins from all reading frames. We determined cis-factors and trans-factors influencing translation of the human C9ORF72 transcripts. G4C2 translation operates through a 5'-3' cap-dependent scanning mechanism, requiring a CUG codon located upstream of the repeats and an initiator Met-tRNAMeti. Production of poly-GA, poly-GP, and poly-GR proteins from the three frames is influenced by mutation of the same CUG start codon supporting a frameshifting mechanism. RAN translation is also regulated by an upstream open reading frame (uORF) present in mis-spliced C9ORF72 transcripts. Inhibitors of the pre-initiation ribosomal complex and RNA antisense oligonucleotides selectively targeting the 5'-flanking G4C2 sequence block ribosomal scanning and prevent translation. Finally, we identified an unexpected affinity of expanded transcripts for the ribosomal subunits independently from translation.
Mailliot J, Martin F
Viral internal ribosomal entry sites: four classes for one goal Journal Article
In: Wiley Interdiscip Rev RNA, vol. 9, no. 2, pp. none, 2018, ISBN: 29193740.
Abstract | Links | BibTeX | Tags: ERIANI, Unité ARN
@article{,
title = {Viral internal ribosomal entry sites: four classes for one goal},
author = {J Mailliot and F Martin},
url = {https://www.ncbi.nlm.nih.gov/pubmed/29193740?dopt=Abstract},
doi = {10.1002/wrna.1458},
isbn = {29193740},
year = {2018},
date = {2018-01-01},
journal = {Wiley Interdiscip Rev RNA},
volume = {9},
number = {2},
pages = {none},
abstract = {To ensure efficient propagation, viruses need to rapidly produce viral proteins after cell entrance. Since viral genomes do not encode any components of the protein biosynthesis machinery, viral proteins must be produced by the host cell. To hi-jack the host cellular translation, viruses use a great variety of distinct strategies. Many single-stranded positive-sensed RNA viruses contain so-called internal ribosome entry sites (IRESs). IRESs are structural RNA motifs that have evolved to specific folds that recruit the host ribosomes on the viral coding sequences in order to synthesize viral proteins. In host canonical translation, recruitment of the translation machinery components is essentially guided by the 5' cap (m7 G) of mRNA. In contrast, IRESs are able to promote efficient ribosome assembly internally and in cap-independent manner. IRESs have been categorized into four classes, based on their length, nucleotide sequence, secondary and tertiary structures, as well as their mode of action. Classes I and II require the assistance of cellular auxiliary factors, the eukaryotic intiation factors (eIF), for efficient ribosome assembly. Class III IRESs require only a subset of eIFs whereas Class IV, which are the more compact, can promote translation without any eIFs. Extensive functional and structural investigations of IRESs over the past decades have allowed a better understanding of their mode of action for viral translation. Because viral translation has a pivotal role in the infectious program, IRESs are therefore attractive targets for therapeutic purposes. For further resources related to this article, please visit the WIREs website.},
keywords = {ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
To ensure efficient propagation, viruses need to rapidly produce viral proteins after cell entrance. Since viral genomes do not encode any components of the protein biosynthesis machinery, viral proteins must be produced by the host cell. To hi-jack the host cellular translation, viruses use a great variety of distinct strategies. Many single-stranded positive-sensed RNA viruses contain so-called internal ribosome entry sites (IRESs). IRESs are structural RNA motifs that have evolved to specific folds that recruit the host ribosomes on the viral coding sequences in order to synthesize viral proteins. In host canonical translation, recruitment of the translation machinery components is essentially guided by the 5' cap (m7 G) of mRNA. In contrast, IRESs are able to promote efficient ribosome assembly internally and in cap-independent manner. IRESs have been categorized into four classes, based on their length, nucleotide sequence, secondary and tertiary structures, as well as their mode of action. Classes I and II require the assistance of cellular auxiliary factors, the eukaryotic intiation factors (eIF), for efficient ribosome assembly. Class III IRESs require only a subset of eIFs whereas Class IV, which are the more compact, can promote translation without any eIFs. Extensive functional and structural investigations of IRESs over the past decades have allowed a better understanding of their mode of action for viral translation. Because viral translation has a pivotal role in the infectious program, IRESs are therefore attractive targets for therapeutic purposes. For further resources related to this article, please visit the WIREs website.
Gross L, Schaeffer L, Alghoul F, Hayek H, Allmang C, Eriani G, Martin F
Tracking the m7G-cap during translation initiation by crosslinking methods Journal Article
In: Methods, vol. 137, pp. 3-10, 2018, ISBN: 29307728.
Abstract | Links | BibTeX | Tags: Cap-dependent translation Chemical crosslinking Histone H4 mRNA Ribosome UV crosslinking eIF4E, ERIANI, Unité ARN
@article{,
title = {Tracking the m^{7}G-cap during translation initiation by crosslinking methods},
author = {L Gross and L Schaeffer and F Alghoul and H Hayek and C Allmang and G Eriani and F Martin},
url = {https://www.ncbi.nlm.nih.gov/pubmed/29307728?dopt=Abstract},
doi = {10.1016/j.ymeth.2017.12.019},
isbn = {29307728},
year = {2018},
date = {2018-01-01},
journal = {Methods},
volume = {137},
pages = {3-10},
abstract = {In eukaryotes, cap-dependent translation initiation is a sophisticated process that requires numerous trans-acting factors, the eukaryotic Initiation Factors (eIFs). Their main function is to assist the ribosome for accurate AUG start codon recognition. The whole process requires a 5'-3' scanning step and is therefore highly dynamic. Therefore translation requires a complex interplay between eIFs through assembly/release cycles. Here, we describe an original approach to assess the dynamic features of translation initiation. The principle is to use the m7Gcap located at the 5' extremity of mRNAs as a tracker to monitor RNA and protein components that are in its vicinity. Cap-binding molecules are trapped by chemical and UV crosslinking. The combination of cap crosslinking methods in cell-free translation systems with the use of specific translation inhibitors for different steps such as edeine, GMP-PNP or cycloheximide allowed assessing the cap fate during eukaryotic translation. Here, we followed the position of the cap in the histone H4 mRNA and the cap binding proteins during H4 mRNA translation.},
keywords = {Cap-dependent translation Chemical crosslinking Histone H4 mRNA Ribosome UV crosslinking eIF4E, ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
In eukaryotes, cap-dependent translation initiation is a sophisticated process that requires numerous trans-acting factors, the eukaryotic Initiation Factors (eIFs). Their main function is to assist the ribosome for accurate AUG start codon recognition. The whole process requires a 5'-3' scanning step and is therefore highly dynamic. Therefore translation requires a complex interplay between eIFs through assembly/release cycles. Here, we describe an original approach to assess the dynamic features of translation initiation. The principle is to use the m7Gcap located at the 5' extremity of mRNAs as a tracker to monitor RNA and protein components that are in its vicinity. Cap-binding molecules are trapped by chemical and UV crosslinking. The combination of cap crosslinking methods in cell-free translation systems with the use of specific translation inhibitors for different steps such as edeine, GMP-PNP or cycloheximide allowed assessing the cap fate during eukaryotic translation. Here, we followed the position of the cap in the histone H4 mRNA and the cap binding proteins during H4 mRNA translation.
Gribling-Burrer A S, Eriani G, Allmang C
Modification of Selenoprotein mRNAs by Cap Tri-methylation Book Chapter
In: Chavatte, L (Ed.): Selenoproteins: Methods and Protocols, vol. 1661, pp. 125-141, Springer Protocols, Humana Press, 2018, ISBN: 28917041.
Abstract | Links | BibTeX | Tags: 2, 7G cap, Cap hypermethylation Cap immunoprecipitation Selenoprotein mRNAs TMG cap Tgs1 m3 2, ERIANI, Unité ARN
@inbook{,
title = {Modification of Selenoprotein mRNAs by Cap Tri-methylation},
author = {A S Gribling-Burrer and G Eriani and C Allmang},
editor = {L Chavatte},
url = {https://www.ncbi.nlm.nih.gov/pubmed/28917041?dopt=Abstract},
doi = {1007/978-1-4939-7258-6_9},
isbn = {28917041},
year = {2018},
date = {2018-01-01},
booktitle = {Selenoproteins: Methods and Protocols},
volume = {1661},
pages = {125-141},
publisher = {Springer Protocols, Humana Press},
series = {Methods in Molecular Biology},
abstract = {Several selenoprotein mRNAs undergo 5' cap maturation events whereby their classical monomethylated m7G cap becomes trimethylated (m32,2,7G) by the trimethylguanosine synthase 1 (Tgs1). Here, we describe immunoprecipitation methods for the detection of endogenous m32,2,7G-capped selenoprotein mRNAs from total cell extracts or after polysome fractionation of cytoplasmic extracts. We have also developed a method for the in vitro cap hypermethylation of selenoprotein mRNA transcripts using purified Tgs1 enzyme.},
keywords = {2, 7G cap, Cap hypermethylation Cap immunoprecipitation Selenoprotein mRNAs TMG cap Tgs1 m3 2, ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Several selenoprotein mRNAs undergo 5' cap maturation events whereby their classical monomethylated m7G cap becomes trimethylated (m32,2,7G) by the trimethylguanosine synthase 1 (Tgs1). Here, we describe immunoprecipitation methods for the detection of endogenous m32,2,7G-capped selenoprotein mRNAs from total cell extracts or after polysome fractionation of cytoplasmic extracts. We have also developed a method for the in vitro cap hypermethylation of selenoprotein mRNA transcripts using purified Tgs1 enzyme.
Eriani G, Martin F
START: STructure-Assisted RNA Translation Journal Article
In: RNA Biol, vol. 15, no. 9, pp. 1250-1253, 2018, ISBN: 30176155.
Abstract | Links | BibTeX | Tags: Ded1/DDX3 RNA helicase Ribosome Scanning Translation initiation messenger RNA, ERIANI, Unité ARN
@article{,
title = {START: STructure-Assisted RNA Translation},
author = {G Eriani and F Martin},
url = {https://www.ncbi.nlm.nih.gov/pubmed/30176155?dopt=Abstract},
doi = {10.1080/15476286.2018.1518855},
isbn = {30176155},
year = {2018},
date = {2018-01-01},
journal = {RNA Biol},
volume = {15},
number = {9},
pages = {1250-1253},
abstract = {Cap-dependent translation initiation begins by assembly of a pre-initiation ribosomal complex that scans the 5' Untranslated Region in order to localise the start codon. During this process, RNA secondary structures are melted by RNA helicases. Guenther et al reported that the yeast helicase Ded1, an orthologue of the mammalian DDX3 helicase, is responsible for this activity. When Ded1 is non-functional, RNA structures in the 5'UTR promote translation initiation on Alternative Translation Initiation Sites (ATIS) lead to uORF translation and consequently down-regulation of the main ORF. This mechanism is driven by the sole presence of RNA secondary structures located downstream of ATIS. Translation initiation mediated by RNA structures is found in other messenger RNAs. We propose to name this novel mechanism STructure-Assisted-RNA-Translation or START.},
keywords = {Ded1/DDX3 RNA helicase Ribosome Scanning Translation initiation messenger RNA, ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Cap-dependent translation initiation begins by assembly of a pre-initiation ribosomal complex that scans the 5' Untranslated Region in order to localise the start codon. During this process, RNA secondary structures are melted by RNA helicases. Guenther et al reported that the yeast helicase Ded1, an orthologue of the mammalian DDX3 helicase, is responsible for this activity. When Ded1 is non-functional, RNA structures in the 5'UTR promote translation initiation on Alternative Translation Initiation Sites (ATIS) lead to uORF translation and consequently down-regulation of the main ORF. This mechanism is driven by the sole presence of RNA secondary structures located downstream of ATIS. Translation initiation mediated by RNA structures is found in other messenger RNAs. We propose to name this novel mechanism STructure-Assisted-RNA-Translation or START.
2017
Kobeissy F, Shaito A, Kaplan A, Baki L, Hayek H, Dagher-Hamalian C, Nehme A, Ghali R, Abidi E, Husari A, Zeidan A, Zouein F A, Zibara K
Acute Exposure to Cigarette Smoking Followed by Myocardial Infarction Aggravates Renal Damage in an In Vivo Mouse Model. Journal Article
In: Oxid Med Cell Longev, vol. 2017, pp. 5135241, 2017, ISBN: 29177025.
Abstract | Links | BibTeX | Tags: ERIANI, Unité ARN
@article{,
title = {Acute Exposure to Cigarette Smoking Followed by Myocardial Infarction Aggravates Renal Damage in an \textit{In Vivo} Mouse Model.},
author = {F Kobeissy and A Shaito and A Kaplan and L Baki and H Hayek and C Dagher-Hamalian and A Nehme and R Ghali and E Abidi and A Husari and A Zeidan and F A Zouein and K Zibara},
url = {https://www.ncbi.nlm.nih.gov/pubmed/29177025?dopt=Abstract},
doi = {10.1155/2017/5135241},
isbn = {29177025},
year = {2017},
date = {2017-01-01},
journal = {Oxid Med Cell Longev},
volume = {2017},
pages = {5135241},
abstract = {Cigarette smoking (S) is a risk factor for progressive chronic kidney disease, renal dysfunction, and renal failure. In this study, the effect of smoking on kidney function was investigated in a mouse model of myocardial infarction (MI) using 4 groups: control (C), smoking (S), MI, and S+MI. Histological analysis of S+MI group showed alterations in kidney structure including swelling of the proximal convoluted tubules (PCTs), thinning of the epithelial lining, focal loss of the brush border of PCTs, and patchy glomerular retraction. Molecular analysis revealed that nephrin expression was significantly reduced in the S+MI group, whereas sodium-hydrogen exchanger-1 (NHE-1) was significantly increased, suggesting altered glomerular filtration and kidney functions. Moreover, S+MI group, but not S alone, showed a significant increase in the expression of connective tissue growth factor (CTGF) and fibrotic proteins fibronectin (FN) and α-smooth muscle actin (SMA), in comparison to controls, in addition to a significant increase in mRNA levels of IL-6 and TNF-α inflammatory markers. Finally, reactive oxygen species (ROS) production was significantly accentuated in S+MI group concomitant with a significant increase in NOX-4 protein levels. In conclusion, smoking aggravates murine acute renal damage caused by MI at the structural and molecular levels by exacerbating renal dysfunction.},
keywords = {ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Cigarette smoking (S) is a risk factor for progressive chronic kidney disease, renal dysfunction, and renal failure. In this study, the effect of smoking on kidney function was investigated in a mouse model of myocardial infarction (MI) using 4 groups: control (C), smoking (S), MI, and S+MI. Histological analysis of S+MI group showed alterations in kidney structure including swelling of the proximal convoluted tubules (PCTs), thinning of the epithelial lining, focal loss of the brush border of PCTs, and patchy glomerular retraction. Molecular analysis revealed that nephrin expression was significantly reduced in the S+MI group, whereas sodium-hydrogen exchanger-1 (NHE-1) was significantly increased, suggesting altered glomerular filtration and kidney functions. Moreover, S+MI group, but not S alone, showed a significant increase in the expression of connective tissue growth factor (CTGF) and fibrotic proteins fibronectin (FN) and α-smooth muscle actin (SMA), in comparison to controls, in addition to a significant increase in mRNA levels of IL-6 and TNF-α inflammatory markers. Finally, reactive oxygen species (ROS) production was significantly accentuated in S+MI group concomitant with a significant increase in NOX-4 protein levels. In conclusion, smoking aggravates murine acute renal damage caused by MI at the structural and molecular levels by exacerbating renal dysfunction.
Gribling-Burrer A S, Leichter M, Wurth L, Huttin A, Schlotter F, Troffer-Charlier N, Cura V, Barkats M, Cavarelli J, Massenet S, Allmang C
SECIS-binding protein 2 interacts with the SMN complex and the methylosome for selenoprotein mRNP assembly and translation. Journal Article
In: Nucleic Acids Res, vol. 45, no. 9, pp. 5399-5413, 2017, ISBN: 28115638.
Abstract | Links | BibTeX | Tags: ERIANI, Unité ARN
@article{,
title = {SECIS-binding protein 2 interacts with the SMN complex and the methylosome for selenoprotein mRNP assembly and translation.},
author = {A S Gribling-Burrer and M Leichter and L Wurth and A Huttin and F Schlotter and N Troffer-Charlier and V Cura and M Barkats and J Cavarelli and S Massenet and C Allmang},
url = {https://www.ncbi.nlm.nih.gov/pubmed/28115638?dopt=Abstract},
doi = {10.1093/nar/gkx031},
isbn = {28115638},
year = {2017},
date = {2017-01-01},
journal = {Nucleic Acids Res},
volume = {45},
number = {9},
pages = {5399-5413},
abstract = {Selenoprotein synthesis requires the co-translational recoding of a UGASec codon. This process involves an RNA structural element, called Selenocysteine Insertion Sequence (SECIS) and the SECIS binding protein 2 (SBP2). Several selenoprotein mRNAs undergo unusual cap hypermethylation by the trimethylguanosine synthase 1 (Tgs1), which is recruited by the ubiquitous Survival of MotoNeurons (SMN) protein. SMN, the protein involved in spinal muscular atrophy, is part of a chaperone complex that collaborates with the methylosome for RNP assembly. Here, we analyze the role of individual SMN and methylosome components in selenoprotein mRNP assembly and translation. We show that SBP2 interacts directly with four proteins of the SMN complex and the methylosome core proteins. Nevertheless, SBP2 is not a methylation substrate of the methylosome. We found that both SMN and methylosome complexes are required for efficient translation of the selenoprotein GPx1 in vivo We establish that the steady-state level of several selenoprotein mRNAs, major regulators of oxidative stress damage in neurons, is specifically reduced in the spinal cord of SMN-deficient mice and that cap hypermethylation of GPx1 mRNA is affected. Altogether we identified a new function of the SMN complex and the methylosome in selenoprotein mRNP assembly and expression.},
keywords = {ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Selenoprotein synthesis requires the co-translational recoding of a UGASec codon. This process involves an RNA structural element, called Selenocysteine Insertion Sequence (SECIS) and the SECIS binding protein 2 (SBP2). Several selenoprotein mRNAs undergo unusual cap hypermethylation by the trimethylguanosine synthase 1 (Tgs1), which is recruited by the ubiquitous Survival of MotoNeurons (SMN) protein. SMN, the protein involved in spinal muscular atrophy, is part of a chaperone complex that collaborates with the methylosome for RNP assembly. Here, we analyze the role of individual SMN and methylosome components in selenoprotein mRNP assembly and translation. We show that SBP2 interacts directly with four proteins of the SMN complex and the methylosome core proteins. Nevertheless, SBP2 is not a methylation substrate of the methylosome. We found that both SMN and methylosome complexes are required for efficient translation of the selenoprotein GPx1 in vivo We establish that the steady-state level of several selenoprotein mRNAs, major regulators of oxidative stress damage in neurons, is specifically reduced in the spinal cord of SMN-deficient mice and that cap hypermethylation of GPx1 mRNA is affected. Altogether we identified a new function of the SMN complex and the methylosome in selenoprotein mRNP assembly and expression.
Gross L, Vicens Q, Einhorn E, Noireterre A, Schaeffer L, Kuhn L, Imler JL, Eriani G, Meignin C, Martin F
The IRES5'UTR of the dicistrovirus cricket paralysis virus is a type III IRES containing an essential pseudoknot structure Journal Article
In: Nucleic Acids Res, vol. 45, no. 15, pp. 8993-9004, 2017, ISBN: 28911115.
Abstract | Links | BibTeX | Tags: ERIANI, meignin, PPSE, Unité ARN
@article{,
title = {The IRES5'UTR of the dicistrovirus cricket paralysis virus is a type III IRES containing an essential pseudoknot structure},
author = {L Gross and Q Vicens and E Einhorn and A Noireterre and L Schaeffer and L Kuhn and JL Imler and G Eriani and C Meignin and F Martin},
url = {https://www.ncbi.nlm.nih.gov/pubmed/28911115?dopt=Abstract},
doi = {10.1093/nar/gkx622},
isbn = {28911115},
year = {2017},
date = {2017-01-01},
urldate = {2017-01-01},
journal = {Nucleic Acids Res},
volume = {45},
number = {15},
pages = {8993-9004},
abstract = {Cricket paralysis virus (CrPV) is a dicistrovirus. Its positive-sense single-stranded RNA genome contains two internal ribosomal entry sites (IRESs). The 5' untranslated region (5'UTR) IRES5'UTR mediates translation of non-structural proteins encoded by ORF1 whereas the well-known intergenic region (IGR) IRESIGR is required for translation of structural proteins from open reading frame 2 in the late phase of infection. Concerted action of both IRES is essential for host translation shut-off and viral translation. IRESIGR has been extensively studied, in contrast the IRES5'UTR remains largely unexplored. Here, we define the minimal IRES element required for efficient translation initiation in drosophila S2 cell-free extracts. We show that IRES5'UTR promotes direct recruitment of the ribosome on the cognate viral AUG start codon without any scanning step, using a Hepatitis-C virus-related translation initiation mechanism. Mass spectrometry analysis revealed that IRES5'UTR recruits eukaryotic initiation factor 3, confirming that it belongs to type III class of IRES elements. Using Selective 2'-hydroxyl acylation analyzed by primer extension and DMS probing, we established a secondary structure model of 5'UTR and of the minimal IRES5'UTR. The IRES5'UTR contains a pseudoknot structure that is essential for proper folding and ribosome recruitment. Overall, our results pave the way for studies addressing the synergy and interplay between the two IRES from CrPV.},
keywords = {ERIANI, meignin, PPSE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Cricket paralysis virus (CrPV) is a dicistrovirus. Its positive-sense single-stranded RNA genome contains two internal ribosomal entry sites (IRESs). The 5' untranslated region (5'UTR) IRES5'UTR mediates translation of non-structural proteins encoded by ORF1 whereas the well-known intergenic region (IGR) IRESIGR is required for translation of structural proteins from open reading frame 2 in the late phase of infection. Concerted action of both IRES is essential for host translation shut-off and viral translation. IRESIGR has been extensively studied, in contrast the IRES5'UTR remains largely unexplored. Here, we define the minimal IRES element required for efficient translation initiation in drosophila S2 cell-free extracts. We show that IRES5'UTR promotes direct recruitment of the ribosome on the cognate viral AUG start codon without any scanning step, using a Hepatitis-C virus-related translation initiation mechanism. Mass spectrometry analysis revealed that IRES5'UTR recruits eukaryotic initiation factor 3, confirming that it belongs to type III class of IRES elements. Using Selective 2'-hydroxyl acylation analyzed by primer extension and DMS probing, we established a secondary structure model of 5'UTR and of the minimal IRES5'UTR. The IRES5'UTR contains a pseudoknot structure that is essential for proper folding and ribosome recruitment. Overall, our results pave the way for studies addressing the synergy and interplay between the two IRES from CrPV.
Haimov O, Sinvani H, Martin F, Ulitsky I, Emmanuel R, Tamarkin-Ben-Harush A, Vardy A, Dikstein R
In: Mol Cell Biol, vol. 37, no. 15, pp. e00150-00117, 2017, ISBN: 28584194.
Abstract | Links | BibTeX | Tags: ERIANI, RPS10 RPS10e RPS3 TISU eIF1A short 5′UTR translation initiation, Unité ARN
@article{,
title = {Efficient and Accurate Translation Initiation Directed by TISU Involves RPS3 and RPS10e Binding and Differential Eukaryotic Initiation Factor 1A Regulation},
author = {O Haimov and H Sinvani and F Martin and I Ulitsky and R Emmanuel and A Tamarkin-Ben-Harush and A Vardy and R Dikstein},
url = {https://www.ncbi.nlm.nih.gov/pubmed/28584194?dopt=Abstract},
doi = {10.1128/MCB.00150-17},
isbn = {28584194},
year = {2017},
date = {2017-01-01},
journal = {Mol Cell Biol},
volume = {37},
number = {15},
pages = {e00150-00117},
abstract = {Canonical translation initiation involves ribosomal scanning but short 5' UTR mRNAs are translated in a scanning-independent manner. The extent and mechanism of scanning independent translation is not fully understood. Here we report that short 5' UTR mRNAs constitute a substantial fraction of the translatome. Short 5' UTR mRNAs are enriched with TISU, a 12-nucleotide element directing efficient scanning-independent translation. Comprehensive mutagenesis revealed that each AUG flanking nucleotides of TISU contributes to translational strength but only few are important for accuracy. Using site-specific UV crosslinking of ribosomal complexes assembled on TISU mRNA we demonstrate specific binding of TISU to ribosomal proteins at the E and the A sites. We identified RPS3 as the major TISU-binding protein in the 48S complex A-site. Upon 80S formation RPS3 interaction is weakened and switched to RPS10e (former name RPS10). We further demonstrate that TISU is particularly dependent on eIF1A which interacts with both RPS3 and RPS10e. Our findings suggest that the cap-recruited ribosome specifically binds the TISU nucleotides at the A and the E sites in cooperation with eIF1A to promote scanning arrest.},
keywords = {ERIANI, RPS10 RPS10e RPS3 TISU eIF1A short 5′UTR translation initiation, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Canonical translation initiation involves ribosomal scanning but short 5' UTR mRNAs are translated in a scanning-independent manner. The extent and mechanism of scanning independent translation is not fully understood. Here we report that short 5' UTR mRNAs constitute a substantial fraction of the translatome. Short 5' UTR mRNAs are enriched with TISU, a 12-nucleotide element directing efficient scanning-independent translation. Comprehensive mutagenesis revealed that each AUG flanking nucleotides of TISU contributes to translational strength but only few are important for accuracy. Using site-specific UV crosslinking of ribosomal complexes assembled on TISU mRNA we demonstrate specific binding of TISU to ribosomal proteins at the E and the A sites. We identified RPS3 as the major TISU-binding protein in the 48S complex A-site. Upon 80S formation RPS3 interaction is weakened and switched to RPS10e (former name RPS10). We further demonstrate that TISU is particularly dependent on eIF1A which interacts with both RPS3 and RPS10e. Our findings suggest that the cap-recruited ribosome specifically binds the TISU nucleotides at the A and the E sites in cooperation with eIF1A to promote scanning arrest.
2016
Kowalska J., Martin F., Jemielity J.
Synthetic Capped mRNAs for Cap-Specific Photo-Cross-Linking Experiments. Book Section
In: Rhoads, R. (Ed.): Synthetic mRNA: Production, Introduction Into Cells, and Physiological Consequences, vol. 1428, pp. 31-43, Springer Protocols, Humana Press, 2016.
Abstract | BibTeX | Tags: 5′, 6-thioguanosine, analogs, Binding, Cap, ERIANI, Histone, mRNA, Photo-cross-linking, stability, Transcription
@incollection{,
title = {Synthetic Capped mRNAs for Cap-Specific Photo-Cross-Linking Experiments.},
author = { J. Kowalska and F. Martin and J. Jemielity},
editor = { R. Rhoads},
year = {2016},
date = {2016-01-01},
booktitle = {Synthetic mRNA: Production, Introduction Into Cells, and Physiological Consequences},
volume = {1428},
pages = {31-43},
publisher = {Springer Protocols, Humana Press},
series = {Methods in Molecular Biology},
abstract = {he 7-methylguanosine triphosphate cap present at the 5' ends of eukaryotic mRNAs plays numerous roles in mRNA expression and metabolism. The identification and studies on cap-binding partners can be significantly advanced using tailored chemical tools such as synthetic cap analogues or RNAs carrying modified cap structures. Here we provide protocols for the production of mRNAs specifically labeled within the 5' cap with a nucleoside capable of being photo-activated, either 6-thioguanosine or 7-methyl-6-thioguanosine, which can be used in photo-cross-linking experiments to identify or characterize cap-binding biomolecules. We also describe a protocol for the cross-linking experiments with capped RNAs to map histone H4 cap-binding pocket.},
keywords = {5′, 6-thioguanosine, analogs, Binding, Cap, ERIANI, Histone, mRNA, Photo-cross-linking, stability, Transcription},
pubstate = {published},
tppubtype = {incollection}
}
he 7-methylguanosine triphosphate cap present at the 5' ends of eukaryotic mRNAs plays numerous roles in mRNA expression and metabolism. The identification and studies on cap-binding partners can be significantly advanced using tailored chemical tools such as synthetic cap analogues or RNAs carrying modified cap structures. Here we provide protocols for the production of mRNAs specifically labeled within the 5' cap with a nucleoside capable of being photo-activated, either 6-thioguanosine or 7-methyl-6-thioguanosine, which can be used in photo-cross-linking experiments to identify or characterize cap-binding biomolecules. We also describe a protocol for the cross-linking experiments with capped RNAs to map histone H4 cap-binding pocket.
Wang Y, Zhou X L, Ruan Z R, Liu R J, Eriani G, Wang E D
A Human Disease-causing Point Mutation in Mitochondrial Threonyl-tRNA Synthetase Induces Both Structural and Functional Defects. Journal Article
In: J Biol Chem, vol. 291, no. 12, pp. 6507-6520, 2016, ISBN: 26811336.
Abstract | Links | BibTeX | Tags: alternative splicing aminoacyl-tRNA synthetase enzyme kinetics mitochondria mitochondrial disease threonyl-tRNA synthetase, ERIANI, Unité ARN
@article{,
title = {A Human Disease-causing Point Mutation in Mitochondrial Threonyl-tRNA Synthetase Induces Both Structural and Functional Defects.},
author = {Y Wang and X L Zhou and Z R Ruan and R J Liu and G Eriani and E D Wang},
url = {http://www.ncbi.nlm.nih.gov/pubmed/26811336?dopt=Abstract},
doi = {10.1074/jbc.M115.700849},
isbn = {26811336},
year = {2016},
date = {2016-01-01},
journal = {J Biol Chem},
volume = {291},
number = {12},
pages = {6507-6520},
abstract = {Mitochondria require all translational components, including aminoacyl-tRNA synthetases (aaRSs), to complete organelle protein synthesis. Some aaRS mutations cause mitochondrial disorders, including human mitochondrial threonyl-tRNA synthetase (hmtThrRS) (encoded by TARS2), the P282L mutation of which causes mitochondrial encephalomyopathies. However, its catalytic and structural consequences remain unclear. Herein, we cloned TARS2 and purified the wild-type and P282L mutant hmtThrRS. hmtThrRS misactivates non-cognate Ser and uses post-transfer editing to clear erroneously synthesized products. In vitro and in vivo analyses revealed that the mutation induces a decrease in Thr activation, aminoacylation, and proofreading activities and a change in the protein structure and/or stability, which might cause reduced catalytic efficiency. We also identified a splicing variant of TARS2 mRNA lacking exons 8 and 9, the protein product of which is targeted into mitochondria. In HEK293T cells, the variant does not dimerize and cannot complement the ThrRS knock-out strain in yeast, suggesting that the truncated protein is inactive and might have a non-canonical function, as observed for other aaRS fragments. The present study describes the aminoacylation and editing properties of hmtThrRS, clarifies the molecular consequences of the P282L mutation, and shows that the yeast ThrRS-deletion model is suitable to test pathology-associated point mutations or alternative splicing variants of mammalian aaRS mRNAs.},
keywords = {alternative splicing aminoacyl-tRNA synthetase enzyme kinetics mitochondria mitochondrial disease threonyl-tRNA synthetase, ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Mitochondria require all translational components, including aminoacyl-tRNA synthetases (aaRSs), to complete organelle protein synthesis. Some aaRS mutations cause mitochondrial disorders, including human mitochondrial threonyl-tRNA synthetase (hmtThrRS) (encoded by TARS2), the P282L mutation of which causes mitochondrial encephalomyopathies. However, its catalytic and structural consequences remain unclear. Herein, we cloned TARS2 and purified the wild-type and P282L mutant hmtThrRS. hmtThrRS misactivates non-cognate Ser and uses post-transfer editing to clear erroneously synthesized products. In vitro and in vivo analyses revealed that the mutation induces a decrease in Thr activation, aminoacylation, and proofreading activities and a change in the protein structure and/or stability, which might cause reduced catalytic efficiency. We also identified a splicing variant of TARS2 mRNA lacking exons 8 and 9, the protein product of which is targeted into mitochondria. In HEK293T cells, the variant does not dimerize and cannot complement the ThrRS knock-out strain in yeast, suggesting that the truncated protein is inactive and might have a non-canonical function, as observed for other aaRS fragments. The present study describes the aminoacylation and editing properties of hmtThrRS, clarifies the molecular consequences of the P282L mutation, and shows that the yeast ThrRS-deletion model is suitable to test pathology-associated point mutations or alternative splicing variants of mammalian aaRS mRNAs.
Wang M, Liu H, Zheng J, Chen B, Zhou M, Fan W, Wang H, Liang X, Zhou X, Eriani G, Jiang P, Guan M X
In: J Biol Chem, vol. 291, no. 40, pp. 21029-21041, 2016, ISBN: 27519417.
Abstract | Links | BibTeX | Tags: diabetes hearing mitochondrial DNA (mtDNA) mitochondrial disease mutant pathogenesis post-translational modification (PTM) transfer RNA (tRNA), ERIANI, Unité ARN
@article{,
title = {A deafness and diabetes associated tRNA mutation caused the deficient pseudouridinylation at position 55 in tRNAGlu and mitochondrial dysfunction.},
author = {M Wang and H Liu and J Zheng and B Chen and M Zhou and W Fan and H Wang and X Liang and X Zhou and G Eriani and P Jiang and M X Guan},
url = {http://www.ncbi.nlm.nih.gov/pubmed/27519417?dopt=Abstract},
doi = {10.1074/jbc.M116.739482},
isbn = {27519417},
year = {2016},
date = {2016-01-01},
journal = {J Biol Chem},
volume = {291},
number = {40},
pages = {21029-21041},
abstract = {Several mitochondrial tRNA mutations have been associated with maternally inherited diabetes and deafness (MIDD). However, the pathophysiology of these tRNA mutations remains poorly understood. In this report, we identified the novel homoplasmic 14692A>G mutation in the mitochondrial tRNAGlu gene among three Han Chinese families with maternally inherited diabetes and deafness. The m.14692A>G mutation affected a highly conserved uridine at position 55 of TΨC loop of tRNAGlu. The uridine is modified to pseudouridine (Ψ55), which plays an important role in the structure and function of this tRNA. Using lymphoblastoid cell lines derived from a Chinese family, we demonstrated that the m.14692A>G mutation caused the loss of Ψ55 modification and increased the angiogenin-mediated endonucleolytic cleavage in mutant tRNAGlu. The destabilization of base-pairing (18A-Ψ55) caused by the m.14692A>G mutation perturbed the conformation and stability of tRNAGlu. Approximately 65% decrease in the steady-state level of tRNAGlu was observed in mutant cells, compared to control cells. A failure in tRNAGlu metabolism impaired mitochondrial translation, especially for polypeptides with high proportion of glutamic acid codons such as MT-ND1, MT-ND6 and MT-CO2 in mutant cells. An impairment of mitochondrial translation caused the defective respiratory capacity, especially reducing activities of complexes I and IV. Furthermore, marked decreases in the levels of mitochondrial ATP and membrane potential were observed in mutant cells. These mitochondrial dysfunctions caused an increasing production of reactive oxygen species in the mutant cells. Our findings may provide new insights into pathophysiology of MIDD, which was primarily manifested by the deficient nucleotide modification of mitochondrial tRNAGlu.},
keywords = {diabetes hearing mitochondrial DNA (mtDNA) mitochondrial disease mutant pathogenesis post-translational modification (PTM) transfer RNA (tRNA), ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Several mitochondrial tRNA mutations have been associated with maternally inherited diabetes and deafness (MIDD). However, the pathophysiology of these tRNA mutations remains poorly understood. In this report, we identified the novel homoplasmic 14692A>G mutation in the mitochondrial tRNAGlu gene among three Han Chinese families with maternally inherited diabetes and deafness. The m.14692A>G mutation affected a highly conserved uridine at position 55 of TΨC loop of tRNAGlu. The uridine is modified to pseudouridine (Ψ55), which plays an important role in the structure and function of this tRNA. Using lymphoblastoid cell lines derived from a Chinese family, we demonstrated that the m.14692A>G mutation caused the loss of Ψ55 modification and increased the angiogenin-mediated endonucleolytic cleavage in mutant tRNAGlu. The destabilization of base-pairing (18A-Ψ55) caused by the m.14692A>G mutation perturbed the conformation and stability of tRNAGlu. Approximately 65% decrease in the steady-state level of tRNAGlu was observed in mutant cells, compared to control cells. A failure in tRNAGlu metabolism impaired mitochondrial translation, especially for polypeptides with high proportion of glutamic acid codons such as MT-ND1, MT-ND6 and MT-CO2 in mutant cells. An impairment of mitochondrial translation caused the defective respiratory capacity, especially reducing activities of complexes I and IV. Furthermore, marked decreases in the levels of mitochondrial ATP and membrane potential were observed in mutant cells. These mitochondrial dysfunctions caused an increasing production of reactive oxygen species in the mutant cells. Our findings may provide new insights into pathophysiology of MIDD, which was primarily manifested by the deficient nucleotide modification of mitochondrial tRNAGlu.
McShane A, Hok E, Tomberlin J, Eriani G, Geslain R
The Enzymatic Paradox of Yeast Arginyl-tRNA Synthetase: Exclusive Arginine Transfer Controlled by a Flexible Mechanism of tRNA Recognition. Journal Article
In: PLoS One, vol. 11, no. 2, pp. e0148460, 2016, ISBN: 26844776.
Abstract | Links | BibTeX | Tags: ERIANI, Unité ARN
@article{,
title = {The Enzymatic Paradox of Yeast Arginyl-tRNA Synthetase: Exclusive Arginine Transfer Controlled by a Flexible Mechanism of tRNA Recognition.},
author = {A McShane and E Hok and J Tomberlin and G Eriani and R Geslain},
url = {http://www.ncbi.nlm.nih.gov/pubmed/26844776?dopt=Abstract},
doi = {10.1371/journal.pone.0148460},
isbn = {26844776},
year = {2016},
date = {2016-01-01},
journal = {PLoS One},
volume = {11},
number = {2},
pages = {e0148460},
abstract = {Identity determinants are essential for the accurate recognition of transfer RNAs by aminoacyl-tRNA synthetases. To date, arginine determinants in the yeast Saccharomyces cerevisiae have been identified exclusively in vitro and only on a limited number of tRNA Arginine isoacceptors. In the current study, we favor a full cellular approach and expand the investigation of arginine determinants to all four tRNA Arg isoacceptors. More precisely, this work scrutinizes the relevance of the tRNA nucleotides at position 20, 35 and 36 in the yeast arginylation reaction. We built 21 mutants by site-directed mutagenesis and tested their functionality in YAL5, a previously engineered yeast knockout deficient for the expression of tRNA Arg CCG. Arginylation levels were also monitored using Northern blot. Our data collected in vivo correlate with previous observations. C35 is the prominent arginine determinant followed by G36 or U36 (G/U36). In addition, although there is no major arginine determinant in the D loop, the recognition of tRNA Arg ICG relies to some extent on the nucleotide at position 20. This work refines the existing model for tRNA Arg recognition. Our observations indicate that yeast Arginyl-tRNA synthetase (yArgRS) relies on distinct mechanisms to aminoacylate the four isoacceptors. Finally, according to our refined model, yArgRS is able to accommodate tRNA Arg scaffolds presenting N34, C/G35 and G/A/U36 anticodons while maintaining specificity. We discuss the mechanistic and potential physiological implications of these findings.},
keywords = {ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Identity determinants are essential for the accurate recognition of transfer RNAs by aminoacyl-tRNA synthetases. To date, arginine determinants in the yeast Saccharomyces cerevisiae have been identified exclusively in vitro and only on a limited number of tRNA Arginine isoacceptors. In the current study, we favor a full cellular approach and expand the investigation of arginine determinants to all four tRNA Arg isoacceptors. More precisely, this work scrutinizes the relevance of the tRNA nucleotides at position 20, 35 and 36 in the yeast arginylation reaction. We built 21 mutants by site-directed mutagenesis and tested their functionality in YAL5, a previously engineered yeast knockout deficient for the expression of tRNA Arg CCG. Arginylation levels were also monitored using Northern blot. Our data collected in vivo correlate with previous observations. C35 is the prominent arginine determinant followed by G36 or U36 (G/U36). In addition, although there is no major arginine determinant in the D loop, the recognition of tRNA Arg ICG relies to some extent on the nucleotide at position 20. This work refines the existing model for tRNA Arg recognition. Our observations indicate that yeast Arginyl-tRNA synthetase (yArgRS) relies on distinct mechanisms to aminoacylate the four isoacceptors. Finally, according to our refined model, yArgRS is able to accommodate tRNA Arg scaffolds presenting N34, C/G35 and G/A/U36 anticodons while maintaining specificity. We discuss the mechanistic and potential physiological implications of these findings.
Martin F, Ménétret J F, Simonetti A, Myasnikov A G, Vicens Q, Prongidi-Fix L, Natchiar S K, Klaholz B P, Eriani G
Ribosomal 18S rRNA base pairs with mRNA during eukaryotic translation initiation. Journal Article
In: Nat Commun, vol. 7, pp. 12622, 2016, ISBN: 27554013.
Abstract | Links | BibTeX | Tags: ERIANI, Unité ARN
@article{,
title = {Ribosomal 18S rRNA base pairs with mRNA during eukaryotic translation initiation.},
author = {F Martin and J F Ménétret and A Simonetti and A G Myasnikov and Q Vicens and L Prongidi-Fix and S K Natchiar and B P Klaholz and G Eriani},
url = {http://www.ncbi.nlm.nih.gov/pubmed/27554013?dopt=Abstract},
doi = {10.1038/ncomms12622},
isbn = {27554013},
year = {2016},
date = {2016-01-01},
journal = {Nat Commun},
volume = {7},
pages = {12622},
abstract = {Eukaryotic mRNAs often contain a Kozak sequence that helps tether the ribosome to the AUG start codon. The mRNA of histone H4 (h4) does not undergo classical ribosome scanning but has evolved a specific tethering mechanism. The cryo-EM structure of the rabbit ribosome complex with mouse h4 shows that the mRNA forms a folded, repressive structure at the mRNA entry site on the 40S subunit next to the tip of helix 16 of 18S ribosomal RNA (rRNA). Toe-printing and mutational assays reveal that an interaction exists between a purine-rich sequence in h4 mRNA and a complementary UUUC sequence of helix h16. Together the present data establish that the h4 mRNA harbours a sequence complementary to an 18S rRNA sequence which tethers the mRNA to the ribosome to promote proper start codon positioning, complementing the interactions of the 40S subunit with the Kozak sequence that flanks the AUG start codon.},
keywords = {ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Eukaryotic mRNAs often contain a Kozak sequence that helps tether the ribosome to the AUG start codon. The mRNA of histone H4 (h4) does not undergo classical ribosome scanning but has evolved a specific tethering mechanism. The cryo-EM structure of the rabbit ribosome complex with mouse h4 shows that the mRNA forms a folded, repressive structure at the mRNA entry site on the 40S subunit next to the tip of helix 16 of 18S ribosomal RNA (rRNA). Toe-printing and mutational assays reveal that an interaction exists between a purine-rich sequence in h4 mRNA and a complementary UUUC sequence of helix h16. Together the present data establish that the h4 mRNA harbours a sequence complementary to an 18S rRNA sequence which tethers the mRNA to the ribosome to promote proper start codon positioning, complementing the interactions of the 40S subunit with the Kozak sequence that flanks the AUG start codon.
Kowalska J, Martin F, Jemielity J
Synthetic Capped mRNAs for Cap-Specific Photo-Cross-Linking Experiments. Book Chapter
In: Rhoads, R (Ed.): Synthetic mRNA: Production, Introduction Into Cells, and Physiological Consequences, vol. 1428, pp. 31-43, Springer Protocols, Humana Press, 2016, ISBN: 27236790.
Abstract | Links | BibTeX | Tags: cap analogs 6-thioguanosine Cap binding Histone mRNA Photo-cross-linking Transcription mRNA stability, ERIANI, Unité ARN
@inbook{,
title = {Synthetic Capped mRNAs for Cap-Specific Photo-Cross-Linking Experiments.},
author = {J Kowalska and F Martin and J Jemielity},
editor = {R Rhoads},
url = {http://www.ncbi.nlm.nih.gov/pubmed/27236790?dopt=Abstract},
doi = {10.1007/978-1-4939-3625-0_2},
isbn = {27236790},
year = {2016},
date = {2016-01-01},
booktitle = {Synthetic mRNA: Production, Introduction Into Cells, and Physiological Consequences},
volume = {1428},
pages = {31-43},
publisher = {Springer Protocols, Humana Press},
series = {Methods in Molecular Biology},
abstract = {he 7-methylguanosine triphosphate cap present at the 5' ends of eukaryotic mRNAs plays numerous roles in mRNA expression and metabolism. The identification and studies on cap-binding partners can be significantly advanced using tailored chemical tools such as synthetic cap analogues or RNAs carrying modified cap structures. Here we provide protocols for the production of mRNAs specifically labeled within the 5' cap with a nucleoside capable of being photo-activated, either 6-thioguanosine or 7-methyl-6-thioguanosine, which can be used in photo-cross-linking experiments to identify or characterize cap-binding biomolecules. We also describe a protocol for the cross-linking experiments with capped RNAs to map histone H4 cap-binding pocket.},
keywords = {cap analogs 6-thioguanosine Cap binding Histone mRNA Photo-cross-linking Transcription mRNA stability, ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
he 7-methylguanosine triphosphate cap present at the 5' ends of eukaryotic mRNAs plays numerous roles in mRNA expression and metabolism. The identification and studies on cap-binding partners can be significantly advanced using tailored chemical tools such as synthetic cap analogues or RNAs carrying modified cap structures. Here we provide protocols for the production of mRNAs specifically labeled within the 5' cap with a nucleoside capable of being photo-activated, either 6-thioguanosine or 7-methyl-6-thioguanosine, which can be used in photo-cross-linking experiments to identify or characterize cap-binding biomolecules. We also describe a protocol for the cross-linking experiments with capped RNAs to map histone H4 cap-binding pocket.
2015
Yan W, Ye Q, Tan M, Chen X, Eriani G, Wang E D
Modulation of aminoacylation and editing properties of leucyl-tRNA synthetase by a conserved structural module. Journal Article
In: J Biol Chem, vol. 290, no. 19, pp. 12256-12267, 2015, ISBN: 25817995.
Abstract | Links | BibTeX | Tags: aminoacyl tRNA synthetase aminoacylation editing enzyme evolution protein synthesis stem contact fold transfer RNA (tRNA), ERIANI, Unité ARN
@article{,
title = {Modulation of aminoacylation and editing properties of leucyl-tRNA synthetase by a conserved structural module.},
author = {W Yan and Q Ye and M Tan and X Chen and G Eriani and E D Wang},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25817995?dopt=Abstract},
doi = {10.1074/jbc.M115.639492},
isbn = {25817995},
year = {2015},
date = {2015-01-01},
journal = {J Biol Chem},
volume = {290},
number = {19},
pages = {12256-12267},
abstract = {A conserved structural module following the KMSKS catalytic loop exhibits α-α-β-α topology in class Ia and Ib aminoacyl-tRNA synthetases. However, the function of this domain has received little attention. Here, we describe the effect this module has on the aminoacylation and editing capacities of leucyl-tRNA synthetases (LeuRSs) by characterizing the key residues from various species. Mutation of highly conserved basic residues on the third α-helix of this domain impairs the affinity of LeuRS for the anticodon stem of tRNALeu, which decreases both aminoacylation and editing activities. Two glycine residues on this α-helix contribute to flexibility, leucine activation and editing of LeuRS from Escherichia coli (EcLeuRS). Acidic residues on the β-strand enhance the editing activity of EcLeuRS and sense the size of the tRNALeu D-loop. Incorporation of these residues stimulates the tRNA-dependent editing activity of the chimeric minimalist enzyme MmLeuRS fused with the connective polypeptide 1 (CP1) editing domain and leucine-specific domain of (LSD) from EcLeuRS. Together, these results reveal the stem contact (SC)-fold to be functional as well as a structural linker between the catalytic site and tRNA binding domain. Sequence comparison of the EcLeuRS SC-fold domain with editing-deficient enzymes suggests that key residues of this module have evolved an adaptive strategy to follow the editing functions of LeuRSs.},
keywords = {aminoacyl tRNA synthetase aminoacylation editing enzyme evolution protein synthesis stem contact fold transfer RNA (tRNA), ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
A conserved structural module following the KMSKS catalytic loop exhibits α-α-β-α topology in class Ia and Ib aminoacyl-tRNA synthetases. However, the function of this domain has received little attention. Here, we describe the effect this module has on the aminoacylation and editing capacities of leucyl-tRNA synthetases (LeuRSs) by characterizing the key residues from various species. Mutation of highly conserved basic residues on the third α-helix of this domain impairs the affinity of LeuRS for the anticodon stem of tRNALeu, which decreases both aminoacylation and editing activities. Two glycine residues on this α-helix contribute to flexibility, leucine activation and editing of LeuRS from Escherichia coli (EcLeuRS). Acidic residues on the β-strand enhance the editing activity of EcLeuRS and sense the size of the tRNALeu D-loop. Incorporation of these residues stimulates the tRNA-dependent editing activity of the chimeric minimalist enzyme MmLeuRS fused with the connective polypeptide 1 (CP1) editing domain and leucine-specific domain of (LSD) from EcLeuRS. Together, these results reveal the stem contact (SC)-fold to be functional as well as a structural linker between the catalytic site and tRNA binding domain. Sequence comparison of the EcLeuRS SC-fold domain with editing-deficient enzymes suggests that key residues of this module have evolved an adaptive strategy to follow the editing functions of LeuRSs.
Ruan Z R, Fang Z P, Ye Q, Lei H Y, Eriani G, Zhou X L, Wang E D
Identification of Lethal Mutations in Yeast Threonyl-tRNA Synthetase Revealing Critical Residues in Its Human Homolog. Journal Article
In: J Biol Chem, vol. 290, no. 3, pp. 1664-1678, 2015, ISBN: 25416776.
Abstract | Links | BibTeX | Tags: aminoacyl tRNA synthetase aminoacylation editing mutagenesis protein structure transfer RNA (tRNA) translation, ERIANI, Unité ARN
@article{,
title = {Identification of Lethal Mutations in Yeast Threonyl-tRNA Synthetase Revealing Critical Residues in Its Human Homolog.},
author = {Z R Ruan and Z P Fang and Q Ye and H Y Lei and G Eriani and X L Zhou and E D Wang},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25416776?dopt=Abstract},
doi = {10.1074/jbc.M114.599886},
isbn = {25416776},
year = {2015},
date = {2015-01-01},
journal = {J Biol Chem},
volume = {290},
number = {3},
pages = {1664-1678},
abstract = {Aminoacyl-tRNA synthetases (aaRSs) are a group of ancient enzymes catalyzing aminoacylation and editing reactions for protein biosynthesis. Increasing evidence suggests that these critical enzymes are often associated with mammalian disorders. Therefore, complete determination of the enzymes functions is essential for informed diagnosis and treatment. Here, we show that a yeast knockout strain for the threonyl-tRNA synthetase (ThrRS) gene is an excellent platform for such an investigation. Saccharomyces cerevisiae ThrRS (ScThrRS) has a unique modular structure containing four structural domains and a eukaryotic-specific N-terminal extension. Using randomly mutated libraries of the ThrRS gene (thrS) and a genetic screen, a set of loss-of-function mutants were identified. The mutations affected the synthetic and editing activities and influenced the dimer interface. The results also highlighted the role of the N-terminal extension for enzymatic activity and protein stability. To gain insights into the pathological mechanisms induced by mutated aaRSs, we systematically introduced the loss-of-function mutations into the human cytoplasmic ThrRS gene. All mutations induced similar detrimental effects, showing that the yeast model could be used to study pathology-associated point mutations in mammalian aaRSs.},
keywords = {aminoacyl tRNA synthetase aminoacylation editing mutagenesis protein structure transfer RNA (tRNA) translation, ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Aminoacyl-tRNA synthetases (aaRSs) are a group of ancient enzymes catalyzing aminoacylation and editing reactions for protein biosynthesis. Increasing evidence suggests that these critical enzymes are often associated with mammalian disorders. Therefore, complete determination of the enzymes functions is essential for informed diagnosis and treatment. Here, we show that a yeast knockout strain for the threonyl-tRNA synthetase (ThrRS) gene is an excellent platform for such an investigation. Saccharomyces cerevisiae ThrRS (ScThrRS) has a unique modular structure containing four structural domains and a eukaryotic-specific N-terminal extension. Using randomly mutated libraries of the ThrRS gene (thrS) and a genetic screen, a set of loss-of-function mutants were identified. The mutations affected the synthetic and editing activities and influenced the dimer interface. The results also highlighted the role of the N-terminal extension for enzymatic activity and protein stability. To gain insights into the pathological mechanisms induced by mutated aaRSs, we systematically introduced the loss-of-function mutations into the human cytoplasmic ThrRS gene. All mutations induced similar detrimental effects, showing that the yeast model could be used to study pathology-associated point mutations in mammalian aaRSs.
Lei H Y, Zhou X L, Ruan Z R, Sun W C, Eriani G, Wang E D
Calpain Cleaves Most Components in the Multiple Aminoacyl-tRNA Synthetase Complex and Affects Their Functions. Journal Article
In: J Biol Chem, vol. 290, no. 43, pp. 26314-26327, 2015, ISBN: 26324710.
Abstract | Links | BibTeX | Tags: aminoacyl tRNA synthetase aminoacylation calpain protein fragments protein secretion proteolysis stress, ERIANI, Unité ARN
@article{,
title = {Calpain Cleaves Most Components in the Multiple Aminoacyl-tRNA Synthetase Complex and Affects Their Functions.},
author = {H Y Lei and X L Zhou and Z R Ruan and W C Sun and G Eriani and E D Wang},
url = {http://www.ncbi.nlm.nih.gov/pubmed/26324710?dopt=Abstract},
doi = {10.1074/jbc.M115.681999},
isbn = {26324710},
year = {2015},
date = {2015-01-01},
journal = {J Biol Chem},
volume = {290},
number = {43},
pages = {26314-26327},
abstract = {Nine aminoacyl-tRNA synthetases (aaRSs) and three scaffold proteins form a super multiple aminoacyl-tRNA synthetase complex (MSC) in the human cytoplasm. Domains that have been added progressively to MSC components during evolution are linked by unstructured flexible peptides, producing an elongated and multiarmed MSC structure that is easily attacked by proteases in vivo. A yeast two-hybrid screen for proteins interacting with LeuRS, a representative MSC member, identified calpain 2, a calcium-activated neutral cysteine protease. Calpain 2 and calpain 1 could partially hydrolyze most MSC components to generate specific fragments that resembled those reported previously. The cleavage sites of calpain in ArgRS, GlnRS, and p43 were precisely mapped. After cleavage, their N-terminal regions were removed. Sixty-three amino acid residues were removed from the N terminus of ArgRS to form ArgRSΔN63; GlnRS formed GlnRSΔN198, and p43 formed p43ΔN106. GlnRSΔN198 had a much weaker affinity for its substrates, tRNA(Gln) and glutamine. p43ΔN106 was the same as the previously reported p43-derived apoptosis-released factor. The formation of p43ΔN106 by calpain depended on Ca(2+) and could be specifically inhibited by calpeptin and by RNAi of the regulatory subunit of calpain in vivo. These results showed, for the first time, that calpain plays an essential role in dissociating the MSC and might regulate the canonical and non-canonical functions of certain components of the MSC.},
keywords = {aminoacyl tRNA synthetase aminoacylation calpain protein fragments protein secretion proteolysis stress, ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Nine aminoacyl-tRNA synthetases (aaRSs) and three scaffold proteins form a super multiple aminoacyl-tRNA synthetase complex (MSC) in the human cytoplasm. Domains that have been added progressively to MSC components during evolution are linked by unstructured flexible peptides, producing an elongated and multiarmed MSC structure that is easily attacked by proteases in vivo. A yeast two-hybrid screen for proteins interacting with LeuRS, a representative MSC member, identified calpain 2, a calcium-activated neutral cysteine protease. Calpain 2 and calpain 1 could partially hydrolyze most MSC components to generate specific fragments that resembled those reported previously. The cleavage sites of calpain in ArgRS, GlnRS, and p43 were precisely mapped. After cleavage, their N-terminal regions were removed. Sixty-three amino acid residues were removed from the N terminus of ArgRS to form ArgRSΔN63; GlnRS formed GlnRSΔN198, and p43 formed p43ΔN106. GlnRSΔN198 had a much weaker affinity for its substrates, tRNA(Gln) and glutamine. p43ΔN106 was the same as the previously reported p43-derived apoptosis-released factor. The formation of p43ΔN106 by calpain depended on Ca(2+) and could be specifically inhibited by calpeptin and by RNAi of the regulatory subunit of calpain in vivo. These results showed, for the first time, that calpain plays an essential role in dissociating the MSC and might regulate the canonical and non-canonical functions of certain components of the MSC.
Eriani G, Karam J, Jacinto J, Richard E Morris, Geslain R
MIST, a Novel Approach to Reveal Hidden Substrate Specificity in Aminoacyl-tRNA Synthetases. Journal Article
In: PLoS One, vol. 10, no. 6, pp. e0130042, 2015, ISBN: 26067673.
Abstract | Links | BibTeX | Tags: ERIANI, Unité ARN
@article{,
title = {MIST, a Novel Approach to Reveal Hidden Substrate Specificity in Aminoacyl-tRNA Synthetases.},
author = {G Eriani and J Karam and J Jacinto and E Morris Richard and R Geslain},
url = {http://www.ncbi.nlm.nih.gov/pubmed/26067673?dopt=Abstract},
doi = {10.1371/journal.pone.0130042},
isbn = {26067673},
year = {2015},
date = {2015-01-01},
journal = {PLoS One},
volume = {10},
number = {6},
pages = {e0130042},
abstract = {Aminoacyl-tRNA synthetases (AARSs) constitute a family of RNA-binding proteins, that participate in the translation of the genetic code, by covalently linking amino acids to appropriate tRNAs. Due to their fundamental importance for cell life, AARSs are likely to be one of the most ancient families of enzymes and have therefore been characterized extensively. Paradoxically, little is known about their capacity to discriminate tRNAs mainly because of the practical challenges that represent precise and systematic tRNA identification. This work describes a new technical and conceptual approach named MIST (Microarray Identification of Shifted tRNAs) designed to study the formation of tRNA/AARS complexes independently from the aminoacylation reaction. MIST combines electrophoretic mobility shift assays with microarray analyses. Although MIST is a non-cellular assay, it fully integrates the notion of tRNA competition. In this study we focus on yeast cytoplasmic Arginyl-tRNA synthetase (yArgRS) and investigate in depth its ability to discriminate cellular tRNAs. We report that yArgRS in submicromolar concentrations binds cognate and non-cognate tRNAs with a wide range of apparent affinities. In particular, we demonstrate that yArgRS binds preferentially to type II tRNAs but does not support their misaminoacylation. Our results reveal important new trends in tRNA/AARS complex formation and potential deep physiological implications.},
keywords = {ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Aminoacyl-tRNA synthetases (AARSs) constitute a family of RNA-binding proteins, that participate in the translation of the genetic code, by covalently linking amino acids to appropriate tRNAs. Due to their fundamental importance for cell life, AARSs are likely to be one of the most ancient families of enzymes and have therefore been characterized extensively. Paradoxically, little is known about their capacity to discriminate tRNAs mainly because of the practical challenges that represent precise and systematic tRNA identification. This work describes a new technical and conceptual approach named MIST (Microarray Identification of Shifted tRNAs) designed to study the formation of tRNA/AARS complexes independently from the aminoacylation reaction. MIST combines electrophoretic mobility shift assays with microarray analyses. Although MIST is a non-cellular assay, it fully integrates the notion of tRNA competition. In this study we focus on yeast cytoplasmic Arginyl-tRNA synthetase (yArgRS) and investigate in depth its ability to discriminate cellular tRNAs. We report that yArgRS in submicromolar concentrations binds cognate and non-cognate tRNAs with a wide range of apparent affinities. In particular, we demonstrate that yArgRS binds preferentially to type II tRNAs but does not support their misaminoacylation. Our results reveal important new trends in tRNA/AARS complex formation and potential deep physiological implications.
Chicher J, Simonetti A, Kuhn L, Schaeffer L, Hammann P, Eriani G, Martin F
Purification of mRNA-programmed translation initiation complexes suitable for mass spectrometry analysis. Journal Article
In: Proteomics, vol. 15, no. 14, pp. 2417-2425, 2015, ISBN: 25914180.
Abstract | Links | BibTeX | Tags: ERIANI, PPSE, Unité ARN
@article{,
title = {Purification of mRNA-programmed translation initiation complexes suitable for mass spectrometry analysis.},
author = {J Chicher and A Simonetti and L Kuhn and L Schaeffer and P Hammann and G Eriani and F Martin},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25914180?dopt=Abstract},
doi = {10.1002/pmic.201400628},
isbn = {25914180},
year = {2015},
date = {2015-01-01},
journal = {Proteomics},
volume = {15},
number = {14},
pages = {2417-2425},
abstract = {Liquid Chromatography coupled to tandem Mass Spectrometry (nanoLC-MS/MS) is a powerful analytical technique for the identification and mass analysis of complex protein mixtures. Here we present a combination of methods developed for the extensive/deep proteomic analysis of purified ribosome/mRNA particles assembled in rabbit reticulocyte lysate (RRL). Ribosomes are assembled on chimeric biotinylated mRNA-DNA molecules immobilized on streptavidin-coated beads and incubated with RRL to form initiation complexes. After washing steps, the complexes are trypsin-digested directly on the beads in semi-native condition or after their elution from the beads in denaturing Laemmli buffer. The nanoLC-MS/MS analysis performed on complexes assembled on β-globin, viral HCV and histone H4 mRNAs revealed significant differences in initiation factors composition in agreement with models of translation initiation used by these different types of mRNAs. Using Laemmli-denaturing condition induces release of deeply buried peptides from the ribosome and eukaryotic initiation factor 3 (eIF3) allowing the identification of the nearly complete set of ribosomal proteins. This article is protected by copyright. All rights reserved.},
keywords = {ERIANI, PPSE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Liquid Chromatography coupled to tandem Mass Spectrometry (nanoLC-MS/MS) is a powerful analytical technique for the identification and mass analysis of complex protein mixtures. Here we present a combination of methods developed for the extensive/deep proteomic analysis of purified ribosome/mRNA particles assembled in rabbit reticulocyte lysate (RRL). Ribosomes are assembled on chimeric biotinylated mRNA-DNA molecules immobilized on streptavidin-coated beads and incubated with RRL to form initiation complexes. After washing steps, the complexes are trypsin-digested directly on the beads in semi-native condition or after their elution from the beads in denaturing Laemmli buffer. The nanoLC-MS/MS analysis performed on complexes assembled on β-globin, viral HCV and histone H4 mRNAs revealed significant differences in initiation factors composition in agreement with models of translation initiation used by these different types of mRNAs. Using Laemmli-denaturing condition induces release of deeply buried peptides from the ribosome and eukaryotic initiation factor 3 (eIF3) allowing the identification of the nearly complete set of ribosomal proteins. This article is protected by copyright. All rights reserved.
2014
Wurth L, Gribling-Burrer A S, Verheggen C, Leichter M, Takeuchi A, Baudrey S, Martin F, Krol A, Bertrand E, Allmang C
Hypermethylated-capped selenoprotein mRNAs in mammals. Journal Article
In: Nucleic Acids Res, vol. 42, no. 13, pp. 8663-8677, 2014, ISBN: 25013170.
Abstract | Links | BibTeX | Tags: ERIANI, Unité ARN
@article{,
title = {Hypermethylated-capped selenoprotein mRNAs in mammals.},
author = {L Wurth and A S Gribling-Burrer and C Verheggen and M Leichter and A Takeuchi and S Baudrey and F Martin and A Krol and E Bertrand and C Allmang},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25013170},
doi = {10.1093/nar/gku580},
isbn = {25013170},
year = {2014},
date = {2014-01-01},
journal = {Nucleic Acids Res},
volume = {42},
number = {13},
pages = {8663-8677},
abstract = {Mammalian mRNAs are generated by complex and coordinated biogenesis pathways and acquire 5'-end m7G caps that play fundamental roles in processing and translation. Here we show that several selenoprotein mRNAs are not recognized efficiently by translation initiation factor eIF4E because they bear a hypermethylated cap. This cap modification is acquired via a 5'-end maturation pathway similar to that of the small nucle(ol)ar RNAs (sn- and snoRNAs). Our findings also establish that the trimethylguanosine synthase 1 (Tgs1) interacts with selenoprotein mRNAs for cap hypermethylation and that assembly chaperones and core proteins devoted to sn- and snoRNP maturation contribute to recruiting Tgs1 to selenoprotein mRNPs. We further demonstrate that the hypermethylated-capped selenoprotein mRNAs localize to the cytoplasm, are associated with polysomes and thus translated. Moreover, we found that the activity of Tgs1, but not of eIF4E, is required for the synthesis of the GPx1 selenoprotein in vivo.},
keywords = {ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Mammalian mRNAs are generated by complex and coordinated biogenesis pathways and acquire 5'-end m7G caps that play fundamental roles in processing and translation. Here we show that several selenoprotein mRNAs are not recognized efficiently by translation initiation factor eIF4E because they bear a hypermethylated cap. This cap modification is acquired via a 5'-end maturation pathway similar to that of the small nucle(ol)ar RNAs (sn- and snoRNAs). Our findings also establish that the trimethylguanosine synthase 1 (Tgs1) interacts with selenoprotein mRNAs for cap hypermethylation and that assembly chaperones and core proteins devoted to sn- and snoRNP maturation contribute to recruiting Tgs1 to selenoprotein mRNPs. We further demonstrate that the hypermethylated-capped selenoprotein mRNAs localize to the cytoplasm, are associated with polysomes and thus translated. Moreover, we found that the activity of Tgs1, but not of eIF4E, is required for the synthesis of the GPx1 selenoprotein in vivo.
Ray S, Blaise M, Roy B, Ghosh S, Kern D, Banerjee R
Fusion with Anticodon Binding Domain of GluRS is Not Sufficient to Alter the Substrate Specificity of a Chimeric Glu-Q-RS. Journal Article
In: Protein J, vol. 33, no. 1, pp. 48-60, 2014, ISBN: 24374508.
Abstract | Links | BibTeX | Tags: ERIANI, Unité ARN
@article{,
title = {Fusion with Anticodon Binding Domain of GluRS is Not Sufficient to Alter the Substrate Specificity of a Chimeric Glu-Q-RS.},
author = {S Ray and M Blaise and B Roy and S Ghosh and D Kern and R Banerjee},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24374508},
doi = {10.1007/s10930-013-9537-7},
isbn = {24374508},
year = {2014},
date = {2014-01-01},
journal = {Protein J},
volume = {33},
number = {1},
pages = {48-60},
abstract = {Glutamyl-queuosine-tRNAAsp synthetase (Glu-Q-RS) is a paralog of glutamyl-tRNA synthetase (GluRS) and is found in more than forty species of proteobacteria, cyanobacteria, and actinobacteria. Glu-Q-RS shows striking structural similarity with N-terminal catalytic domain of GluRS (NGluRS) but it lacks the C-terminal anticodon binding domain (CGluRS). In spite of structural similarities, Glu-Q-RS and NGluRS differ in their functional properties. Glu-Q-RS glutamylates the Q34 nucleotide of the anticodon of tRNAAsp whereas NGluRS constitutes the catalytic domain of GluRS catalyzing the transfer of Glu on the acceptor end of tRNAGlu. Since NGluRS is able to catalyze aminoacylation of only tRNAGlu the glutamylation capacity of tRNAAsp by Glu-Q-RS is surprising. To understand the substrate specificity of Glu-Q-RS we undertook a systemic approach by investigating the biophysical and biochemical properties of the NGluRS (1-301), CGluRS (314-471) and Glu-Q-RS-CGluRS, (1-298 of Glu-Q-RS fused to 314-471 from GluRS). Circular dichroism, fluorescence spectroscopy and differential scanning calorimetry analyses revealed absence of N-terminal domain (1-298 of Glu-Q-RS) and C-terminal domain (314-471 from GluRS) communication in chimera, in contrast to the native full length GluRS. The chimeric Glu-Q-RS is still able to aminoacylate tRNAAsp but has also the capacity to bind tRNAGlu. However the chimeric protein is unable to aminoacylate tRNAGlu probably as a consequence of the lack of domain-domain communication.},
keywords = {ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Glutamyl-queuosine-tRNAAsp synthetase (Glu-Q-RS) is a paralog of glutamyl-tRNA synthetase (GluRS) and is found in more than forty species of proteobacteria, cyanobacteria, and actinobacteria. Glu-Q-RS shows striking structural similarity with N-terminal catalytic domain of GluRS (NGluRS) but it lacks the C-terminal anticodon binding domain (CGluRS). In spite of structural similarities, Glu-Q-RS and NGluRS differ in their functional properties. Glu-Q-RS glutamylates the Q34 nucleotide of the anticodon of tRNAAsp whereas NGluRS constitutes the catalytic domain of GluRS catalyzing the transfer of Glu on the acceptor end of tRNAGlu. Since NGluRS is able to catalyze aminoacylation of only tRNAGlu the glutamylation capacity of tRNAAsp by Glu-Q-RS is surprising. To understand the substrate specificity of Glu-Q-RS we undertook a systemic approach by investigating the biophysical and biochemical properties of the NGluRS (1-301), CGluRS (314-471) and Glu-Q-RS-CGluRS, (1-298 of Glu-Q-RS fused to 314-471 from GluRS). Circular dichroism, fluorescence spectroscopy and differential scanning calorimetry analyses revealed absence of N-terminal domain (1-298 of Glu-Q-RS) and C-terminal domain (314-471 from GluRS) communication in chimera, in contrast to the native full length GluRS. The chimeric Glu-Q-RS is still able to aminoacylate tRNAAsp but has also the capacity to bind tRNAGlu. However the chimeric protein is unable to aminoacylate tRNAGlu probably as a consequence of the lack of domain-domain communication.
Ray S, Banerjee V, Blaise M, Banerjee B, Das K P, Kern D, Banerjee R
Critical Role of Zinc Ion on E. coli Glutamyl-Queuosine-tRNAAsp Synthetase (Glu-Q-RS) Structure and Function. Journal Article
In: Protein J, vol. 33, no. 2, pp. 143-149, 2014, ISBN: 24505021.
Abstract | Links | BibTeX | Tags: ERIANI, Unité ARN
@article{,
title = {Critical Role of Zinc Ion on E. coli Glutamyl-Queuosine-tRNA^{Asp} Synthetase (Glu-Q-RS) Structure and Function.},
author = {S Ray and V Banerjee and M Blaise and B Banerjee and K P Das and D Kern and R Banerjee},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24505021?dopt=Abstract},
doi = {10.1007/s10930-014-9546-1},
isbn = {24505021},
year = {2014},
date = {2014-01-01},
journal = {Protein J},
volume = {33},
number = {2},
pages = {143-149},
abstract = {Glutamyl-queuosine-tRNAAsp synthetase (Glu-Q-RS) and glutamyl-tRNA synthetase (GluRS), differ widely by their function although they share close structural resemblance within their catalytic core of GluRS. In particular both Escherichia coli GluRS and Glu-Q-RS contain a single zinc-binding site in their putative tRNA acceptor stem-binding domain. It has been shown that the zinc is crucial for correct positioning of the tRNAGlu acceptor-end in the active site of E. coli GluRS. To address the role of zinc ion in Glu-Q-RS, the C101S/C103S Glu-Q-RS variant is constructed. Energy dispersive X-ray fluorescence show that the zinc ion still remained coordinated but the variant became structurally labile and acquired aggregation capacity. The extent of aggregation of the protein is significantly decreased in presence of the small substrates and more particularly by adenosine triphosphate. Addition of zinc increased significantly the solubility of the variant. The aminoacylation assay reveals a decrease in activity of the variant even after addition of zinc as compared to the wild-type, although the secondary structure of the protein is not altered as shown by the Fourier transform infrared spectroscopy study.},
keywords = {ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Glutamyl-queuosine-tRNAAsp synthetase (Glu-Q-RS) and glutamyl-tRNA synthetase (GluRS), differ widely by their function although they share close structural resemblance within their catalytic core of GluRS. In particular both Escherichia coli GluRS and Glu-Q-RS contain a single zinc-binding site in their putative tRNA acceptor stem-binding domain. It has been shown that the zinc is crucial for correct positioning of the tRNAGlu acceptor-end in the active site of E. coli GluRS. To address the role of zinc ion in Glu-Q-RS, the C101S/C103S Glu-Q-RS variant is constructed. Energy dispersive X-ray fluorescence show that the zinc ion still remained coordinated but the variant became structurally labile and acquired aggregation capacity. The extent of aggregation of the protein is significantly decreased in presence of the small substrates and more particularly by adenosine triphosphate. Addition of zinc increased significantly the solubility of the variant. The aminoacylation assay reveals a decrease in activity of the variant even after addition of zinc as compared to the wild-type, although the secondary structure of the protein is not altered as shown by the Fourier transform infrared spectroscopy study.
Nowakowska M, Kowalska J, Martin F, d'Orchymont A, Zuberek J, Lukaszewicz M, Darzynkiewicz E, Jemielity J
Cap analogs containing 6-thioguanosine - reagents for the synthesis of mRNAs selectively photo-crosslinkable with cap-binding biomolecules. Journal Article
In: Org Biomol Chem, vol. 12, no. 27, pp. 4841-4847, 2014, ISBN: 24763507.
Abstract | Links | BibTeX | Tags: ERIANI, Unité ARN
@article{,
title = {Cap analogs containing 6-thioguanosine - reagents for the synthesis of mRNAs selectively photo-crosslinkable with cap-binding biomolecules.},
author = {M Nowakowska and J Kowalska and F Martin and A d'Orchymont and J Zuberek and M Lukaszewicz and E Darzynkiewicz and J Jemielity},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24763507},
doi = {10.1039/c4ob00059e},
isbn = {24763507},
year = {2014},
date = {2014-01-01},
journal = {Org Biomol Chem},
volume = {12},
number = {27},
pages = {4841-4847},
abstract = {Numerous biomolecules recognize the 7-methylguanosine cap structure present at the 5' ends of eukaryotic mRNAs. Photo-crosslinking is a valuable technique to study these interactions. We report three anti-reverse cap analogs containing a photo-activable nucleoside, 6-thioguanosine (6SG), that enable the synthesis of capped RNAs with 6SG positioned exclusively as the first transcribed nucleotide. The effect of the 6-thioguanosine moiety on binding to the translation factor eIF4E and the efficiency of mRNA translation was determined. The utility of mRNAs with a 6SG-modified cap in crosslinking experiments is shown by mapping the histone H4 cap-binding pocket.},
keywords = {ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Numerous biomolecules recognize the 7-methylguanosine cap structure present at the 5' ends of eukaryotic mRNAs. Photo-crosslinking is a valuable technique to study these interactions. We report three anti-reverse cap analogs containing a photo-activable nucleoside, 6-thioguanosine (6SG), that enable the synthesis of capped RNAs with 6SG positioned exclusively as the first transcribed nucleotide. The effect of the 6-thioguanosine moiety on binding to the translation factor eIF4E and the efficiency of mRNA translation was determined. The utility of mRNAs with a 6SG-modified cap in crosslinking experiments is shown by mapping the histone H4 cap-binding pocket.
Zhou X L, Ruan Z R, Wang M, Fang Z P, Wang Y, Chen Y, Liu R J, Eriani G, Wang E D
A minimalist mitochondrial threonyl-tRNA synthetase exhibits tRNA-isoacceptor specificity during proofreading. Journal Article
In: Nucleic Acids Res, vol. 42, no. 22, pp. 13873-13886, 2014, ISBN: 25414329.
Abstract | Links | BibTeX | Tags: ERIANI, Unité ARN
@article{,
title = {A minimalist mitochondrial threonyl-tRNA synthetase exhibits tRNA-isoacceptor specificity during proofreading.},
author = {X L Zhou and Z R Ruan and M Wang and Z P Fang and Y Wang and Y Chen and R J Liu and G Eriani and E D Wang},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25414329?dopt=Abstract},
doi = {10.1093/nar/gku1218},
isbn = {25414329},
year = {2014},
date = {2014-01-01},
journal = {Nucleic Acids Res},
volume = {42},
number = {22},
pages = {13873-13886},
abstract = {Yeast mitochondria contain a minimalist threonyl-tRNA synthetase (ThrRS) composed only of the catalytic core and tRNA binding domain but lacking the entire editing domain. Besides the usual tRNAThr2, some budding yeasts, such as Saccharomyces cerevisiae, also contain a non-canonical tRNAThr1 with an enlarged 8-nucleotide anticodon loop, reprograming the usual leucine CUN codons to threonine. This raises interesting questions about the aminoacylation fidelity of such ThrRSs and the possible contribution of the two tRNAThrs during editing. Here, we found that, despite the absence of the editing domain, S. cerevisiae mitochondrial ThrRS (ScmtThrRS) harbors a tRNA-dependent pre-transfer editing activity. Remarkably, only the usual tRNAThr2 stimulated pre-transfer editing, thus, establishing the first example of a synthetase exhibiting tRNA-isoacceptor specificity during pre-transfer editing. We also showed that the failure of tRNAThr1 to stimulate tRNA-dependent pre-transfer editing was due to the lack of an editing domain. Using assays of the complementation of a ScmtThrRS gene knockout strain, we showed that the catalytic core and tRNA binding domain of ScmtThrRS co-evolved to recognize the unusual tRNAThr1. In combination, the results provide insights into the tRNA-dependent editing process and suggest that tRNA-dependent pre-transfer editing takes place in the aminoacylation catalytic core.},
keywords = {ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Yeast mitochondria contain a minimalist threonyl-tRNA synthetase (ThrRS) composed only of the catalytic core and tRNA binding domain but lacking the entire editing domain. Besides the usual tRNAThr2, some budding yeasts, such as Saccharomyces cerevisiae, also contain a non-canonical tRNAThr1 with an enlarged 8-nucleotide anticodon loop, reprograming the usual leucine CUN codons to threonine. This raises interesting questions about the aminoacylation fidelity of such ThrRSs and the possible contribution of the two tRNAThrs during editing. Here, we found that, despite the absence of the editing domain, S. cerevisiae mitochondrial ThrRS (ScmtThrRS) harbors a tRNA-dependent pre-transfer editing activity. Remarkably, only the usual tRNAThr2 stimulated pre-transfer editing, thus, establishing the first example of a synthetase exhibiting tRNA-isoacceptor specificity during pre-transfer editing. We also showed that the failure of tRNAThr1 to stimulate tRNA-dependent pre-transfer editing was due to the lack of an editing domain. Using assays of the complementation of a ScmtThrRS gene knockout strain, we showed that the catalytic core and tRNA binding domain of ScmtThrRS co-evolved to recognize the unusual tRNAThr1. In combination, the results provide insights into the tRNA-dependent editing process and suggest that tRNA-dependent pre-transfer editing takes place in the aminoacylation catalytic core.
Majzoub K, Hafirassou M L, Meignin C, Goto A, Marzi S, Fedorova A, Verdier Y, Vinh J, Hoffmann J A, Martin F, Baumert T F, Schuster C, Imler JL
RACK1 Controls IRES-Mediated Translation of Viruses. Journal Article
In: Cell, vol. 159, no. 5, pp. 1086-1095, 2014, ISBN: 25416947.
Abstract | Links | BibTeX | Tags: ERIANI, hoffmann, imler, M3i, meignin, ROMBY, Unité ARN
@article{,
title = {RACK1 Controls IRES-Mediated Translation of Viruses.},
author = {K Majzoub and M L Hafirassou and C Meignin and A Goto and S Marzi and A Fedorova and Y Verdier and J Vinh and J A Hoffmann and F Martin and T F Baumert and C Schuster and JL Imler},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25416947},
doi = {10.1016/j.cell.2014.10.041},
isbn = {25416947},
year = {2014},
date = {2014-01-01},
journal = {Cell},
volume = {159},
number = {5},
pages = {1086-1095},
abstract = {Fighting viral infections is hampered by the scarcity of viral targets and their variability, resulting in development of resistance. Viruses depend on cellular molecules-which are attractive alternative targets-for their life cycle, provided that they are dispensable for normal cell functions. Using the model organism Drosophila melanogaster, we identify the ribosomal protein RACK1 as a cellular factor required for infection by internal ribosome entry site (IRES)-containing viruses. We further show that RACK1 is an essential determinant for hepatitis C virus translation and infection, indicating that its function is conserved for distantly related human and fly viruses. Inhibition of RACK1 does not affect Drosophila or human cell viability and proliferation, and RACK1-silenced adult flies are viable, indicating that this protein is not essential for general translation. Our findings demonstrate a specific function for RACK1 in selective mRNA translation and uncover a target for the development of broad antiviral intervention.},
keywords = {ERIANI, hoffmann, imler, M3i, meignin, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Fighting viral infections is hampered by the scarcity of viral targets and their variability, resulting in development of resistance. Viruses depend on cellular molecules-which are attractive alternative targets-for their life cycle, provided that they are dispensable for normal cell functions. Using the model organism Drosophila melanogaster, we identify the ribosomal protein RACK1 as a cellular factor required for infection by internal ribosome entry site (IRES)-containing viruses. We further show that RACK1 is an essential determinant for hepatitis C virus translation and infection, indicating that its function is conserved for distantly related human and fly viruses. Inhibition of RACK1 does not affect Drosophila or human cell viability and proliferation, and RACK1-silenced adult flies are viable, indicating that this protein is not essential for general translation. Our findings demonstrate a specific function for RACK1 in selective mRNA translation and uncover a target for the development of broad antiviral intervention.
Vicens Q, Westhof E
Biogenesis of Circular RNAs. Journal Article
In: Cell, vol. 159, no. 1, pp. 13-14, 2014, ISBN: 25259915.
Abstract | Links | BibTeX | Tags: ERIANI, Unité ARN, WESTHOF
@article{,
title = {Biogenesis of Circular RNAs.},
author = {Q Vicens and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25259915?dopt=Abstract},
doi = {10.1016/j.cell.2014.09.005},
isbn = {25259915},
year = {2014},
date = {2014-01-01},
journal = {Cell},
volume = {159},
number = {1},
pages = {13-14},
abstract = {Circular RNAs are generated during splicing through various mechanisms. Ashwal-Fluss et al. demonstrate that exon circularization and linear splicing compete with each other in a tissue-specific fashion, and Zhang et al. show that exon circularization depends on flanking intronic complementary sequences. Both papers show that several types of circular RNA transcripts can be produced from a single gene.},
keywords = {ERIANI, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Circular RNAs are generated during splicing through various mechanisms. Ashwal-Fluss et al. demonstrate that exon circularization and linear splicing compete with each other in a tissue-specific fashion, and Zhang et al. show that exon circularization depends on flanking intronic complementary sequences. Both papers show that several types of circular RNA transcripts can be produced from a single gene.
Voortman L M, Vulović M, Maletta M, Voigt A, Franken E M, Simonetti A, Peters P J, van Vliet L J, Rieger B
Quantifying resolution limiting factors in subtomogram averaged cryo-electron tomography using simulations. Journal Article
In: J Struct Biol, vol. 187, no. 2, pp. 103-111, 2014, ISBN: 24998892.
Abstract | Links | BibTeX | Tags: Acquisition protocol Cryo-EM Ribosome Subtomogram averaging TEM image simulation Tilted CTF correction Tomography, ERIANI, Unité ARN
@article{,
title = {Quantifying resolution limiting factors in subtomogram averaged cryo-electron tomography using simulations.},
author = {L M Voortman and M Vulović and M Maletta and A Voigt and E M Franken and A Simonetti and P J Peters and L J van Vliet and B Rieger},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24998892},
doi = {10.1016/j.jsb.2014.06.007},
isbn = {24998892},
year = {2014},
date = {2014-01-01},
journal = {J Struct Biol},
volume = {187},
number = {2},
pages = {103-111},
abstract = {Cryo-electron tomography (CET) is the only available technique capable of characterizing the structure of biological macromolecules in conditions close to the native state. With the advent of subtomogram averaging, as a post-processing step to CET, resolutions in the (sub-) nanometer range have become within reach. In addition to advances in instrumentation and experiments, the reconstruction scheme has improved by inclusion of more accurate contrast transfer function (CTF) correction methods, better defocus estimation, and better alignments of the tilt-series and subtomograms. To quantify the importance of each contribution, we have split the full process from data collection to reconstruction into different steps. For the purpose of evaluation we have acquired tilt-series of ribosomes in such a way that we could precisely determine the defocus of each macromolecule. Then, we simulated tilt-series using the InSilicoTEM package and applied tomogram reconstruction and subtomogram averaging. Through large scale simulations under different conditions and parameter settings we find that tilt-series alignment is the resolution limiting factor for our experimental data. Using simulations, we find that when this alignment inaccuracy is alleviated, tilted CTF correction improves the final resolution, or equivalently, the same resolution can be achieved using less particles. Furthermore, we predict from which resolution onwards better CTF correction and defocus estimation methods are required. We obtain a final average using 3198 ribosomes with a resolution of 2.2nm on the experimental data. Our simulations suggest that with the same number of particles a resolution of 1.2nm could be achieved by improving the tilt-series alignment.},
keywords = {Acquisition protocol Cryo-EM Ribosome Subtomogram averaging TEM image simulation Tilted CTF correction Tomography, ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Cryo-electron tomography (CET) is the only available technique capable of characterizing the structure of biological macromolecules in conditions close to the native state. With the advent of subtomogram averaging, as a post-processing step to CET, resolutions in the (sub-) nanometer range have become within reach. In addition to advances in instrumentation and experiments, the reconstruction scheme has improved by inclusion of more accurate contrast transfer function (CTF) correction methods, better defocus estimation, and better alignments of the tilt-series and subtomograms. To quantify the importance of each contribution, we have split the full process from data collection to reconstruction into different steps. For the purpose of evaluation we have acquired tilt-series of ribosomes in such a way that we could precisely determine the defocus of each macromolecule. Then, we simulated tilt-series using the InSilicoTEM package and applied tomogram reconstruction and subtomogram averaging. Through large scale simulations under different conditions and parameter settings we find that tilt-series alignment is the resolution limiting factor for our experimental data. Using simulations, we find that when this alignment inaccuracy is alleviated, tilted CTF correction improves the final resolution, or equivalently, the same resolution can be achieved using less particles. Furthermore, we predict from which resolution onwards better CTF correction and defocus estimation methods are required. We obtain a final average using 3198 ribosomes with a resolution of 2.2nm on the experimental data. Our simulations suggest that with the same number of particles a resolution of 1.2nm could be achieved by improving the tilt-series alignment.
Schwenzer H, Scheper G C, Zorn N, Moulinier L, Gaudry A, Leize E, Martin F, Florentz C, Poch O, Sissler M
Released selective pressure on a structural domain gives new insights on the functional relaxation of mitochondrial aspartyl-tRNA synthetase. Journal Article
In: Biochimie, vol. 100, pp. 18-26, 2014, ISBN: 24120687.
Abstract | Links | BibTeX | Tags: Aminoacyl-tRNA synthetase Bioinformatics MTS Mitochondria Molecular biology Translation aaRS aminoacyl-tRNA synthetase (specificity is indicated by the name of the amino acid abbreviated in a three-letter code, e.g. AspRS stands for aspartyl-tRNA synthetase) mitochondrial mitochondrial targeting sequence mt, ERIANI, FLORENTZ, SISSLER, transferred to the cognate tRNA, Unité ARN
@article{,
title = {Released selective pressure on a structural domain gives new insights on the functional relaxation of mitochondrial aspartyl-tRNA synthetase.},
author = {H Schwenzer and G C Scheper and N Zorn and L Moulinier and A Gaudry and E Leize and F Martin and C Florentz and O Poch and M Sissler},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24120687},
doi = {10.1016/j.biochi.2013.09.027},
isbn = {24120687},
year = {2014},
date = {2014-01-01},
journal = {Biochimie},
volume = {100},
pages = {18-26},
abstract = {Mammalian mitochondrial aminoacyl-tRNA synthetases are nuclear-encoded enzymes that are essential for mitochondrial protein synthesis. Due to an endosymbiotic origin of the mitochondria, many of them share structural domains with homologous bacterial enzymes of same specificity. This is also the case for human mitochondrial aspartyl-tRNA synthetase (AspRS) that shares the so-called bacterial insertion domain with bacterial homologs. The function of this domain in the mitochondrial proteins is unclear. Here, we show by bioinformatic analyses that the sequences coding for the bacterial insertion domain are less conserved in opisthokont and protist than in bacteria and viridiplantae. The divergence suggests a loss of evolutionary pressure on this domain for non-plant mitochondrial AspRSs. This discovery is further connected with the herein described occurrence of alternatively spliced transcripts of the mRNAs coding for some mammalian mitochondrial AspRSs. Interestingly, the spliced transcripts alternately lack one of the four exons that code for the bacterial insertion domain. Although we showed that the human alternative transcript is present in all tested tissues; co-exists with the full-length form, possesses 5'- and 3'-UTRs, a poly-A tail and is bound to polysomes, we were unable to detect the corresponding protein. The relaxed selective pressure combined with the occurrence of alternative splicing, involving a single structural sub-domain, favors the hypothesis of the loss of function of this domain for AspRSs of mitochondrial location. This evolutionary divergence is in line with other characteristics, established for the human mt-AspRS, that indicate a functional relaxation of non-viridiplantae mt-AspRSs when compared to bacterial and plant ones, despite their common ancestry.},
keywords = {Aminoacyl-tRNA synthetase Bioinformatics MTS Mitochondria Molecular biology Translation aaRS aminoacyl-tRNA synthetase (specificity is indicated by the name of the amino acid abbreviated in a three-letter code, e.g. AspRS stands for aspartyl-tRNA synthetase) mitochondrial mitochondrial targeting sequence mt, ERIANI, FLORENTZ, SISSLER, transferred to the cognate tRNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Mammalian mitochondrial aminoacyl-tRNA synthetases are nuclear-encoded enzymes that are essential for mitochondrial protein synthesis. Due to an endosymbiotic origin of the mitochondria, many of them share structural domains with homologous bacterial enzymes of same specificity. This is also the case for human mitochondrial aspartyl-tRNA synthetase (AspRS) that shares the so-called bacterial insertion domain with bacterial homologs. The function of this domain in the mitochondrial proteins is unclear. Here, we show by bioinformatic analyses that the sequences coding for the bacterial insertion domain are less conserved in opisthokont and protist than in bacteria and viridiplantae. The divergence suggests a loss of evolutionary pressure on this domain for non-plant mitochondrial AspRSs. This discovery is further connected with the herein described occurrence of alternatively spliced transcripts of the mRNAs coding for some mammalian mitochondrial AspRSs. Interestingly, the spliced transcripts alternately lack one of the four exons that code for the bacterial insertion domain. Although we showed that the human alternative transcript is present in all tested tissues; co-exists with the full-length form, possesses 5'- and 3'-UTRs, a poly-A tail and is bound to polysomes, we were unable to detect the corresponding protein. The relaxed selective pressure combined with the occurrence of alternative splicing, involving a single structural sub-domain, favors the hypothesis of the loss of function of this domain for AspRSs of mitochondrial location. This evolutionary divergence is in line with other characteristics, established for the human mt-AspRS, that indicate a functional relaxation of non-viridiplantae mt-AspRSs when compared to bacterial and plant ones, despite their common ancestry.
2013
Simonetti A, Marzi S, Billas I M, Tsai A, Fabbretti A, Myasnikov A G, Roblin P, Vaiana A C, Hazemann I, Eiler D, Steitz T A, Puglisi J D, Gualerzi C O, Klaholz B P
Involvement of protein IF2 N domain in ribosomal subunit joining revealed from architecture and function of the full-length initiation factor. Journal Article
In: Proc Natl Acad Sci U S A, vol. 110, no. 39, pp. 15656-61, 2013, ISBN: 24029017.
Abstract | Links | BibTeX | Tags: ERIANI, integrated structural biology protein synthesis, ROMBY, Unité ARN
@article{,
title = {Involvement of protein IF2 N domain in ribosomal subunit joining revealed from architecture and function of the full-length initiation factor.},
author = {A Simonetti and S Marzi and I M Billas and A Tsai and A Fabbretti and A G Myasnikov and P Roblin and A C Vaiana and I Hazemann and D Eiler and T A Steitz and J D Puglisi and C O Gualerzi and B P Klaholz},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24029017?dopt=Abstract},
doi = {10.1073/pnas.1309578110},
isbn = {24029017},
year = {2013},
date = {2013-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {110},
number = {39},
pages = {15656-61},
abstract = {Translation initiation factor 2 (IF2) promotes 30S initiation complex (IC) formation and 50S subunit joining, which produces the 70S IC. The architecture of full-length IF2, determined by small angle X-ray diffraction and cryo electron microscopy, reveals a more extended conformation of IF2 in solution and on the ribosome than in the crystal. The N-terminal domain is only partially visible in the 30S IC, but in the 70S IC, it stabilizes interactions between IF2 and the L7/L12 stalk of the 50S, and on its deletion, proper N-formyl-methionyl(fMet)-tRNAfMet positioning and efficient transpeptidation are affected. Accordingly, fast kinetics and single-molecule fluorescence data indicate that the N terminus promotes 70S IC formation by stabilizing the productive sampling of the 50S subunit during 30S IC joining. Together, our data highlight the dynamics of IF2-dependent ribosomal subunit joining and the role played by the N terminus of IF2 in this process.},
keywords = {ERIANI, integrated structural biology protein synthesis, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Translation initiation factor 2 (IF2) promotes 30S initiation complex (IC) formation and 50S subunit joining, which produces the 70S IC. The architecture of full-length IF2, determined by small angle X-ray diffraction and cryo electron microscopy, reveals a more extended conformation of IF2 in solution and on the ribosome than in the crystal. The N-terminal domain is only partially visible in the 30S IC, but in the 70S IC, it stabilizes interactions between IF2 and the L7/L12 stalk of the 50S, and on its deletion, proper N-formyl-methionyl(fMet)-tRNAfMet positioning and efficient transpeptidation are affected. Accordingly, fast kinetics and single-molecule fluorescence data indicate that the N terminus promotes 70S IC formation by stabilizing the productive sampling of the 50S subunit during 30S IC joining. Together, our data highlight the dynamics of IF2-dependent ribosomal subunit joining and the role played by the N terminus of IF2 in this process.
Simonetti A, Marzi S, Fabbretti A, Hazemann I, Jenner L, Urzhumtsev A, Gualerzi C O, Klaholz B P
Structure of the protein core of translation initiation factor 2 in apo, GTP-bound and GDP-bound forms. Journal Article
In: Acta Crystallogr D Biol Crystallogr, vol. 69, no. Pt 6, pp. 925-33, 2013, ISBN: 23695237.
Abstract |