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2015
Durand S, Braun F, Lioliou E, Romilly C, Helfer A C, Kuhn L, Quittot N, Nicolas P, Romby P, Condon C
A Nitric Oxide Regulated Small RNA Controls Expression of Genes Involved in Redox Homeostasis in Bacillus subtilis. Journal Article
In: PLoS Genet, vol. 11, no. 2, pp. e1004957, 2015, ISBN: 25643072.
Abstract | Links | BibTeX | Tags: PPSE, ROMBY, Unité ARN
@article{,
title = {A Nitric Oxide Regulated Small RNA Controls Expression of Genes Involved in Redox Homeostasis in Bacillus subtilis.},
author = {S Durand and F Braun and E Lioliou and C Romilly and A C Helfer and L Kuhn and N Quittot and P Nicolas and P Romby and C Condon},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25643072?dopt=Abstract},
doi = {10.1371/journal.pgen.1004957},
isbn = {25643072},
year = {2015},
date = {2015-01-01},
journal = {PLoS Genet},
volume = {11},
number = {2},
pages = {e1004957},
abstract = {RsaE is the only known trans-acting small regulatory RNA (sRNA) besides the ubiquitous 6S RNA that is conserved between the human pathogen Staphylococcus aureus and the soil-dwelling Firmicute Bacillus subtilis. Although a number of RsaE targets are known in S. aureus, neither the environmental signals that lead to its expression nor its physiological role are known. Here we show that expression of the B. subtilis homolog of RsaE is regulated by the presence of nitric oxide (NO) in the cellular milieu. Control of expression by NO is dependent on the ResDE two-component system in B. subtilis and we determined that the same is true in S. aureus. Transcriptome and proteome analyses revealed that many genes with functions related to oxidative stress and oxidation-reduction reactions were up-regulated in a B. subtilis strain lacking this sRNA. We have thus renamed it RoxS. The prediction of RoxS-dependent mRNA targets also suggested a significant enrichment for mRNAs related to respiration and electron transfer. Among the potential direct mRNA targets, we have validated the ppnKB mRNA, encoding an NAD+/NADH kinase, both in vivo and in vitro. RoxS controls both translation initiation and the stability of this transcript, in the latter case via two independent pathways implicating RNase Y and RNase III. Furthermore, RNase Y intervenes at an additional level by processing the 5' end of the RoxS sRNA removing about 20 nucleotides. Processing of RoxS allows it to interact more efficiently with a second target, the sucCD mRNA, encoding succinyl-CoA synthase, thus expanding the repertoire of targets recognized by this sRNA.},
keywords = {PPSE, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
RsaE is the only known trans-acting small regulatory RNA (sRNA) besides the ubiquitous 6S RNA that is conserved between the human pathogen Staphylococcus aureus and the soil-dwelling Firmicute Bacillus subtilis. Although a number of RsaE targets are known in S. aureus, neither the environmental signals that lead to its expression nor its physiological role are known. Here we show that expression of the B. subtilis homolog of RsaE is regulated by the presence of nitric oxide (NO) in the cellular milieu. Control of expression by NO is dependent on the ResDE two-component system in B. subtilis and we determined that the same is true in S. aureus. Transcriptome and proteome analyses revealed that many genes with functions related to oxidative stress and oxidation-reduction reactions were up-regulated in a B. subtilis strain lacking this sRNA. We have thus renamed it RoxS. The prediction of RoxS-dependent mRNA targets also suggested a significant enrichment for mRNAs related to respiration and electron transfer. Among the potential direct mRNA targets, we have validated the ppnKB mRNA, encoding an NAD+/NADH kinase, both in vivo and in vitro. RoxS controls both translation initiation and the stability of this transcript, in the latter case via two independent pathways implicating RNase Y and RNase III. Furthermore, RNase Y intervenes at an additional level by processing the 5' end of the RoxS sRNA removing about 20 nucleotides. Processing of RoxS allows it to interact more efficiently with a second target, the sucCD mRNA, encoding succinyl-CoA synthase, thus expanding the repertoire of targets recognized by this sRNA.
Duval M, Simonetti A, Caldelari I, Marzi S
Multiple ways to regulate translation initiation in bacteria: mechanisms, regulatory circuits, dynamics. Journal Article
In: Biochimie, vol. 114, pp. 18-29, 2015, ISBN: 25792421.
Abstract | Links | BibTeX | Tags: ROMBY, Unité ARN
@article{,
title = {Multiple ways to regulate translation initiation in bacteria: mechanisms, regulatory circuits, dynamics.},
author = {M Duval and A Simonetti and I Caldelari and S Marzi},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25792421?dopt=Abstract},
doi = {10.1016/j.biochi.2015.03.007},
isbn = {25792421},
year = {2015},
date = {2015-01-01},
journal = {Biochimie},
volume = {114},
pages = {18-29},
abstract = {To adapt their metabolism rapidly and constantly in response to environmental variations, bacteria often target the translation initiation process, during which the ribosome assembles on the mRNA. Here, we review different mechanisms of regulation mediated by cis-acting elements, sRNAs and proteins, showing, when possible, their intimate connection with the translational apparatus. Indeed the ribosome itself could play a direct role in several regulatory mechanisms. Different features of the regulatory signals (sequences, structures and their positions on the mRNA) are contributing to the large variety of regulatory mechanisms. Ribosome heterogeneity, variation of individual cells responses and the spatial and temporal organization of the translation process add more layers of complexity. This hampers to define manageable set of rules for bacterial translation initiation control.},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
To adapt their metabolism rapidly and constantly in response to environmental variations, bacteria often target the translation initiation process, during which the ribosome assembles on the mRNA. Here, we review different mechanisms of regulation mediated by cis-acting elements, sRNAs and proteins, showing, when possible, their intimate connection with the translational apparatus. Indeed the ribosome itself could play a direct role in several regulatory mechanisms. Different features of the regulatory signals (sequences, structures and their positions on the mRNA) are contributing to the large variety of regulatory mechanisms. Ribosome heterogeneity, variation of individual cells responses and the spatial and temporal organization of the translation process add more layers of complexity. This hampers to define manageable set of rules for bacterial translation initiation control.
2014
Morfoisse F, Kuchnio A, Frainay C, Gomez-Brouchet A, Delisle M B, Marzi S, Helfer A C, Hantelys F, Pujol F, Guillermet-Guibert J, Bousquet C, Dewerchin M, Pyronnet S, Prats A C, Carmeliet P, Garmy-Susini B
Hypoxia Induces VEGF-C Expression in Metastatic Tumor Cells via a HIF-1α-Independent Translation-Mediated Mechanism. Journal Article
In: Cell Rep, vol. 6, no. 1, pp. 155-167, 2014, ISBN: 24388748.
Abstract | Links | BibTeX | Tags: ROMBY, Unité ARN
@article{,
title = {Hypoxia Induces VEGF-C Expression in Metastatic Tumor Cells via a HIF-1α-Independent Translation-Mediated Mechanism.},
author = {F Morfoisse and A Kuchnio and C Frainay and A Gomez-Brouchet and M B Delisle and S Marzi and A C Helfer and F Hantelys and F Pujol and J Guillermet-Guibert and C Bousquet and M Dewerchin and S Pyronnet and A C Prats and P Carmeliet and B Garmy-Susini},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24388748?dopt=Abstract},
doi = {10.1016/j.celrep.2013.12.011},
isbn = {24388748},
year = {2014},
date = {2014-01-01},
journal = {Cell Rep},
volume = {6},
number = {1},
pages = {155-167},
abstract = {Various tumors metastasize via lymph vessels and lymph nodes to distant organs. Even though tumors are hypoxic, the mechanisms of how hypoxia regulates lymphangiogenesis remain poorly characterized. Here, we show that hypoxia reduced vascular endothelial growth factor C (VEGF-C) transcription and cap-dependent translation via the upregulation of hypophosphorylated 4E-binding protein 1 (4E-BP1). However, initiation of VEGF-C translation was induced by hypoxia through an internal ribosome entry site (IRES)-dependent mechanism. IRES-dependent VEGF-C translation was independent of hypoxia-inducible factor 1α (HIF-1α) signaling. Notably, the VEGF-C IRES activity was higher in metastasizing tumor cells in lymph nodes than in primary tumors, most likely because lymph vessels in these lymph nodes were severely hypoxic. Overall, this transcription-independent but translation-dependent upregulation of VEGF-C in hypoxia stimulates lymphangiogenesis in tumors and lymph nodes and may contribute to lymphatic metastasis.},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Various tumors metastasize via lymph vessels and lymph nodes to distant organs. Even though tumors are hypoxic, the mechanisms of how hypoxia regulates lymphangiogenesis remain poorly characterized. Here, we show that hypoxia reduced vascular endothelial growth factor C (VEGF-C) transcription and cap-dependent translation via the upregulation of hypophosphorylated 4E-binding protein 1 (4E-BP1). However, initiation of VEGF-C translation was induced by hypoxia through an internal ribosome entry site (IRES)-dependent mechanism. IRES-dependent VEGF-C translation was independent of hypoxia-inducible factor 1α (HIF-1α) signaling. Notably, the VEGF-C IRES activity was higher in metastasizing tumor cells in lymph nodes than in primary tumors, most likely because lymph vessels in these lymph nodes were severely hypoxic. Overall, this transcription-independent but translation-dependent upregulation of VEGF-C in hypoxia stimulates lymphangiogenesis in tumors and lymph nodes and may contribute to lymphatic metastasis.
Tomasini A, François P, Howden B P, Fechter P, Romby P, Caldelari I
The importance of regulatory RNAs in Staphylococcus aureus. Journal Article
In: Infect Genet Evol, vol. 21, no. C, pp. 616-626, 2014, ISBN: 24291227.
Abstract | Links | BibTeX | Tags: Regulatory RNA Staphylococcus Virulence, ROMBY, Unité ARN
@article{,
title = {The importance of regulatory RNAs in Staphylococcus aureus.},
author = {A Tomasini and P François and B P Howden and P Fechter and P Romby and I Caldelari},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24291227},
doi = {10.1016/j.meegid.2013.11.016},
isbn = {24291227},
year = {2014},
date = {2014-01-01},
journal = {Infect Genet Evol},
volume = {21},
number = {C},
pages = {616-626},
abstract = {RNA molecules with regulatory functions in pathogenic bacteria have benefited from a renewed interest these two last decades. In Staphylococcus aureus, recent genome-wide approaches have led to the discovery that almost 10-20% of genes code for RNAs with critical regulatory roles in adaptive processes. These RNAs include trans-acting RNAs, which mostly act through binding to target mRNAs, and cis-acting RNAs, which include regulatory regions of mRNAs responding to various metabolic signals. Besides recent analysis of S. aureus transcriptome has revealed an unprecedented existence of pervasive transcription generating a high number of weakly expressed antisense RNAs along the genome as well as numerous mRNAs with overlapped regions. Here, we will illustrate the diversity of trans-acting RNAs and illustrate how they are integrated into complex regulatory circuits, which link metabolism, stress response and virulence.},
keywords = {Regulatory RNA Staphylococcus Virulence, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
RNA molecules with regulatory functions in pathogenic bacteria have benefited from a renewed interest these two last decades. In Staphylococcus aureus, recent genome-wide approaches have led to the discovery that almost 10-20% of genes code for RNAs with critical regulatory roles in adaptive processes. These RNAs include trans-acting RNAs, which mostly act through binding to target mRNAs, and cis-acting RNAs, which include regulatory regions of mRNAs responding to various metabolic signals. Besides recent analysis of S. aureus transcriptome has revealed an unprecedented existence of pervasive transcription generating a high number of weakly expressed antisense RNAs along the genome as well as numerous mRNAs with overlapped regions. Here, we will illustrate the diversity of trans-acting RNAs and illustrate how they are integrated into complex regulatory circuits, which link metabolism, stress response and virulence.
Sesto N, Touchon M, Andrade J M, Kondo J, Rocha E P, Arraiano C M, Archambaud C, Westhof E, Romby P, Cossart P
A PNPase Dependent CRISPR System in Listeria. Journal Article
In: PLoS Genet, vol. 10, no. 1, pp. e1004065, 2014, ISBN: 24415952.
Abstract | Links | BibTeX | Tags: ROMBY, Unité ARN, WESTHOF
@article{,
title = {A PNPase Dependent CRISPR System in Listeria.},
author = {N Sesto and M Touchon and J M Andrade and J Kondo and E P Rocha and C M Arraiano and C Archambaud and E Westhof and P Romby and P Cossart},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24415952?dopt=Abstract},
doi = {10.1371/journal.pgen.1004065},
isbn = {24415952},
year = {2014},
date = {2014-01-01},
journal = {PLoS Genet},
volume = {10},
number = {1},
pages = {e1004065},
abstract = {The human bacterial pathogen Listeria monocytogenes is emerging as a model organism to study RNA-mediated regulation in pathogenic bacteria. A class of non-coding RNAs called CRISPRs (clustered regularly interspaced short palindromic repeats) has been described to confer bacterial resistance against invading bacteriophages and conjugative plasmids. CRISPR function relies on the activity of CRISPR associated (cas) genes that encode a large family of proteins with nuclease or helicase activities and DNA and RNA binding domains. Here, we characterized a CRISPR element (RliB) that is expressed and processed in the L. monocytogenes strain EGD-e, which is completely devoid of cas genes. Structural probing revealed that RliB has an unexpected secondary structure comprising basepair interactions between the repeats and the adjacent spacers in place of canonical hairpins formed by the palindromic repeats. Moreover, in contrast to other CRISPR-Cas systems identified in Listeria, RliB-CRISPR is ubiquitously present among Listeria genomes at the same genomic locus and is never associated with the cas genes. We showed that RliB-CRISPR is a substrate for the endogenously encoded polynucleotide phosphorylase (PNPase) enzyme. The spacers of the different Listeria RliB-CRISPRs share many sequences with temperate and virulent phages. Furthermore, we show that a cas-less RliB-CRISPR lowers the acquisition frequency of a plasmid carrying the matching protospacer, provided that trans encoded cas genes of a second CRISPR-Cas system are present in the genome. Importantly, we show that PNPase is required for RliB-CRISPR mediated DNA interference. Altogether, our data reveal a yet undescribed CRISPR system whose both processing and activity depend on PNPase, highlighting a new and unexpected function for PNPase in "CRISPRology".},
keywords = {ROMBY, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
The human bacterial pathogen Listeria monocytogenes is emerging as a model organism to study RNA-mediated regulation in pathogenic bacteria. A class of non-coding RNAs called CRISPRs (clustered regularly interspaced short palindromic repeats) has been described to confer bacterial resistance against invading bacteriophages and conjugative plasmids. CRISPR function relies on the activity of CRISPR associated (cas) genes that encode a large family of proteins with nuclease or helicase activities and DNA and RNA binding domains. Here, we characterized a CRISPR element (RliB) that is expressed and processed in the L. monocytogenes strain EGD-e, which is completely devoid of cas genes. Structural probing revealed that RliB has an unexpected secondary structure comprising basepair interactions between the repeats and the adjacent spacers in place of canonical hairpins formed by the palindromic repeats. Moreover, in contrast to other CRISPR-Cas systems identified in Listeria, RliB-CRISPR is ubiquitously present among Listeria genomes at the same genomic locus and is never associated with the cas genes. We showed that RliB-CRISPR is a substrate for the endogenously encoded polynucleotide phosphorylase (PNPase) enzyme. The spacers of the different Listeria RliB-CRISPRs share many sequences with temperate and virulent phages. Furthermore, we show that a cas-less RliB-CRISPR lowers the acquisition frequency of a plasmid carrying the matching protospacer, provided that trans encoded cas genes of a second CRISPR-Cas system are present in the genome. Importantly, we show that PNPase is required for RliB-CRISPR mediated DNA interference. Altogether, our data reveal a yet undescribed CRISPR system whose both processing and activity depend on PNPase, highlighting a new and unexpected function for PNPase in "CRISPRology".
Romilly C, Lays C, Tomasini A, Caldelari I, Benito Y, Hammann P, Geissmann T, Boisset S, Romby P, Vandenesch F
A Non-Coding RNA Promotes Bacterial Persistence and Decreases Virulence by Regulating a Regulator in Staphylococcus aureus. Journal Article
In: PLoS Pathog, vol. 10, no. 3, pp. e1003979, 2014, ISBN: 24651379.
Abstract | Links | BibTeX | Tags: PPSE, ROMBY, Unité ARN
@article{,
title = {A Non-Coding RNA Promotes Bacterial Persistence and Decreases Virulence by Regulating a Regulator in Staphylococcus aureus.},
author = {C Romilly and C Lays and A Tomasini and I Caldelari and Y Benito and P Hammann and T Geissmann and S Boisset and P Romby and F Vandenesch},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24651379?dopt=Abstract},
doi = {10.1371/journal.ppat.1003979},
isbn = {24651379},
year = {2014},
date = {2014-01-01},
journal = {PLoS Pathog},
volume = {10},
number = {3},
pages = {e1003979},
abstract = {Staphylococcus aureus produces a high number of RNAs for which the functions are poorly understood. Several non-coding RNAs carry a C-rich sequence suggesting that they regulate mRNAs at the post-transcriptional level. We demonstrate that the Sigma B-dependent RsaA RNA represses the synthesis of the global transcriptional regulator MgrA by forming an imperfect duplex with the Shine and Dalgarno sequence and a loop-loop interaction within the coding region of the target mRNA. These two recognition sites are required for translation repression. Consequently, RsaA causes enhanced production of biofilm and a decreased synthesis of capsule formation in several strain backgrounds. These phenotypes led to a decreased protection of S. aureus against opsonophagocytic killing by polymorphonuclear leukocytes compared to the mutant strains lacking RsaA. Mice animal models showed that RsaA attenuates the severity of acute systemic infections and enhances chronic catheter infection. RsaA takes part in a regulatory network that contributes to the complex interactions of S. aureus with the host immune system to moderate invasiveness and favour chronic infections. It is the first example of a conserved small RNA in S. aureus functioning as a virulence suppressor of acute infections. Because S. aureus is essentially a human commensal, we propose that RsaA has been positively selected through evolution to support commensalism and saprophytic interactions with the host.},
keywords = {PPSE, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Staphylococcus aureus produces a high number of RNAs for which the functions are poorly understood. Several non-coding RNAs carry a C-rich sequence suggesting that they regulate mRNAs at the post-transcriptional level. We demonstrate that the Sigma B-dependent RsaA RNA represses the synthesis of the global transcriptional regulator MgrA by forming an imperfect duplex with the Shine and Dalgarno sequence and a loop-loop interaction within the coding region of the target mRNA. These two recognition sites are required for translation repression. Consequently, RsaA causes enhanced production of biofilm and a decreased synthesis of capsule formation in several strain backgrounds. These phenotypes led to a decreased protection of S. aureus against opsonophagocytic killing by polymorphonuclear leukocytes compared to the mutant strains lacking RsaA. Mice animal models showed that RsaA attenuates the severity of acute systemic infections and enhances chronic catheter infection. RsaA takes part in a regulatory network that contributes to the complex interactions of S. aureus with the host immune system to moderate invasiveness and favour chronic infections. It is the first example of a conserved small RNA in S. aureus functioning as a virulence suppressor of acute infections. Because S. aureus is essentially a human commensal, we propose that RsaA has been positively selected through evolution to support commensalism and saprophytic interactions with the host.
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.
2013
Duval M, Korepanov A, Fuchsbauer O, Fechter P, Haller A, Fabbretti A, Choulier L, Micura R, Klaholz B P, Romby P, Springer M, Marzi S
Escherichia coli Ribosomal Protein S1 Unfolds Structured mRNAs Onto the Ribosome for Active Translation Initiation. Journal Article
In: PLoS Biol, vol. 11, no. 12, pp. e1001731, 2013, ISBN: 24339747.
Abstract | Links | BibTeX | Tags: ROMBY, Unité ARN
@article{,
title = {Escherichia coli Ribosomal Protein S1 Unfolds Structured mRNAs Onto the Ribosome for Active Translation Initiation.},
author = {M Duval and A Korepanov and O Fuchsbauer and P Fechter and A Haller and A Fabbretti and L Choulier and R Micura and B P Klaholz and P Romby and M Springer and S Marzi},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24339747?dopt=Abstract},
doi = {10.1371/journal.pbio.1001731},
isbn = {24339747},
year = {2013},
date = {2013-01-01},
journal = {PLoS Biol},
volume = {11},
number = {12},
pages = {e1001731},
abstract = {Regulation of translation initiation is well appropriate to adapt cell growth in response to stress and environmental changes. Many bacterial mRNAs adopt structures in their 5' untranslated regions that modulate the accessibility of the 30S ribosomal subunit. Structured mRNAs interact with the 30S in a two-step process where the docking of a folded mRNA precedes an accommodation step. Here, we used a combination of experimental approaches in vitro (kinetic of mRNA unfolding and binding experiments to analyze mRNA-protein or mRNA-ribosome complexes, toeprinting assays to follow the formation of ribosomal initiation complexes) and in vivo (genetic) to monitor the action of ribosomal protein S1 on the initiation of structured and regulated mRNAs. We demonstrate that r-protein S1 endows the 30S with an RNA chaperone activity that is essential for the docking and the unfolding of structured mRNAs, and for the correct positioning of the initiation codon inside the decoding channel. The first three OB-fold domains of S1 retain all its activities (mRNA and 30S binding, RNA melting activity) on the 30S subunit. S1 is not required for all mRNAs and acts differently on mRNAs according to the signals present at their 5' ends. This work shows that S1 confers to the ribosome dynamic properties to initiate translation of a large set of mRNAs with diverse structural features.},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Regulation of translation initiation is well appropriate to adapt cell growth in response to stress and environmental changes. Many bacterial mRNAs adopt structures in their 5' untranslated regions that modulate the accessibility of the 30S ribosomal subunit. Structured mRNAs interact with the 30S in a two-step process where the docking of a folded mRNA precedes an accommodation step. Here, we used a combination of experimental approaches in vitro (kinetic of mRNA unfolding and binding experiments to analyze mRNA-protein or mRNA-ribosome complexes, toeprinting assays to follow the formation of ribosomal initiation complexes) and in vivo (genetic) to monitor the action of ribosomal protein S1 on the initiation of structured and regulated mRNAs. We demonstrate that r-protein S1 endows the 30S with an RNA chaperone activity that is essential for the docking and the unfolding of structured mRNAs, and for the correct positioning of the initiation codon inside the decoding channel. The first three OB-fold domains of S1 retain all its activities (mRNA and 30S binding, RNA melting activity) on the 30S subunit. S1 is not required for all mRNAs and acts differently on mRNAs according to the signals present at their 5' ends. This work shows that S1 confers to the ribosome dynamic properties to initiate translation of a large set of mRNAs with diverse structural features.
Duval M, Romilly C, Helfer A C, Fuchsbauer O, Romby P, Marzi S
Footprinting methods for mapping RNA-protein and RNA-RNA interactions. Book Section
In: Klostermeier, D; Hammann, C (Ed.): RNA Structure and Folding, pp. 29-50, Verlag Walter de Gruyter, Berlin, 2013, ISBN: 9783110284959/ISSN.
Abstract | Links | BibTeX | Tags: ROMBY, Unité ARN
@incollection{,
title = {Footprinting methods for mapping RNA-protein and RNA-RNA interactions.},
author = {M Duval and C Romilly and A C Helfer and O Fuchsbauer and P Romby and S Marzi},
editor = {D Klostermeier and C Hammann},
url = {http://www.degruyter.com/view/books/9783110284959/9783110284959.29/9783110284959.29.xml?format=EBOK},
doi = {10.1515/9783110284959},
isbn = {9783110284959/ISSN},
year = {2013},
date = {2013-01-01},
booktitle = {RNA Structure and Folding},
pages = {29-50},
publisher = {Verlag Walter de Gruyter},
address = {Berlin},
abstract = {Footprinting is currently used to study protein-nucleic acid complexes and more specifically protein-RNA interactions. The method is based on the accessibility of each nucleotide of RNA bound to a ligand against chemical modifications or enzymatic cleavages. It provides information on the regions of interaction on the RNA sequence, and on the RNA conformational changes, which undergo upon ligand binding. Although these approaches are well appropriate to analyze stable RNA-protein or RNA-RNA complexes, it is however difficult to gain knowledge on transient and dynamic complexes. Here, we provide a brief guide on RNA footprinting, discuss the mechanism of action of the most currently used chemical and enzymatic probes, and illustrate the advantages and limitations of the approaches with several examples.},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {incollection}
}
Footprinting is currently used to study protein-nucleic acid complexes and more specifically protein-RNA interactions. The method is based on the accessibility of each nucleotide of RNA bound to a ligand against chemical modifications or enzymatic cleavages. It provides information on the regions of interaction on the RNA sequence, and on the RNA conformational changes, which undergo upon ligand binding. Although these approaches are well appropriate to analyze stable RNA-protein or RNA-RNA complexes, it is however difficult to gain knowledge on transient and dynamic complexes. Here, we provide a brief guide on RNA footprinting, discuss the mechanism of action of the most currently used chemical and enzymatic probes, and illustrate the advantages and limitations of the approaches with several examples.
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 | Links | BibTeX | Tags: ERIANI, ROMBY, Unité ARN
@article{,
title = {Structure of the protein core of translation initiation factor 2 in apo, GTP-bound and GDP-bound forms.},
author = {A Simonetti and S Marzi and A Fabbretti and I Hazemann and L Jenner and A Urzhumtsev and C O Gualerzi and B P Klaholz},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23695237?dopt=Abstract},
doi = {10.1107/S0907444913006422},
isbn = {23695237},
year = {2013},
date = {2013-01-01},
journal = {Acta Crystallogr D Biol Crystallogr},
volume = {69},
number = {Pt 6},
pages = {925-33},
abstract = {Translation initiation factor 2 (IF2) is involved in the early steps of bacterial protein synthesis. It promotes the stabilization of the initiator tRNA on the 30S initiation complex (IC) and triggers GTP hydrolysis upon ribosomal subunit joining. While the structure of an archaeal homologue (a/eIF5B) is known, there are significant sequence and functional differences in eubacterial IF2, while the trimeric eukaryotic IF2 is completely unrelated. Here, the crystal structure of the apo IF2 protein core from Thermus thermophilus has been determined by MAD phasing and the structures of GTP and GDP complexes were also obtained. The IF2-GTP complex was trapped by soaking with GTP in the cryoprotectant. The structures revealed conformational changes of the protein upon nucleotide binding, in particular in the P-loop region, which extend to the functionally relevant switch II region. The latter carries a catalytically important and conserved histidine residue which is observed in different conformations in the GTP and GDP complexes. Overall, this work provides the first crystal structure of a eubacterial IF2 and suggests that activation of GTP hydrolysis may occur by a conformational repositioning of the histidine residue.},
keywords = {ERIANI, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Translation initiation factor 2 (IF2) is involved in the early steps of bacterial protein synthesis. It promotes the stabilization of the initiator tRNA on the 30S initiation complex (IC) and triggers GTP hydrolysis upon ribosomal subunit joining. While the structure of an archaeal homologue (a/eIF5B) is known, there are significant sequence and functional differences in eubacterial IF2, while the trimeric eukaryotic IF2 is completely unrelated. Here, the crystal structure of the apo IF2 protein core from Thermus thermophilus has been determined by MAD phasing and the structures of GTP and GDP complexes were also obtained. The IF2-GTP complex was trapped by soaking with GTP in the cryoprotectant. The structures revealed conformational changes of the protein upon nucleotide binding, in particular in the P-loop region, which extend to the functionally relevant switch II region. The latter carries a catalytically important and conserved histidine residue which is observed in different conformations in the GTP and GDP complexes. Overall, this work provides the first crystal structure of a eubacterial IF2 and suggests that activation of GTP hydrolysis may occur by a conformational repositioning of the histidine residue.
2012
Song J, Lays C, Vandenesch F, Benito Y, Bes M, Chu Y, Lina G, Romby P, Geissmann T, Boisset S
In: PLoS One, vol. 7, no. 5, pp. e37294, 2012, ISBN: 22629378.
Abstract | Links | BibTeX | Tags: ROMBY, Unité ARN
@article{,
title = {The Expression of Small Regulatory RNAs in Clinical Samples Reflects the Different Life Styles of Staphylococcus aureus in Colonization vs. Infection.},
author = {J Song and C Lays and F Vandenesch and Y Benito and M Bes and Y Chu and G Lina and P Romby and T Geissmann and S Boisset},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22629378?dopt=Abstract
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0037294},
isbn = {22629378},
year = {2012},
date = {2012-01-01},
journal = {PLoS One},
volume = {7},
number = {5},
pages = {e37294},
abstract = {Small RNAs (sRNAs) are involved in the post-transcriptional regulation of metabolic pathways and in responses to stress and virulence. We analyzed the expression levels of five sRNAs of Staphylococcus aureus during human colonization or infection. Total RNA was isolated from nasal carriers, abscesses and cystic fibrosis patients (20 subjects per condition). The expression levels of the sRNAs were measured in the clinical samples and compared with those of the corresponding strains grown in vitro. Five sRNAs were encoded and expressed in all clinical strains in vitro. In vivo, the global expression of the five sRNAs was extremely variable in the abscessed patients, more homogeneous in the cystic fibrosis patients, and highly uniform in the nasal carrier samples. The expression levels of the sRNAs in vivo resembled those obtained at exponential phase or late exponential phase of growth in vitro, for three and one sRNA respectively; while for one sRNA, the expression was always higher in vivo as compared to in vitro growth. The in vitro conditions do not uniformly mimic the in vivo conditions for sRNA expression. Nasal colonization is associated with a unique expression pattern of sRNA that might reflect the commensalism of S. aureus in this niche.},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Small RNAs (sRNAs) are involved in the post-transcriptional regulation of metabolic pathways and in responses to stress and virulence. We analyzed the expression levels of five sRNAs of Staphylococcus aureus during human colonization or infection. Total RNA was isolated from nasal carriers, abscesses and cystic fibrosis patients (20 subjects per condition). The expression levels of the sRNAs were measured in the clinical samples and compared with those of the corresponding strains grown in vitro. Five sRNAs were encoded and expressed in all clinical strains in vitro. In vivo, the global expression of the five sRNAs was extremely variable in the abscessed patients, more homogeneous in the cystic fibrosis patients, and highly uniform in the nasal carrier samples. The expression levels of the sRNAs in vivo resembled those obtained at exponential phase or late exponential phase of growth in vitro, for three and one sRNA respectively; while for one sRNA, the expression was always higher in vivo as compared to in vitro growth. The in vitro conditions do not uniformly mimic the in vivo conditions for sRNA expression. Nasal colonization is associated with a unique expression pattern of sRNA that might reflect the commensalism of S. aureus in this niche.
Romilly C, Chevalier C, Marzi S, Masquida B, Geissmann T, Vandenesch F, Westhof E, Romby P
Loop-loop interactions involved in antisense regulation are processed by the endoribonuclease III in Staphylococcus aureus. Journal Article
In: RNA Biol, vol. 9, no. 12, pp. 1461-1472, 2012, ISBN: 23134978.
Abstract | Links | BibTeX | Tags: ROMBY, Unité ARN, WESTHOF
@article{,
title = {Loop-loop interactions involved in antisense regulation are processed by the endoribonuclease III in Staphylococcus aureus.},
author = {C Romilly and C Chevalier and S Marzi and B Masquida and T Geissmann and F Vandenesch and E Westhof and P Romby},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23134978?dopt=Abstract},
doi = {10.4161/rna.22710},
isbn = {23134978},
year = {2012},
date = {2012-01-01},
journal = {RNA Biol},
volume = {9},
number = {12},
pages = {1461-1472},
abstract = {The endoribonuclease III (RNase III) belongs to the enzyme family known to process double-stranded RNAs. Staphylococcus aureus RNase III was shown to regulate, in concert with the quorum sensing induced RNAIII, the degradation of several mRNAs encoding virulence factors and the transcriptional repressor of toxins Rot. Two of the mRNA-RNAIII complexes involve fully base paired loop-loop interactions with similar sequences that are cleaved by RNase III at a unique position. We show here that the sequence of the base pairs within the loop-loop interaction was not critical for RNase III cleavage, but that the co-axial stacking of three consecutive helices provides an ideal topology for RNase III recognition. In contrast, RNase III induces several strong cleavages in a regular helix, which carries a sequence similar to the loop-loop interaction. The introduction of a bulged loop that interrupts the regular helix restrains the number of cleavages. This work shows that S. aureus RNase III is able to bind and cleave a variety of RNA-mRNA substrates, and that specific structure elements direct the action of RNase III.},
keywords = {ROMBY, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
The endoribonuclease III (RNase III) belongs to the enzyme family known to process double-stranded RNAs. Staphylococcus aureus RNase III was shown to regulate, in concert with the quorum sensing induced RNAIII, the degradation of several mRNAs encoding virulence factors and the transcriptional repressor of toxins Rot. Two of the mRNA-RNAIII complexes involve fully base paired loop-loop interactions with similar sequences that are cleaved by RNase III at a unique position. We show here that the sequence of the base pairs within the loop-loop interaction was not critical for RNase III cleavage, but that the co-axial stacking of three consecutive helices provides an ideal topology for RNase III recognition. In contrast, RNase III induces several strong cleavages in a regular helix, which carries a sequence similar to the loop-loop interaction. The introduction of a bulged loop that interrupts the regular helix restrains the number of cleavages. This work shows that S. aureus RNase III is able to bind and cleave a variety of RNA-mRNA substrates, and that specific structure elements direct the action of RNase III.
Romilly C, Caldelari I, Parmentier D, Lioliou E, Romby P, Fechter P
Current knowledge on regulatory RNAs and their machineries in Staphylococcus aureus Journal Article
In: RNA Biol, vol. 9, no. 4, pp. 402-413, 2012, ISBN: 22546940.
Abstract | Links | BibTeX | Tags: ROMBY, Staphylococcus aureus Gene regulation Peptides Regulatory RNAs RNA-binding proteins Virulence, Unité ARN
@article{,
title = {Current knowledge on regulatory RNAs and their machineries in Staphylococcus aureus},
author = {C Romilly and I Caldelari and D Parmentier and E Lioliou and P Romby and P Fechter},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22546940},
doi = {0.4161/rna.20103},
isbn = {22546940},
year = {2012},
date = {2012-01-01},
journal = {RNA Biol},
volume = {9},
number = {4},
pages = {402-413},
abstract = {Staphylococcus aureus is one of the major human pathogens, which causes numerous community-associated and hospital-acquired infections. The regulation of the expression of numerous virulence factors is coordinated by complex interplays between two component systems, transcriptional regulatory proteins, and regulatory RNAs. Recent studies have identified numerous novel RNAs comprising cis-acting regulatory RNAs, antisense RNAs, small non coding RNAs and small mRNAs encoding peptides. We present here several examples of RNAs regulating S. aureus pathogenicity and describe various aspects of antisense regulation.},
keywords = {ROMBY, Staphylococcus aureus Gene regulation Peptides Regulatory RNAs RNA-binding proteins Virulence, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Staphylococcus aureus is one of the major human pathogens, which causes numerous community-associated and hospital-acquired infections. The regulation of the expression of numerous virulence factors is coordinated by complex interplays between two component systems, transcriptional regulatory proteins, and regulatory RNAs. Recent studies have identified numerous novel RNAs comprising cis-acting regulatory RNAs, antisense RNAs, small non coding RNAs and small mRNAs encoding peptides. We present here several examples of RNAs regulating S. aureus pathogenicity and describe various aspects of antisense regulation.
Marzi S, Romby P
RNA mimicry, a decoy for regulatory proteins. Journal Article
In: Mol Microbiol, vol. 83, no. 1, pp. 1-6, 2012, ISBN: 22098101, (Article first published online: 21 NOV 2011).
Abstract | Links | BibTeX | Tags: ROMBY, Unité ARN
@article{,
title = {RNA mimicry, a decoy for regulatory proteins.},
author = {S Marzi and P Romby},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22098101},
doi = {10.1111/j.1365-2958.2011.07911.x},
isbn = {22098101},
year = {2012},
date = {2012-01-01},
journal = {Mol Microbiol},
volume = {83},
number = {1},
pages = {1-6},
abstract = {Small non-coding RNA molecules (sRNA) are key regulators participating in complex networks, which adapt metabolism in response to environmental changes. In this issue of Molecular Microbiology, and in a related paper in Proc. Natl. Acad. Sci. USA, Moreno and colleagues and Sonnleitner and colleagues report on novel sRNAs, which act as decoys to inhibit the activity of the master post-transcriptional regulatory protein Crc. Crc is a key protein involved in carbon catabolite repression that optimizes metabolism improving the adaptation of the bacteria to their diverse habitats. Crc is a novel RNA-binding protein that regulates translation of multiple target mRNAs. Two regulatory sRNAs in Pseudomonas putida mimic the natural mRNA targets of Crc and counteract the action of Crc by sequestrating the protein when catabolite repression is absent. Crc trapping by a sRNA is a mechanism reminiscent to the regulation of the repressor of secondary metabolites (RsmA) in Pseudomonas, and highlights the suitability of RNA-dependent regulation to rapidly adjust cell growth in response to environmental changes.},
note = {Article first published online: 21 NOV 2011},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Small non-coding RNA molecules (sRNA) are key regulators participating in complex networks, which adapt metabolism in response to environmental changes. In this issue of Molecular Microbiology, and in a related paper in Proc. Natl. Acad. Sci. USA, Moreno and colleagues and Sonnleitner and colleagues report on novel sRNAs, which act as decoys to inhibit the activity of the master post-transcriptional regulatory protein Crc. Crc is a key protein involved in carbon catabolite repression that optimizes metabolism improving the adaptation of the bacteria to their diverse habitats. Crc is a novel RNA-binding protein that regulates translation of multiple target mRNAs. Two regulatory sRNAs in Pseudomonas putida mimic the natural mRNA targets of Crc and counteract the action of Crc by sequestrating the protein when catabolite repression is absent. Crc trapping by a sRNA is a mechanism reminiscent to the regulation of the repressor of secondary metabolites (RsmA) in Pseudomonas, and highlights the suitability of RNA-dependent regulation to rapidly adjust cell growth in response to environmental changes.
Lioliou E, Sharma C M, Caldelari I, Helfer A C, Fechter P, Vandenesch F, Vogel J, Romby P
Global Regulatory Functions of the Staphylococcus aureus Endoribonuclease III in Gene Expression. Journal Article
In: PLoS Genet, vol. 8, no. 6, pp. e1002782, 2012, ISBN: 22761586.
Abstract | Links | BibTeX | Tags: ROMBY, Unité ARN
@article{,
title = {Global Regulatory Functions of the Staphylococcus aureus Endoribonuclease III in Gene Expression.},
author = {E Lioliou and C M Sharma and I Caldelari and A C Helfer and P Fechter and F Vandenesch and J Vogel and P Romby},
url = {http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002782 http://www.ncbi.nlm.nih.gov/pubmed/22761586?dopt=Abstract},
isbn = {22761586},
year = {2012},
date = {2012-01-01},
journal = {PLoS Genet},
volume = {8},
number = {6},
pages = {e1002782},
abstract = {RNA turnover plays an important role in both virulence and adaptation to stress in the Gram-positive human pathogen Staphylococcus aureus. However, the molecular players and mechanisms involved in these processes are poorly understood. Here, we explored the functions of S. aureus endoribonuclease III (RNase III), a member of the ubiquitous family of double-strand-specific endoribonucleases. To define genomic transcripts that are bound and processed by RNase III, we performed deep sequencing on cDNA libraries generated from RNAs that were co-immunoprecipitated with wild-type RNase III or two different cleavage-defective mutant variants in vivo. Several newly identified RNase III targets were validated by independent experimental methods. We identified various classes of structured RNAs as RNase III substrates and demonstrated that this enzyme is involved in the maturation of rRNAs and tRNAs, regulates the turnover of mRNAs and non-coding RNAs, and autoregulates its synthesis by cleaving within the coding region of its own mRNA. Moreover, we identified a positive effect of RNase III on protein synthesis based on novel mechanisms. RNase III-mediated cleavage in the 5' untranslated region (5'UTR) enhanced the stability and translation of cspA mRNA, which encodes the major cold-shock protein. Furthermore, RNase III cleaved overlapping 5'UTRs of divergently transcribed genes to generate leaderless mRNAs, which constitutes a novel way to co-regulate neighboring genes. In agreement with recent findings, low abundance antisense RNAs covering 44% of the annotated genes were captured by co-immunoprecipitation with RNase III mutant proteins. Thus, in addition to gene regulation, RNase III is associated with RNA quality control of pervasive transcription. Overall, this study illustrates the complexity of post-transcriptional regulation mediated by RNase III.},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
RNA turnover plays an important role in both virulence and adaptation to stress in the Gram-positive human pathogen Staphylococcus aureus. However, the molecular players and mechanisms involved in these processes are poorly understood. Here, we explored the functions of S. aureus endoribonuclease III (RNase III), a member of the ubiquitous family of double-strand-specific endoribonucleases. To define genomic transcripts that are bound and processed by RNase III, we performed deep sequencing on cDNA libraries generated from RNAs that were co-immunoprecipitated with wild-type RNase III or two different cleavage-defective mutant variants in vivo. Several newly identified RNase III targets were validated by independent experimental methods. We identified various classes of structured RNAs as RNase III substrates and demonstrated that this enzyme is involved in the maturation of rRNAs and tRNAs, regulates the turnover of mRNAs and non-coding RNAs, and autoregulates its synthesis by cleaving within the coding region of its own mRNA. Moreover, we identified a positive effect of RNase III on protein synthesis based on novel mechanisms. RNase III-mediated cleavage in the 5' untranslated region (5'UTR) enhanced the stability and translation of cspA mRNA, which encodes the major cold-shock protein. Furthermore, RNase III cleaved overlapping 5'UTRs of divergently transcribed genes to generate leaderless mRNAs, which constitutes a novel way to co-regulate neighboring genes. In agreement with recent findings, low abundance antisense RNAs covering 44% of the annotated genes were captured by co-immunoprecipitation with RNase III mutant proteins. Thus, in addition to gene regulation, RNase III is associated with RNA quality control of pervasive transcription. Overall, this study illustrates the complexity of post-transcriptional regulation mediated by RNase III.
Lioliou E, Romilly C, Geissman T, Vandenesch F, Romby P
RNA-mediated regulation of virulence gene expression: another layer of complexity Book Chapter
In: Filloux, A (Ed.): Bacterial Regulatory Networks, pp. 143-166, Caister Academic Press, Norwich, UK, 2012.
Abstract | Links | BibTeX | Tags: ROMBY, Unité ARN
@inbook{,
title = {RNA-mediated regulation of virulence gene expression: another layer of complexity},
author = {E Lioliou and C Romilly and T Geissman and F Vandenesch and P Romby},
editor = {A Filloux},
url = {http://www.horizonpress.com/regulatorynetworks},
year = {2012},
date = {2012-01-01},
booktitle = {Bacterial Regulatory Networks},
pages = {143-166},
publisher = {Caister Academic Press},
address = {Norwich, UK},
abstract = {Many pathogenic bacteria cause serious diseases in humans, animals, and plants. Due to the appearance of resistance to multiple antibiotics, it has become important to fully understand the regulatory networks that lead to the production of virulence factors that help the bacteria combat the host defense machinery, acquire nutrients, and survive and/or proliferate within the host. In recent years, complex interplays between transcriptional regulatory proteins, two-component systems, and regulatory RNAs have been described, establishing the gene expression patterns in pathogenic bacteria. In this review, several examples will illustrate the diversity of regulatory RNAs and how they are integrated into the regulatory circuits required for virulence gene expression, with special emphasis on the mechanisms of regulation at the molecular level.},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Many pathogenic bacteria cause serious diseases in humans, animals, and plants. Due to the appearance of resistance to multiple antibiotics, it has become important to fully understand the regulatory networks that lead to the production of virulence factors that help the bacteria combat the host defense machinery, acquire nutrients, and survive and/or proliferate within the host. In recent years, complex interplays between transcriptional regulatory proteins, two-component systems, and regulatory RNAs have been described, establishing the gene expression patterns in pathogenic bacteria. In this review, several examples will illustrate the diversity of regulatory RNAs and how they are integrated into the regulatory circuits required for virulence gene expression, with special emphasis on the mechanisms of regulation at the molecular level.
Jester B C, Romby P, Lioliou E
When ribonucleases come into play in pathogens: a survey of gram-positive bacteria. Journal Article
In: Int J Microbiol, vol. 2012, pp. 592196, 2012, ISSN: ISSN: 1687-918X (Print) ISSN: 1687-9198 (Online), (Epub 2012 Mar 13.).
Abstract | Links | BibTeX | Tags: ROMBY, Unité ARN
@article{,
title = {When ribonucleases come into play in pathogens: a survey of gram-positive bacteria.},
author = {B C Jester and P Romby and E Lioliou},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22550495},
doi = {10.1155/2012/592196},
issn = {ISSN: 1687-918X (Print)
ISSN: 1687-9198 (Online)},
year = {2012},
date = {2012-01-01},
journal = {Int J Microbiol},
volume = {2012},
pages = {592196},
abstract = {It is widely acknowledged that RNA stability plays critical roles in bacterial adaptation and survival in different environments like those encountered when bacteria infect a host. Bacterial ribonucleases acting alone or in concert with regulatory RNAs or RNA binding proteins are the mediators of the regulatory outcome on RNA stability. We will give a current update of what is known about ribonucleases in the model Gram-positive organism Bacillus subtilis and will describe their established roles in virulence in several Gram-positive pathogenic bacteria that are imposing major health concerns worldwide. Implications on bacterial evolution through stabilization/transfer of genetic material (phage or plasmid DNA) as a result of ribonucleases' functions will be covered. The role of ribonucleases in emergence of antibiotic resistance and new concepts in drug design will additionally be discussed.},
note = {Epub 2012 Mar 13.},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
It is widely acknowledged that RNA stability plays critical roles in bacterial adaptation and survival in different environments like those encountered when bacteria infect a host. Bacterial ribonucleases acting alone or in concert with regulatory RNAs or RNA binding proteins are the mediators of the regulatory outcome on RNA stability. We will give a current update of what is known about ribonucleases in the model Gram-positive organism Bacillus subtilis and will describe their established roles in virulence in several Gram-positive pathogenic bacteria that are imposing major health concerns worldwide. Implications on bacterial evolution through stabilization/transfer of genetic material (phage or plasmid DNA) as a result of ribonucleases' functions will be covered. The role of ribonucleases in emergence of antibiotic resistance and new concepts in drug design will additionally be discussed.
Caldelari I, Fechter P, Lioliou E, Chevalier C, Gaspin C, Romby P
A current overview of regulatory RNAs in Staphylococcus aureus Book Chapter
In: Marchfelder, A; Hess, W R (Ed.): Regulatory RNAs in prokaryotes, pp. 51-75, SpringerWienNewYork, 2012.
Abstract | Links | BibTeX | Tags: ROMBY, Unité ARN
@inbook{,
title = {A current overview of regulatory RNAs in Staphylococcus aureus},
author = {I Caldelari and P Fechter and E Lioliou and C Chevalier and C Gaspin and P Romby},
editor = {A Marchfelder and W R Hess},
url = {http://link.springer.com/content/pdf/10.1007%2F978-3-7091-0218-3_3},
doi = {10.1007/978-3-7091-0218-3_3},
year = {2012},
date = {2012-01-01},
booktitle = {Regulatory RNAs in prokaryotes},
pages = {51-75},
publisher = {SpringerWienNewYork},
abstract = {Staphylococcus aureus is a common commensal bacterial species that is usually found in the nose and on the skin of 30 % of healthy adults. However, the bacterium is a remarkably versatile pathogen that is one of the main causes of community as well as hospital-acquired infections (Cheung et al., 2004; Novick, 2003). S. aureus is responsible for systemic infections such as sepsis and endocarditis, which can be difficult to treat due to the acquisition of resistance towards numerous antibiotics in clinical use. S. aureus causes a wide spectrum of human diseases in part due to its ability to produce an array of virulence factors, which are mostly encoded by laterally acquired genomic regions, the so-called pathogenicity islands. These factors include surface proteins responsible for the adhesion and invasion of the host, exoproteins required for host immune evasion, and toxins involved in dissemination in host tissues and acquisition of nutrients (Novick, 2003). Redundancies exist to ensure that a productive infection still occurs even though one factor may be lost. In recent decades, many studies have been carried out to understand how S. aureus is able to coordinate the expression of a large panel of virulence factors at the appropriate time in order to facilitate successful infections (Novick and Geisinger, 2008). These works offer the possibility for developing anti-virulence therapies as alternative strategies for affecting the bacteria viability, i. e. by inhibiting the expression of the virulence factors that cause host damage or the interaction between the pathogen and the host (Clatworthy et al., 2007). Inhibiting virulence instead of viability may have little impact on human flora and result in weaker selective pressure for the development of antibiotic resistance. Hence, determining the regulatory networks and the dynamics involved in virulence and in fast adaptive responses are of prime importance to combating S. aureus infections.},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Staphylococcus aureus is a common commensal bacterial species that is usually found in the nose and on the skin of 30 % of healthy adults. However, the bacterium is a remarkably versatile pathogen that is one of the main causes of community as well as hospital-acquired infections (Cheung et al., 2004; Novick, 2003). S. aureus is responsible for systemic infections such as sepsis and endocarditis, which can be difficult to treat due to the acquisition of resistance towards numerous antibiotics in clinical use. S. aureus causes a wide spectrum of human diseases in part due to its ability to produce an array of virulence factors, which are mostly encoded by laterally acquired genomic regions, the so-called pathogenicity islands. These factors include surface proteins responsible for the adhesion and invasion of the host, exoproteins required for host immune evasion, and toxins involved in dissemination in host tissues and acquisition of nutrients (Novick, 2003). Redundancies exist to ensure that a productive infection still occurs even though one factor may be lost. In recent decades, many studies have been carried out to understand how S. aureus is able to coordinate the expression of a large panel of virulence factors at the appropriate time in order to facilitate successful infections (Novick and Geisinger, 2008). These works offer the possibility for developing anti-virulence therapies as alternative strategies for affecting the bacteria viability, i. e. by inhibiting the expression of the virulence factors that cause host damage or the interaction between the pathogen and the host (Clatworthy et al., 2007). Inhibiting virulence instead of viability may have little impact on human flora and result in weaker selective pressure for the development of antibiotic resistance. Hence, determining the regulatory networks and the dynamics involved in virulence and in fast adaptive responses are of prime importance to combating S. aureus infections.
Helfer A C, Romilly C, Chevalier C, Lioliou E, Marzi S, Romby P
Probing RNA Structure In Vitro with Enzymes and Chemicals. Book Section
In: Hartmann, R K; Bindereif, A; Schön, A; Westhof, E (Ed.): Handbook of RNA Biochemistry: Second, Completely Revised and Enlarged Edition, pp. 205-230, Wiley-VCH, 2012, ISBN: 9783527327645 9783527647064/ISSN.
Abstract | Links | BibTeX | Tags: RNA structure probing in vitro in vivo chemical probes enzymatic probing ribonucleases RNases T1, ROMBY, T2, Unité ARN, V1 lead(II)-induced cleavages dimethylsulfate (DMS) diethylpyrocarbonate (DEPC) 1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate (CMCT) N-ethyl-N-nitrosourea (ENU) N-methylisatoic anhydride (NMIA) 1-methyl-7-nitroisatoic anhydride (1M7) benzoyl cyanide (BzCN)
@incollection{,
title = {Probing RNA Structure In Vitro with Enzymes and Chemicals.},
author = {A C Helfer and C Romilly and C Chevalier and E Lioliou and S Marzi and P Romby},
editor = {R K Hartmann and A Bindereif and A Schön and E Westhof},
url = {http://onlinelibrary.wiley.com/doi/10.1002/9783527647064.ch10/summary},
doi = {10.1002/9783527647064.ch10},
isbn = {9783527327645 9783527647064/ISSN},
year = {2012},
date = {2012-01-01},
booktitle = {Handbook of RNA Biochemistry: Second, Completely Revised and Enlarged Edition},
pages = {205-230},
publisher = {Wiley-VCH},
abstract = {Introduction
Enzymatic and Chemical Probes
In Vivo DMS Modification
Commentary
Troubleshooting
References},
keywords = {RNA structure probing in vitro in vivo chemical probes enzymatic probing ribonucleases RNases T1, ROMBY, T2, Unité ARN, V1 lead(II)-induced cleavages dimethylsulfate (DMS) diethylpyrocarbonate (DEPC) 1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate (CMCT) N-ethyl-N-nitrosourea (ENU) N-methylisatoic anhydride (NMIA) 1-methyl-7-nitroisatoic anhydride (1M7) benzoyl cyanide (BzCN)},
pubstate = {published},
tppubtype = {incollection}
}
Introduction
Enzymatic and Chemical Probes
In Vivo DMS Modification
Commentary
Troubleshooting
References
Enzymatic and Chemical Probes
In Vivo DMS Modification
Commentary
Troubleshooting
References
2011
Simonetti A, Marzi S, Myasnikov A, Menetret J F, Klaholz B P
Insights into translation initiation and termination complexes and into the polysome architecture Book Chapter
In: Rodnina, M; Wintermeyer, W; Green, R (Ed.): Ribosomes Structures, Function, and Dynamics, pp. 113-128, Springer, Wien, 2011.
Abstract | Links | BibTeX | Tags: ENNIFAR, ROMBY, Unité ARN
@inbook{,
title = {Insights into translation initiation and termination complexes and into the polysome architecture},
author = {A Simonetti and S Marzi and A Myasnikov and J F Menetret and B P Klaholz},
editor = {M Rodnina and W Wintermeyer and R Green},
url = {http://www.springerlink.com/content/j5022n7218036w14},
doi = {10.1007/978-3-7091-0215-2_10},
year = {2011},
date = {2011-01-01},
booktitle = {Ribosomes Structures, Function, and Dynamics},
pages = {113-128},
publisher = {Springer},
address = {Wien},
abstract = {Translation initiation is the most strongly regulated phase of protein synthesis during which the synthesis of a given protein is decided on. Initiation is the least conserved step of translation, since bacteria, archaea and eukarya have distinct and very different ways to initiate translation, and many different trans-acting factors are involved in the process. In bacteria, translation initiation comprises the consecutive formation of three major intermediary initiation complexes that are assembled via a multi-step process and that differ in composition and in conformation. At the end of the initiation process, an active 70S ribosomal initiation complex (70S IC) has formed which can enter peptide bond formation.},
keywords = {ENNIFAR, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Translation initiation is the most strongly regulated phase of protein synthesis during which the synthesis of a given protein is decided on. Initiation is the least conserved step of translation, since bacteria, archaea and eukarya have distinct and very different ways to initiate translation, and many different trans-acting factors are involved in the process. In bacteria, translation initiation comprises the consecutive formation of three major intermediary initiation complexes that are assembled via a multi-step process and that differ in composition and in conformation. At the end of the initiation process, an active 70S ribosomal initiation complex (70S IC) has formed which can enter peptide bond formation.
2010
Giuliodori A M, Pietro F Di, Marzi S, Masquida B, Wagner R, Romby P, Gualerzi C O, Pon C L
The cspA mRNA is a thermosensor that modulates translation of the cold-shock protein CspA Journal Article
In: Mol Cell, vol. 37, no. 1, pp. 21-33, 2010, ISBN: 20129052, (1097-4164 (Electronic) 1097-2765 (Linking) Journal Article Research Support, Non-U.S. Gov't).
Abstract | Links | BibTeX | Tags: 5' Untranslated Regions Acclimatization *Cold Temperature Escherichia coli/*genetics/metabolism Escherichia coli Proteins/genetics/*physiology Gene Expression Regulation, Bacterial Heat-Shock Proteins/genetics/*physiology Models, Genetic Nucleic Acid Conformation *Protein Biosynthesis RNA, Messenger/chemistry/*physiology, ROMBY, Unité ARN, WESTHOF
@article{,
title = {The cspA mRNA is a thermosensor that modulates translation of the cold-shock protein CspA},
author = {A M Giuliodori and F Di Pietro and S Marzi and B Masquida and R Wagner and P Romby and C O Gualerzi and C L Pon},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20129052},
isbn = {20129052},
year = {2010},
date = {2010-01-01},
journal = {Mol Cell},
volume = {37},
number = {1},
pages = {21-33},
abstract = {Cold induction of cspA, the paradigm Escherichia coli cold-shock gene, is mainly subject to posttranscriptional control, partly promoted by cis-acting elements of its transcript, whose secondary structure at 37 degrees C and at cold-shock temperature has been elucidated here by enzymatic and chemical probing. The structures, which were also validated by mutagenesis, demonstrate that cspA mRNA undergoes a temperature-dependent structural rearrangement, likely resulting from stabilization in the cold of an otherwise thermodynamically unstable folding intermediate. At low temperature, the "cold-shock" structure is more efficiently translated and somewhat less susceptible to degradation than the 37 degrees C structure. Overall, our data shed light on a molecular mechanism at the basis of the cold-shock response, indicating that cspA mRNA is able to sense temperature downshifts, adopting functionally distinct structures at different temperatures, even without the aid of trans-acting factors. Unlike with other previously studied RNA thermometers, these structural rearrangements do not result from melting of hairpin structures.},
note = {1097-4164 (Electronic)
1097-2765 (Linking)
Journal Article
Research Support, Non-U.S. Gov't},
keywords = {5' Untranslated Regions Acclimatization *Cold Temperature Escherichia coli/*genetics/metabolism Escherichia coli Proteins/genetics/*physiology Gene Expression Regulation, Bacterial Heat-Shock Proteins/genetics/*physiology Models, Genetic Nucleic Acid Conformation *Protein Biosynthesis RNA, Messenger/chemistry/*physiology, ROMBY, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Cold induction of cspA, the paradigm Escherichia coli cold-shock gene, is mainly subject to posttranscriptional control, partly promoted by cis-acting elements of its transcript, whose secondary structure at 37 degrees C and at cold-shock temperature has been elucidated here by enzymatic and chemical probing. The structures, which were also validated by mutagenesis, demonstrate that cspA mRNA undergoes a temperature-dependent structural rearrangement, likely resulting from stabilization in the cold of an otherwise thermodynamically unstable folding intermediate. At low temperature, the "cold-shock" structure is more efficiently translated and somewhat less susceptible to degradation than the 37 degrees C structure. Overall, our data shed light on a molecular mechanism at the basis of the cold-shock response, indicating that cspA mRNA is able to sense temperature downshifts, adopting functionally distinct structures at different temperatures, even without the aid of trans-acting factors. Unlike with other previously studied RNA thermometers, these structural rearrangements do not result from melting of hairpin structures.
2009
Simonetti A, Marzi S, Jenner L, Myasnikov A, Romby P, Yusupova G, Klaholz B P, Yusupov M
A structural view of translation initiation in bacteria Journal Article
In: Cell Mol Life Sci, vol. 66, no. 3, pp. 423-436, 2009, ISBN: 19011758, (1420-9071 (Electronic) Journal Article Research Support, Non-U.S. Gov't).
Abstract | Links | BibTeX | Tags: ROMBY, Unité ARN
@article{,
title = {A structural view of translation initiation in bacteria},
author = {A Simonetti and S Marzi and L Jenner and A Myasnikov and P Romby and G Yusupova and B P Klaholz and M Yusupov},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19011758},
isbn = {19011758},
year = {2009},
date = {2009-01-01},
journal = {Cell Mol Life Sci},
volume = {66},
number = {3},
pages = {423-436},
abstract = {The assembly of the protein synthesis machinery occurs during translation initiation. In bacteria, this process involves the binding of messenger RNA(mRNA) start site and fMet-tRNA(fMet) to the ribosome, which results in the formation of the first codon-anticodon interaction and sets the reading frame for the decoding of the mRNA. This interaction takes place in the peptidyl site of the 30S ribosomal subunit and is controlled by the initiation factors IF1, IF2 and IF3 to form the 30S initiation complex. The binding of the 50S subunit and the ejection of the IFs mark the irreversible transition to the elongation phase. Visualization of these ligands on the ribosome has been achieved by cryo-electron microscopy and X-ray crystallography studies, which has helped to understand the mechanism of translation initiation at the molecular level. Conformational changes associated with different functional states provide a dynamic view of the initiation process and of its regulation.},
note = {1420-9071 (Electronic)
Journal Article
Research Support, Non-U.S. Gov't},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The assembly of the protein synthesis machinery occurs during translation initiation. In bacteria, this process involves the binding of messenger RNA(mRNA) start site and fMet-tRNA(fMet) to the ribosome, which results in the formation of the first codon-anticodon interaction and sets the reading frame for the decoding of the mRNA. This interaction takes place in the peptidyl site of the 30S ribosomal subunit and is controlled by the initiation factors IF1, IF2 and IF3 to form the 30S initiation complex. The binding of the 50S subunit and the ejection of the IFs mark the irreversible transition to the elongation phase. Visualization of these ligands on the ribosome has been achieved by cryo-electron microscopy and X-ray crystallography studies, which has helped to understand the mechanism of translation initiation at the molecular level. Conformational changes associated with different functional states provide a dynamic view of the initiation process and of its regulation.
Romby P, Marzi S, Westhof E
[The atomic structure of the ribosome into the spotlight] Journal Article
In: Med Sci (Paris), vol. 25, no. 11, pp. 977-981, 2009, ISBN: 19951677, (0767-0974 (Print) 0767-0974 (Linking) Journal Article).
Links | BibTeX | Tags: ROMBY, Unité ARN, WESTHOF
@article{,
title = {[The atomic structure of the ribosome into the spotlight]},
author = {P Romby and S Marzi and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19951677},
isbn = {19951677},
year = {2009},
date = {2009-01-01},
journal = {Med Sci (Paris)},
volume = {25},
number = {11},
pages = {977-981},
note = {0767-0974 (Print)
0767-0974 (Linking)
Journal Article},
keywords = {ROMBY, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Romby P, Charpentier E
An overview of RNAs with regulatory functions in gram-positive bacteria Journal Article
In: Cell Mol Life Sci, vol. 67, no. 2, pp. 217-237, 2009, ISBN: 19859665, (1420-9071 (Electronic) 1420-682X (Linking) Journal Article Research Support, Non-U.S. Gov't Review).
Abstract | Links | BibTeX | Tags: Bacterial Gram-Positive Bacteria/*genetics/pathogenicity RNA, Bacterial/genetics/*metabolism RNA, Gene Expression Regulation, ROMBY, Unité ARN, Untranslated/genetics/*metabolism Virulence/genetics
@article{,
title = {An overview of RNAs with regulatory functions in gram-positive bacteria},
author = {P Romby and E Charpentier},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19859665},
isbn = {19859665},
year = {2009},
date = {2009-01-01},
journal = {Cell Mol Life Sci},
volume = {67},
number = {2},
pages = {217-237},
abstract = {During the last decade, RNA molecules with regulatory functions on gene expression have benefited from a renewed interest. In bacteria, recent high throughput computational and experimental approaches have led to the discovery that 10-20% of all genes code for RNAs with critical regulatory roles in metabolic, physiological and pathogenic processes. The trans-acting RNAs comprise the noncoding RNAs, RNAs with a short open reading frame and antisense RNAs. Many of these RNAs act through binding to their target mRNAs while others modulate protein activity or target DNA. The cis-acting RNAs include regulatory regions of mRNAs that can respond to various signals. These RNAs often provide the missing link between sensing changing conditions in the environment and fine-tuning the subsequent biological responses. Information on their various functions and modes of action has been well documented for gram-negative bacteria. Here, we summarize the current knowledge of regulatory RNAs in gram-positive bacteria.},
note = {1420-9071 (Electronic)
1420-682X (Linking)
Journal Article
Research Support, Non-U.S. Gov't
Review},
keywords = {Bacterial Gram-Positive Bacteria/*genetics/pathogenicity RNA, Bacterial/genetics/*metabolism RNA, Gene Expression Regulation, ROMBY, Unité ARN, Untranslated/genetics/*metabolism Virulence/genetics},
pubstate = {published},
tppubtype = {article}
}
During the last decade, RNA molecules with regulatory functions on gene expression have benefited from a renewed interest. In bacteria, recent high throughput computational and experimental approaches have led to the discovery that 10-20% of all genes code for RNAs with critical regulatory roles in metabolic, physiological and pathogenic processes. The trans-acting RNAs comprise the noncoding RNAs, RNAs with a short open reading frame and antisense RNAs. Many of these RNAs act through binding to their target mRNAs while others modulate protein activity or target DNA. The cis-acting RNAs include regulatory regions of mRNAs that can respond to various signals. These RNAs often provide the missing link between sensing changing conditions in the environment and fine-tuning the subsequent biological responses. Information on their various functions and modes of action has been well documented for gram-negative bacteria. Here, we summarize the current knowledge of regulatory RNAs in gram-positive bacteria.
Moreno R, Marzi S, Romby P, Rojo F
In: Nucleic Acids Res, vol. 37, no. 22, pp. 7678-7690, 2009, ISBN: 19825982, (1362-4962 (Electronic) 0305-1048 (Linking) Journal Article Research Support, Non-U.S. Gov't).
Abstract | Links | BibTeX | Tags: 5' Untranslated Regions Bacterial Proteins/genetics/*metabolism Binding Sites Nucleic Acid Conformation *Peptide Chain Initiation, Messenger/chemistry/metabolism Repressor Proteins/*metabolism Trans-Activators/*genetics, ROMBY, Translational Pseudomonas putida/*genetics RNA, Unité ARN
@article{,
title = {The Crc global regulator binds to an unpaired A-rich motif at the Pseudomonas putida alkS mRNA coding sequence and inhibits translation initiation},
author = {R Moreno and S Marzi and P Romby and F Rojo},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19825982},
isbn = {19825982},
year = {2009},
date = {2009-01-01},
journal = {Nucleic Acids Res},
volume = {37},
number = {22},
pages = {7678-7690},
abstract = {Crc is a key global translational regulator in Pseudomonads that orchestrates the hierarchy of induction of several catabolic pathways for amino acids, sugars, hydrocarbons or aromatic compounds. In the presence of amino acids, which are preferred carbon sources, Crc inhibits translation of the Pseudomonas putida alkS and benR mRNAs, which code for transcriptional regulators of genes required to assimilate alkanes (hydrocarbons) and benzoate (an aromatic compound), respectively. Crc binds to the 5'-end of these mRNAs, but the sequence and/or structure recognized, and the way in which it inhibits translation, were unknown. We have determined the secondary structure of the alkS mRNA 5'-end through its sensitivity to several ribonucleases and chemical reagents. Footprinting and band-shift assays using variant alkS mRNAs have shown that Crc specifically binds to a short unpaired A-rich sequence located adjacent to the alkS AUG start codon. This interaction is stable enough to prevent formation of the translational initiation complex. A similar Crc-binding site was localized at benR mRNA, upstream of the Shine-Dalgarno sequence. This allowed predicting binding sites at other Crc-regulated genes, deriving a consensus sequence that will help to validate new Crc targets and to discriminate between direct and indirect effects of this regulator.},
note = {1362-4962 (Electronic)
0305-1048 (Linking)
Journal Article
Research Support, Non-U.S. Gov't},
keywords = {5' Untranslated Regions Bacterial Proteins/genetics/*metabolism Binding Sites Nucleic Acid Conformation *Peptide Chain Initiation, Messenger/chemistry/metabolism Repressor Proteins/*metabolism Trans-Activators/*genetics, ROMBY, Translational Pseudomonas putida/*genetics RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Crc is a key global translational regulator in Pseudomonads that orchestrates the hierarchy of induction of several catabolic pathways for amino acids, sugars, hydrocarbons or aromatic compounds. In the presence of amino acids, which are preferred carbon sources, Crc inhibits translation of the Pseudomonas putida alkS and benR mRNAs, which code for transcriptional regulators of genes required to assimilate alkanes (hydrocarbons) and benzoate (an aromatic compound), respectively. Crc binds to the 5'-end of these mRNAs, but the sequence and/or structure recognized, and the way in which it inhibits translation, were unknown. We have determined the secondary structure of the alkS mRNA 5'-end through its sensitivity to several ribonucleases and chemical reagents. Footprinting and band-shift assays using variant alkS mRNAs have shown that Crc specifically binds to a short unpaired A-rich sequence located adjacent to the alkS AUG start codon. This interaction is stable enough to prevent formation of the translational initiation complex. A similar Crc-binding site was localized at benR mRNA, upstream of the Shine-Dalgarno sequence. This allowed predicting binding sites at other Crc-regulated genes, deriving a consensus sequence that will help to validate new Crc targets and to discriminate between direct and indirect effects of this regulator.
Geissmann T, Marzi S, Romby P
The role of mRNA structure in translational control in bacteria Journal Article
In: RNA Biol, vol. 6, no. 2, pp. 153-160, 2009, ISBN: 19885993, (1555-8584 (Electronic) 1547-6286 (Linking) Journal Article Research Support, Non-U.S. Gov't Review).
Abstract | Links | BibTeX | Tags: Amino Acid, Amino Acid Sequence Bacteria/*genetics Bacterial Proteins/chemistry/genetics Molecular Sequence Data *Nucleic Acid Conformation *Protein Biosynthesis RNA, Messenger/*chemistry Sequence Homology, ROMBY, Unité ARN
@article{,
title = {The role of mRNA structure in translational control in bacteria},
author = {T Geissmann and S Marzi and P Romby},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19885993},
isbn = {19885993},
year = {2009},
date = {2009-01-01},
journal = {RNA Biol},
volume = {6},
number = {2},
pages = {153-160},
abstract = {During the past few years, our knowledge on RNA-based regulation in many organisms has tremendously increased. In bacteria, although transcriptional regulatory proteins remain key players in gene regulation, a wide variety of post-transcriptional regulatory mechanisms discovered highlights the importance of the mRNA structure in the regulation of gene expression. RNA-dependent regulation largely contributes to rapidly adapt the bacterial metabolism in response to environmental changes, stress and in establishment of virulence. Bacteria exploit the extraordinary ability of mRNA to fold into different structures in response to various signals (environmental cues, ligand binding). Induced mRNA conformational rearrangements can potentially regulate transcription, translation and mRNA stability. The present review focuses on the structures of regulatory regions of mRNA that have evolved to permit productive interactions with trans-acting regulators, such as protein or non-coding RNAs. Finally, we describe how particular properties of these regulatory complexes regulate translation initiation.},
note = {1555-8584 (Electronic)
1547-6286 (Linking)
Journal Article
Research Support, Non-U.S. Gov't
Review},
keywords = {Amino Acid, Amino Acid Sequence Bacteria/*genetics Bacterial Proteins/chemistry/genetics Molecular Sequence Data *Nucleic Acid Conformation *Protein Biosynthesis RNA, Messenger/*chemistry Sequence Homology, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
During the past few years, our knowledge on RNA-based regulation in many organisms has tremendously increased. In bacteria, although transcriptional regulatory proteins remain key players in gene regulation, a wide variety of post-transcriptional regulatory mechanisms discovered highlights the importance of the mRNA structure in the regulation of gene expression. RNA-dependent regulation largely contributes to rapidly adapt the bacterial metabolism in response to environmental changes, stress and in establishment of virulence. Bacteria exploit the extraordinary ability of mRNA to fold into different structures in response to various signals (environmental cues, ligand binding). Induced mRNA conformational rearrangements can potentially regulate transcription, translation and mRNA stability. The present review focuses on the structures of regulatory regions of mRNA that have evolved to permit productive interactions with trans-acting regulators, such as protein or non-coding RNAs. Finally, we describe how particular properties of these regulatory complexes regulate translation initiation.
Geissmann T, Chevalier C, Cros M J, Boisset S, Fechter P, Noirot C, Schrenzel J, Francois P, Vandenesch F, Gaspin C, Romby P
A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation Journal Article
In: Nucleic Acids Res, vol. 37, no. 21, pp. 7239-7257, 2009, ISBN: 19786493, (1362-4962 (Electronic) 0305-1048 (Linking) Journal Article Research Support, Non-U.S. Gov't).
Abstract | Links | BibTeX | Tags: Bacillus subtilis/genetics/metabolism Base Sequence Computational Biology Conserved Sequence Gene Expression Profiling *Gene Expression Regulation, Bacterial Molecular Sequence Data Proteomics RNA Stability RNA, Genetic, Messenger/metabolism RNA, ROMBY, Unité ARN, Untranslated/*chemistry/genetics/metabolism Staphylococcus aureus/*genetics Transcription
@article{,
title = {A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation},
author = {T Geissmann and C Chevalier and M J Cros and S Boisset and P Fechter and C Noirot and J Schrenzel and P Francois and F Vandenesch and C Gaspin and P Romby},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19786493},
isbn = {19786493},
year = {2009},
date = {2009-01-01},
journal = {Nucleic Acids Res},
volume = {37},
number = {21},
pages = {7239-7257},
abstract = {Bioinformatic analysis of the intergenic regions of Staphylococcus aureus predicted multiple regulatory regions. From this analysis, we characterized 11 novel noncoding RNAs (RsaA-K) that are expressed in several S. aureus strains under different experimental conditions. Many of them accumulate in the late-exponential phase of growth. All ncRNAs are stable and their expression is Hfq-independent. The transcription of several of them is regulated by the alternative sigma B factor (RsaA, D and F) while the expression of RsaE is agrA-dependent. Six of these ncRNAs are specific to S. aureus, four are conserved in other Staphylococci, and RsaE is also present in Bacillaceae. Transcriptomic and proteomic analysis indicated that RsaE regulates the synthesis of proteins involved in various metabolic pathways. Phylogenetic analysis combined with RNA structure probing, searches for RsaE-mRNA base pairing, and toeprinting assays indicate that a conserved and unpaired UCCC sequence motif of RsaE binds to target mRNAs and prevents the formation of the ribosomal initiation complex. This study unexpectedly shows that most of the novel ncRNAs carry the conserved C-rich motif, suggesting that they are members of a class of ncRNAs that target mRNAs by a shared mechanism.},
note = {1362-4962 (Electronic)
0305-1048 (Linking)
Journal Article
Research Support, Non-U.S. Gov't},
keywords = {Bacillus subtilis/genetics/metabolism Base Sequence Computational Biology Conserved Sequence Gene Expression Profiling *Gene Expression Regulation, Bacterial Molecular Sequence Data Proteomics RNA Stability RNA, Genetic, Messenger/metabolism RNA, ROMBY, Unité ARN, Untranslated/*chemistry/genetics/metabolism Staphylococcus aureus/*genetics Transcription},
pubstate = {published},
tppubtype = {article}
}
Bioinformatic analysis of the intergenic regions of Staphylococcus aureus predicted multiple regulatory regions. From this analysis, we characterized 11 novel noncoding RNAs (RsaA-K) that are expressed in several S. aureus strains under different experimental conditions. Many of them accumulate in the late-exponential phase of growth. All ncRNAs are stable and their expression is Hfq-independent. The transcription of several of them is regulated by the alternative sigma B factor (RsaA, D and F) while the expression of RsaE is agrA-dependent. Six of these ncRNAs are specific to S. aureus, four are conserved in other Staphylococci, and RsaE is also present in Bacillaceae. Transcriptomic and proteomic analysis indicated that RsaE regulates the synthesis of proteins involved in various metabolic pathways. Phylogenetic analysis combined with RNA structure probing, searches for RsaE-mRNA base pairing, and toeprinting assays indicate that a conserved and unpaired UCCC sequence motif of RsaE binds to target mRNAs and prevents the formation of the ribosomal initiation complex. This study unexpectedly shows that most of the novel ncRNAs carry the conserved C-rich motif, suggesting that they are members of a class of ncRNAs that target mRNAs by a shared mechanism.
Fechter P, Chevalier C, Yusupova G, Yusupov M, Romby P, Marzi S
Ribosomal initiation complexes probed by toeprinting and effect of trans-acting translational regulators in bacteria Book Chapter
In: Serganov, A (Ed.): Riboswitches: Methods and Protocols, vol. 540, pp. 247-263, Springer Protocols, Humana Press, 2009, ISBN: 19381565.
Abstract | Links | BibTeX | Tags: Bacteria/*genetics/*metabolism Bacterial Proteins/*metabolism Base Sequence Escherichia coli/metabolism Molecular Biology/*methods Molecular Sequence Data *Peptide Chain Initiation, Bacterial/chemistry/genetics Ribosomes/*metabolism Staphylococcus aureus/metabolism Thermus thermophilus/metabolism, ROMBY, Translational RNA, Unité ARN
@inbook{,
title = {Ribosomal initiation complexes probed by toeprinting and effect of trans-acting translational regulators in bacteria},
author = {P Fechter and C Chevalier and G Yusupova and M Yusupov and P Romby and S Marzi},
editor = {A Serganov},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19381565},
doi = {10.1007/978-1-59745-558-9_18},
isbn = {19381565},
year = {2009},
date = {2009-01-01},
booktitle = {Riboswitches: Methods and Protocols},
volume = {540},
pages = {247-263},
publisher = {Springer Protocols, Humana Press},
series = {Methods in Molecular Biology},
abstract = {Toeprinting was developed to study the formation of ribosomal initiation complexes in bacteria. This approach, based on the inhibition of reverse transcriptase elongation, was used to monitor the effect of ribosomal components and translational factors on the formation of the active ribosomal initiation complex. Moreover, this method offers an easy way to study in vitro how mRNA conformational changes alter ribosome binding at the initiation site. These changes can be induced either by environmental cues (temperature, ion concentration), or by the binding of metabolites, regulatory proteins, and trans-acting RNAs. An experimental guide is given to follow the different steps of the formation of ribosomal initiation complexes in Escherichia coli and Staphylococcus aureus, and to monitor the mechanism of action of several regulators on translation initiation in vitro. Protocols to prepare the ribosome and the subunits are also given for Thermus thermophilus, Staphylococcus aureus, and Escherichia coli.},
keywords = {Bacteria/*genetics/*metabolism Bacterial Proteins/*metabolism Base Sequence Escherichia coli/metabolism Molecular Biology/*methods Molecular Sequence Data *Peptide Chain Initiation, Bacterial/chemistry/genetics Ribosomes/*metabolism Staphylococcus aureus/metabolism Thermus thermophilus/metabolism, ROMBY, Translational RNA, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Toeprinting was developed to study the formation of ribosomal initiation complexes in bacteria. This approach, based on the inhibition of reverse transcriptase elongation, was used to monitor the effect of ribosomal components and translational factors on the formation of the active ribosomal initiation complex. Moreover, this method offers an easy way to study in vitro how mRNA conformational changes alter ribosome binding at the initiation site. These changes can be induced either by environmental cues (temperature, ion concentration), or by the binding of metabolites, regulatory proteins, and trans-acting RNAs. An experimental guide is given to follow the different steps of the formation of ribosomal initiation complexes in Escherichia coli and Staphylococcus aureus, and to monitor the mechanism of action of several regulators on translation initiation in vitro. Protocols to prepare the ribosome and the subunits are also given for Thermus thermophilus, Staphylococcus aureus, and Escherichia coli.
Chevalier C, Geissmann T, Helfer A C, Romby P
Probing mRNA structure and sRNA-mRNA interactions in bacteria using enzymes and lead(II) Book Chapter
In: Serganov, A (Ed.): Riboswitches: Methods and Protocols, vol. 540, pp. 215-232, Springer Protocols, Humana Press, 2009, ISBN: 19381563.
Abstract | Links | BibTeX | Tags: Bacterial/chemical synthesis RNA, Base Sequence Chemical Fractionation Enzymes/*metabolism Hydrolysis/drug effects Lead/*pharmacology Molecular Biology/*methods Molecular Sequence Data Nucleic Acid Conformation/drug effects RNA/metabolism RNA, Messenger/*chemistry/genetics/*metabolism RNA, ROMBY, Unité ARN, Untranslated/chemistry/genetics/*metabolism Staphylococcus aureus/drug effects/*metabolism
@inbook{,
title = {Probing mRNA structure and sRNA-mRNA interactions in bacteria using enzymes and lead(II)},
author = {C Chevalier and T Geissmann and A C Helfer and P Romby},
editor = {A Serganov},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19381563},
doi = {978-1-59745-558-9_16},
isbn = {19381563},
year = {2009},
date = {2009-01-01},
booktitle = {Riboswitches: Methods and Protocols},
volume = {540},
pages = {215-232},
publisher = {Springer Protocols, Humana Press},
series = {Methods in Molecular Biology},
abstract = {Enzymatic probing and lead(II)-induced cleavages have been developed to study the secondary structure of RNA molecules either free or engaged in complex with different ligands. Using a combination of probes with different specificities (unpaired vs. paired regions), it is possible to get information on the accessibility of each nucleotide, on the binding site of a ligand (noncoding RNAs, protein, metabolites), and on RNA conformational changes that accompanied ligand binding or environmental conditions (temperature, pH, ions, etc.). The detection of the cleavages can be conducted by two different ways, which are chosen according to the length of the studied RNA. The first method uses end-labeled RNA molecules and the second one involves primer extension by reverse transcriptase. We provide here an experimental procedure that was designed to map the structure of mRNA and mRNA-sRNA interaction in vitro.},
keywords = {Bacterial/chemical synthesis RNA, Base Sequence Chemical Fractionation Enzymes/*metabolism Hydrolysis/drug effects Lead/*pharmacology Molecular Biology/*methods Molecular Sequence Data Nucleic Acid Conformation/drug effects RNA/metabolism RNA, Messenger/*chemistry/genetics/*metabolism RNA, ROMBY, Unité ARN, Untranslated/chemistry/genetics/*metabolism Staphylococcus aureus/drug effects/*metabolism},
pubstate = {published},
tppubtype = {inbook}
}
Enzymatic probing and lead(II)-induced cleavages have been developed to study the secondary structure of RNA molecules either free or engaged in complex with different ligands. Using a combination of probes with different specificities (unpaired vs. paired regions), it is possible to get information on the accessibility of each nucleotide, on the binding site of a ligand (noncoding RNAs, protein, metabolites), and on RNA conformational changes that accompanied ligand binding or environmental conditions (temperature, pH, ions, etc.). The detection of the cleavages can be conducted by two different ways, which are chosen according to the length of the studied RNA. The first method uses end-labeled RNA molecules and the second one involves primer extension by reverse transcriptase. We provide here an experimental procedure that was designed to map the structure of mRNA and mRNA-sRNA interaction in vitro.
Benelli D, Marzi S, Mancone C, Alonzi T, la Teana A, Londei P
Function and ribosomal localization of aIF6, a translational regulator shared by archaea and eukarya Journal Article
In: Nucleic Acids Res, vol. 37, no. 1, pp. 256-267, 2009, ISBN: 19036786, (1362-4962 (Electronic) Journal Article Research Support, Non-U.S. Gov't).
Abstract | Links | BibTeX | Tags: 23S/chemistry/metabolism Ribosomal Proteins/metabolism Ribosome Subunits, Archaeal Proteins/analysis/chemistry/*metabolism Base Sequence Binding Sites Cell Cycle Cloning, Archaeal/*metabolism Ribosomes/metabolism Sulfolobus solfataricus/*genetics/metabolism, Large, Molecular Eukaryotic Initiation Factors/chemistry Models, Molecular Molecular Sequence Data Prokaryotic Initiation Factors/analysis/chemistry/*metabolism *Protein Biosynthesis RNA, Ribosomal, ROMBY, Unité ARN
@article{,
title = {Function and ribosomal localization of aIF6, a translational regulator shared by archaea and eukarya},
author = {D Benelli and S Marzi and C Mancone and T Alonzi and A la Teana and P Londei},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19036786},
isbn = {19036786},
year = {2009},
date = {2009-01-01},
journal = {Nucleic Acids Res},
volume = {37},
number = {1},
pages = {256-267},
abstract = {The translation factor IF6 is shared by the Archaea and the Eukarya, but is not found in Bacteria. The properties of eukaryal IF6 (eIF6) have been extensively studied, but remain somewhat elusive. eIF6 behaves as a ribosome-anti-association factor and is involved in miRNA-mediated gene silencing; however, it also seems to participate in ribosome synthesis and export. Here we have determined the function and ribosomal localization of the archaeal (Sulfolobus solfataricus) IF6 homologue (aIF6). We find that aIF6 binds specifically to the 50S ribosomal subunits, hindering the formation of 70S ribosomes and strongly inhibiting translation. aIF6 is uniformly expressed along the cell cycle, but it is upregulated following both cold- and heat shock. The aIF6 ribosomal binding site lies in the middle of the 30-S interacting surface of the 50S subunit, including a number of critical RNA and protein determinants involved in subunit association. The data suggest that the IF6 protein evolved in the archaeal-eukaryal lineage to modulate translational efficiency under unfavourable environmental conditions, perhaps acquiring additional functions during eukaryotic evolution.},
note = {1362-4962 (Electronic)
Journal Article
Research Support, Non-U.S. Gov't},
keywords = {23S/chemistry/metabolism Ribosomal Proteins/metabolism Ribosome Subunits, Archaeal Proteins/analysis/chemistry/*metabolism Base Sequence Binding Sites Cell Cycle Cloning, Archaeal/*metabolism Ribosomes/metabolism Sulfolobus solfataricus/*genetics/metabolism, Large, Molecular Eukaryotic Initiation Factors/chemistry Models, Molecular Molecular Sequence Data Prokaryotic Initiation Factors/analysis/chemistry/*metabolism *Protein Biosynthesis RNA, Ribosomal, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The translation factor IF6 is shared by the Archaea and the Eukarya, but is not found in Bacteria. The properties of eukaryal IF6 (eIF6) have been extensively studied, but remain somewhat elusive. eIF6 behaves as a ribosome-anti-association factor and is involved in miRNA-mediated gene silencing; however, it also seems to participate in ribosome synthesis and export. Here we have determined the function and ribosomal localization of the archaeal (Sulfolobus solfataricus) IF6 homologue (aIF6). We find that aIF6 binds specifically to the 50S ribosomal subunits, hindering the formation of 70S ribosomes and strongly inhibiting translation. aIF6 is uniformly expressed along the cell cycle, but it is upregulated following both cold- and heat shock. The aIF6 ribosomal binding site lies in the middle of the 30-S interacting surface of the 50S subunit, including a number of critical RNA and protein determinants involved in subunit association. The data suggest that the IF6 protein evolved in the archaeal-eukaryal lineage to modulate translational efficiency under unfavourable environmental conditions, perhaps acquiring additional functions during eukaryotic evolution.
Myasnikov A G, Simonetti A, Marzi S, Klaholz B P
Structure-function insights into prokaryotic and eukaryotic translation initiation Journal Article
In: Curr Opin Struct Biol, vol. 19, no. 3, pp. 300-9, 2009, ISBN: 19493673, (1879-033X (Electronic) 0959-440X (Linking) Journal Article Research Support, Non-U.S. Gov't Review).
Abstract | Links | BibTeX | Tags: Amino Acid Sequence Eukaryotic Cells/*chemistry/*metabolism Humans Molecular Sequence Data *Peptide Chain Initiation, mino Acid Sequence Eukaryotic Cells/*chemistry/*metabolism Humans Molecular Sequence Data *Peptide Chain Initiation, ROMBY, Transfer/chemistry/metabolism Ribosomes/chemistry/genetics/metabolism, Translational Peptide Initiation Factors/chemistry/metabolism Prokaryotic Cells/*chemistry/*metabolism RNA, Unité ARN
@article{,
title = {Structure-function insights into prokaryotic and eukaryotic translation initiation},
author = {A G Myasnikov and A Simonetti and S Marzi and B P Klaholz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19493673},
isbn = {19493673},
year = {2009},
date = {2009-01-01},
journal = {Curr Opin Struct Biol},
volume = {19},
number = {3},
pages = {300-9},
abstract = {Translation initiation is the rate-limiting and most complexly regulated step of protein synthesis in prokaryotes and eukaryotes. In the last few years, cryo-electron microscopy has provided several novel insights into the universal process of translation initiation. Structures of prokaryotic 30S and 70S ribosomal initiation complexes with initiator transfer RNA (tRNA), messenger RNA (mRNA), and initiation factors have recently revealed the mechanism of initiator tRNA recruitment to the assembling ribosomal machinery, involving molecular rearrangements of the ribosome and associated factors. First three-dimensional pictures of the particularly complex eukaryotic translation initiation machinery have been obtained, revealing how initiation factors tune the ribosome for recruiting the mRNA. A comparison of the available prokaryotic and eukaryotic structures shows that--besides significant differences--some key ribosomal features are universally conserved.},
note = {1879-033X (Electronic)
0959-440X (Linking)
Journal Article
Research Support, Non-U.S. Gov't
Review},
keywords = {Amino Acid Sequence Eukaryotic Cells/*chemistry/*metabolism Humans Molecular Sequence Data *Peptide Chain Initiation, mino Acid Sequence Eukaryotic Cells/*chemistry/*metabolism Humans Molecular Sequence Data *Peptide Chain Initiation, ROMBY, Transfer/chemistry/metabolism Ribosomes/chemistry/genetics/metabolism, Translational Peptide Initiation Factors/chemistry/metabolism Prokaryotic Cells/*chemistry/*metabolism RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Translation initiation is the rate-limiting and most complexly regulated step of protein synthesis in prokaryotes and eukaryotes. In the last few years, cryo-electron microscopy has provided several novel insights into the universal process of translation initiation. Structures of prokaryotic 30S and 70S ribosomal initiation complexes with initiator transfer RNA (tRNA), messenger RNA (mRNA), and initiation factors have recently revealed the mechanism of initiator tRNA recruitment to the assembling ribosomal machinery, involving molecular rearrangements of the ribosome and associated factors. First three-dimensional pictures of the particularly complex eukaryotic translation initiation machinery have been obtained, revealing how initiation factors tune the ribosome for recruiting the mRNA. A comparison of the available prokaryotic and eukaryotic structures shows that--besides significant differences--some key ribosomal features are universally conserved.
Leclerc V, Caldelari I, Veresceaghina N, Reichhart J-M
Phagocytosis in Drosophila melanogaster Immune Response. Book Section
In: Phagocyte-pathogen Interactions, vol. 33, pp. 513–521, DG Russel and S. Gordon, Whasington, DC, 2009.
BibTeX | Tags: M3i, reichhart, ROMBY, Unité ARN
@incollection{leclerc_phagocytosis_2009,
title = {Phagocytosis in Drosophila melanogaster Immune Response.},
author = {V Leclerc and I Caldelari and N Veresceaghina and J-M Reichhart},
year = {2009},
date = {2009-01-01},
booktitle = {Phagocyte-pathogen Interactions},
volume = {33},
pages = {513--521},
publisher = {DG Russel and S. Gordon},
address = {Whasington, DC},
edition = {ASM Press},
keywords = {M3i, reichhart, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {incollection}
}
2008
Chamy L El, Leclerc V, Caldelari I, Reichhart J-M
Sensing of 'danger signals' and pathogen-associated molecular patterns defines binary signaling pathways 'upstream' of Toll Journal Article
In: Nat. Immunol., vol. 9, no. 10, pp. 1165–1170, 2008, ISSN: 1529-2916.
Abstract | Links | BibTeX | Tags: Animals, Fungi, Genetically Modified, Gram-Positive Bacteria, Gram-Positive Bacterial Infections, In Situ Hybridization, M3i, Mycoses, Pattern Recognition, Peptide Hydrolases, Receptors, reichhart, ROMBY, Serine Endopeptidases, Signal Transduction, Toll-Like Receptors, Unité ARN
@article{el_chamy_sensing_2008,
title = {Sensing of 'danger signals' and pathogen-associated molecular patterns defines binary signaling pathways 'upstream' of Toll},
author = {L El Chamy and V Leclerc and I Caldelari and J-M Reichhart},
doi = {10.1038/ni.1643},
issn = {1529-2916},
year = {2008},
date = {2008-10-01},
journal = {Nat. Immunol.},
volume = {9},
number = {10},
pages = {1165--1170},
abstract = {In drosophila, molecular determinants from fungi and Gram-positive bacteria are detected by circulating pattern-recognition receptors. Published findings suggest that such pattern-recognition receptors activate as-yet-unidentified serine-protease cascades that culminate in the cleavage of Spätzle, the endogenous Toll receptor ligand, and trigger the immune response. We demonstrate here that the protease Grass defines a common activation cascade for the detection of fungi and Gram-positive bacteria mediated by pattern-recognition receptors. The serine protease Persephone, shown before to be specific for fungal detection in a cascade activated by secreted fungal proteases, was also required for the sensing of proteases elicited by bacteria in the hemolymph. Hence, Persephone defines a parallel proteolytic cascade activated by 'danger signals' such as abnormal proteolytic activities.},
keywords = {Animals, Fungi, Genetically Modified, Gram-Positive Bacteria, Gram-Positive Bacterial Infections, In Situ Hybridization, M3i, Mycoses, Pattern Recognition, Peptide Hydrolases, Receptors, reichhart, ROMBY, Serine Endopeptidases, Signal Transduction, Toll-Like Receptors, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
In drosophila, molecular determinants from fungi and Gram-positive bacteria are detected by circulating pattern-recognition receptors. Published findings suggest that such pattern-recognition receptors activate as-yet-unidentified serine-protease cascades that culminate in the cleavage of Spätzle, the endogenous Toll receptor ligand, and trigger the immune response. We demonstrate here that the protease Grass defines a common activation cascade for the detection of fungi and Gram-positive bacteria mediated by pattern-recognition receptors. The serine protease Persephone, shown before to be specific for fungal detection in a cascade activated by secreted fungal proteases, was also required for the sensing of proteases elicited by bacteria in the hemolymph. Hence, Persephone defines a parallel proteolytic cascade activated by 'danger signals' such as abnormal proteolytic activities.
Romby P, Wagner E G
Exploring the complex world of RNA regulation Journal Article
In: Biol Cell, vol. 100, no. 1, pp. e1-3, 2008, ISBN: 18072939, (1768-322X (Electronic) Editorial).
Links | BibTeX | Tags: ROMBY, Unité ARN
@article{,
title = {Exploring the complex world of RNA regulation},
author = {P Romby and E G Wagner},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18072939},
isbn = {18072939},
year = {2008},
date = {2008-01-01},
journal = {Biol Cell},
volume = {100},
number = {1},
pages = {e1-3},
note = {1768-322X (Electronic)
Editorial},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Marzi S, Fechter P, Chevalier C, Romby P, Geissmann T
RNA switches regulate initiation of translation in bacteria Journal Article
In: Biol Chem, vol. 389, no. 5, pp. 585-598, 2008, ISBN: 18953726, (1431-6730 (Print) Journal Article Research Support, Non-U.S. Gov't Review).
Abstract | Links | BibTeX | Tags: Animals Bacteria/*genetics Genes, Bacterial/genetics/*immunology RNA, Messenger/biosynthesis/genetics Ribosomes/immunology, ROMBY, Switch/genetics/*immunology Humans Peptide Chain Initiation, Translational/genetics/*immunology Protein Biosynthesis/genetics/*immunology RNA, Unité ARN
@article{,
title = {RNA switches regulate initiation of translation in bacteria},
author = {S Marzi and P Fechter and C Chevalier and P Romby and T Geissmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18953726},
isbn = {18953726},
year = {2008},
date = {2008-01-01},
journal = {Biol Chem},
volume = {389},
number = {5},
pages = {585-598},
abstract = {A large variety of RNA-based mechanisms have been uncovered in all living organisms to regulate gene expression in response to internal and external changes, and to rapidly adapt cell growth in response to these signals. In bacteria, structural elements in the 5' leader regions of mRNAs have direct effects on translation initiation of the downstream coding sequences. The docking and unfolding of these mRNAs on the 30S subunit are critical steps in the initiation process directly modulating and timing translation. Structural elements can also undergo conformational changes in response to environmental cues (i.e., temperature sensors) or upon binding of a variety of trans-acting factors, such as metabolites, non-coding RNAs or regulatory proteins. These RNA switches can temporally regulate translation, leading either to repression or to activation of protein synthesis.},
note = {1431-6730 (Print)
Journal Article
Research Support, Non-U.S. Gov't
Review},
keywords = {Animals Bacteria/*genetics Genes, Bacterial/genetics/*immunology RNA, Messenger/biosynthesis/genetics Ribosomes/immunology, ROMBY, Switch/genetics/*immunology Humans Peptide Chain Initiation, Translational/genetics/*immunology Protein Biosynthesis/genetics/*immunology RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
A large variety of RNA-based mechanisms have been uncovered in all living organisms to regulate gene expression in response to internal and external changes, and to rapidly adapt cell growth in response to these signals. In bacteria, structural elements in the 5' leader regions of mRNAs have direct effects on translation initiation of the downstream coding sequences. The docking and unfolding of these mRNAs on the 30S subunit are critical steps in the initiation process directly modulating and timing translation. Structural elements can also undergo conformational changes in response to environmental cues (i.e., temperature sensors) or upon binding of a variety of trans-acting factors, such as metabolites, non-coding RNAs or regulatory proteins. These RNA switches can temporally regulate translation, leading either to repression or to activation of protein synthesis.
Fechter P, Romby P
Footprinting Book Chapter
In: Muller, S (Ed.): Nucleic Acids from A to Z: a concise encyclopedia, pp. 109, WILEY-VCH Verlag GmbH & Co, 2008.
Links | BibTeX | Tags: ROMBY, Unité ARN
@inbook{,
title = {Footprinting},
author = {P Fechter and P Romby},
editor = {S Muller},
url = {http://books.google.fr/books?id=4xOLLuqKrFgC&pg=PA13&hl=fr&source=gbs_toc_r&cad=4#v=onepage&q&f=false},
doi = {10.1002/9783527622528.ch2},
year = {2008},
date = {2008-01-01},
booktitle = {Nucleic Acids from A to Z: a concise encyclopedia},
pages = {109},
publisher = {WILEY-VCH Verlag GmbH & Co},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Fechter P, Romby P
Chemical and enzymatic structure mapping of RNAs Book Chapter
In: Muller, S (Ed.): Nucleic Acids from A to Z: a concise encyclopedia, pp. 41-43, WILEY-VCH Verlag GmbH & Co, 2008.
Links | BibTeX | Tags: ROMBY, Unité ARN
@inbook{,
title = {Chemical and enzymatic structure mapping of RNAs},
author = {P Fechter and P Romby},
editor = {S Muller},
url = {http://books.google.fr/books?id=4xOLLuqKrFgC&printsec=frontcover&dq=inauthor:%22Sabine+M%C3%BCller%22&hl=fr&sa=X&ei=K2KNT-CQFtDf8QO9qaDJCw&ved=0CDcQ6AEwAQ#v=onepage&q&f=false},
year = {2008},
date = {2008-01-01},
booktitle = {Nucleic Acids from A to Z: a concise encyclopedia},
pages = {41-43},
publisher = {WILEY-VCH Verlag GmbH & Co},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Chevalier C, Huntzinger E, Fechter P, Boisset S, Vandenesch F, Romby P, Geissmann T
Staphylococcus aureus endoribonuclease III purification and properties Journal Article
In: Methods Enzymol, vol. 447, pp. 309-327, 2008, ISBN: 19161850, (1557-7988 (Electronic) Journal Article Research Support, Non-U.S. Gov't).
Abstract | Links | BibTeX | Tags: ROMBY, Unité ARN
@article{,
title = {Staphylococcus aureus endoribonuclease III purification and properties},
author = {C Chevalier and E Huntzinger and P Fechter and S Boisset and F Vandenesch and P Romby and T Geissmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19161850},
isbn = {19161850},
year = {2008},
date = {2008-01-01},
journal = {Methods Enzymol},
volume = {447},
pages = {309-327},
abstract = {Staphylococcus aureus ribonuclease III (Sa-RNase III) belongs to the enzyme family known to process double-stranded RNAs consisting of two turns of the RNA helix. Although the enzyme is thought to play a role in ribosomal RNA processing and gene regulation, the deletion of the rnc gene in S. aureus does not affect cell growth in rich medium. S. aureus RNase III acts in concert with regulatory RNAIII to repress the expression of several mRNAs encoding virulence factors. The action of the RNase is most likely to initiate the degradation of repressed mRNAs leading to an irreversible repression. In this chapter, we describe the overexpression and purification of recombinant RNase III from S. aureus, and we show that its biochemical properties are similar to the orthologous enzyme from Escherichia coli. Both enzymes similarly recognize and cleave different RNA substrates and RNA-mRNA duplexes.},
note = {1557-7988 (Electronic)
Journal Article
Research Support, Non-U.S. Gov't},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Staphylococcus aureus ribonuclease III (Sa-RNase III) belongs to the enzyme family known to process double-stranded RNAs consisting of two turns of the RNA helix. Although the enzyme is thought to play a role in ribosomal RNA processing and gene regulation, the deletion of the rnc gene in S. aureus does not affect cell growth in rich medium. S. aureus RNase III acts in concert with regulatory RNAIII to repress the expression of several mRNAs encoding virulence factors. The action of the RNase is most likely to initiate the degradation of repressed mRNAs leading to an irreversible repression. In this chapter, we describe the overexpression and purification of recombinant RNase III from S. aureus, and we show that its biochemical properties are similar to the orthologous enzyme from Escherichia coli. Both enzymes similarly recognize and cleave different RNA substrates and RNA-mRNA duplexes.
Simonetti A, Marzi S, Myasnikov A G, Fabbretti A, Yusupov M, Gualerzi C O, Klaholz B P
Structure of the 30S translation initiation complex Journal Article
In: Nature, vol. 455, no. 7211, pp. 416-420, 2008, ISBN: 18758445, (1476-4687 (Electronic) Journal Article Research Support, Non-U.S. Gov't).
Abstract | Links | BibTeX | Tags: Cryoelectron Microscopy Crystallography, Messenger/chemistry/genetics/metabolism RNA, Met/chemistry/genetics/metabolism/ultrastructure Ribosome Subunits/chemistry/metabolism/ultrastructure Ribosomes/chemistry/*metabolism/*ultrastructure Thermus thermophilus/*enzymology/genetics/*ultrastructure, Molecular Multiprotein Complexes/*chemistry/genetics/metabolism/*ultrastructure *Peptide Chain Initiation, ROMBY, Transfer, Translational Prokaryotic Initiation Factor-1/chemistry/genetics/metabolism/ultrastructure Prokaryotic Initiation Factor-2/chemistry/genetics/metabolism/ultrastructure Protein Conformation RNA, Unité ARN, X-Ray Guanosine Triphosphate/chemistry/metabolism Models
@article{,
title = {Structure of the 30S translation initiation complex},
author = {A Simonetti and S Marzi and A G Myasnikov and A Fabbretti and M Yusupov and C O Gualerzi and B P Klaholz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18758445},
isbn = {18758445},
year = {2008},
date = {2008-01-01},
journal = {Nature},
volume = {455},
number = {7211},
pages = {416-420},
abstract = {Translation initiation, the rate-limiting step of the universal process of protein synthesis, proceeds through sequential, tightly regulated steps. In bacteria, the correct messenger RNA start site and the reading frame are selected when, with the help of initiation factors IF1, IF2 and IF3, the initiation codon is decoded in the peptidyl site of the 30S ribosomal subunit by the fMet-tRNA(fMet) anticodon. This yields a 30S initiation complex (30SIC) that is an intermediate in the formation of the 70S initiation complex (70SIC) that occurs on joining of the 50S ribosomal subunit to the 30SIC and release of the initiation factors. The localization of IF2 in the 30SIC has proved to be difficult so far using biochemical approaches, but could now be addressed using cryo-electron microscopy and advanced particle separation techniques on the basis of three-dimensional statistical analysis. Here we report the direct visualization of a 30SIC containing mRNA, fMet-tRNA(fMet) and initiation factors IF1 and GTP-bound IF2. We demonstrate that the fMet-tRNA(fMet) is held in a characteristic and precise position and conformation by two interactions that contribute to the formation of a stable complex: one involves the transfer RNA decoding stem which is buried in the 30S peptidyl site, and the other occurs between the carboxy-terminal domain of IF2 and the tRNA acceptor end. The structure provides insights into the mechanism of 70SIC assembly and rationalizes the rapid activation of GTP hydrolysis triggered on 30SIC-50S joining by showing that the GTP-binding domain of IF2 would directly face the GTPase-activated centre of the 50S subunit.},
note = {1476-4687 (Electronic)
Journal Article
Research Support, Non-U.S. Gov't},
keywords = {Cryoelectron Microscopy Crystallography, Messenger/chemistry/genetics/metabolism RNA, Met/chemistry/genetics/metabolism/ultrastructure Ribosome Subunits/chemistry/metabolism/ultrastructure Ribosomes/chemistry/*metabolism/*ultrastructure Thermus thermophilus/*enzymology/genetics/*ultrastructure, Molecular Multiprotein Complexes/*chemistry/genetics/metabolism/*ultrastructure *Peptide Chain Initiation, ROMBY, Transfer, Translational Prokaryotic Initiation Factor-1/chemistry/genetics/metabolism/ultrastructure Prokaryotic Initiation Factor-2/chemistry/genetics/metabolism/ultrastructure Protein Conformation RNA, Unité ARN, X-Ray Guanosine Triphosphate/chemistry/metabolism Models},
pubstate = {published},
tppubtype = {article}
}
Translation initiation, the rate-limiting step of the universal process of protein synthesis, proceeds through sequential, tightly regulated steps. In bacteria, the correct messenger RNA start site and the reading frame are selected when, with the help of initiation factors IF1, IF2 and IF3, the initiation codon is decoded in the peptidyl site of the 30S ribosomal subunit by the fMet-tRNA(fMet) anticodon. This yields a 30S initiation complex (30SIC) that is an intermediate in the formation of the 70S initiation complex (70SIC) that occurs on joining of the 50S ribosomal subunit to the 30SIC and release of the initiation factors. The localization of IF2 in the 30SIC has proved to be difficult so far using biochemical approaches, but could now be addressed using cryo-electron microscopy and advanced particle separation techniques on the basis of three-dimensional statistical analysis. Here we report the direct visualization of a 30SIC containing mRNA, fMet-tRNA(fMet) and initiation factors IF1 and GTP-bound IF2. We demonstrate that the fMet-tRNA(fMet) is held in a characteristic and precise position and conformation by two interactions that contribute to the formation of a stable complex: one involves the transfer RNA decoding stem which is buried in the 30S peptidyl site, and the other occurs between the carboxy-terminal domain of IF2 and the tRNA acceptor end. The structure provides insights into the mechanism of 70SIC assembly and rationalizes the rapid activation of GTP hydrolysis triggered on 30SIC-50S joining by showing that the GTP-binding domain of IF2 would directly face the GTPase-activated centre of the 50S subunit.
Simonetti A, Marzi S, Myasnikov A, Fabbretti A, Yusupov M, Gualerzi C, Klaholz B
2008.
Links | BibTeX | Tags: filter-binding assay, IF1, IF2, initiation factor purification, Ribosome, ROMBY, Thermus thermophilus, translation initiation, Unité ARN
@misc{,
title = {Purification of T. thermophilus translation initiation factors and characterization of the corresponding ribosome complexes by filter-binding assays},
author = {A Simonetti and S Marzi and A Myasnikov and A Fabbretti and M Yusupov and C Gualerzi and B Klaholz},
url = {https://protocolexchange.researchsquare.com/article/nprot-477/v1},
doi = {10.1038/nprot.2008.130},
year = {2008},
date = {2008-01-01},
keywords = {filter-binding assay, IF1, IF2, initiation factor purification, Ribosome, ROMBY, Thermus thermophilus, translation initiation, Unité ARN},
pubstate = {published},
tppubtype = {misc}
}
2007
Mandin P., Repoila F., Vergassola M., Geissmann T., Cossart P.
Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets Journal Article
In: Nucleic Acids Res, vol. 35, no. 3, pp. 962-74, 2007, (1362-4962 (Electronic) Journal Article Research Support, Non-U.S. Gov't).
Abstract | BibTeX | Tags: 5', Assay, Bacterial, Base, Biology, Computational, Data, DNA, Electrophoretic, Flanking, Genes, Genomics, Intergenic/chemistry, Listeria, Messenger/chemistry/*metabolism, Mobility, Molecular, monocytogenes/*genetics/metabolism, Region, RNA, ROMBY, Sequence, Shift, Untranslated/analysis/*genetics/metabolism
@article{,
title = {Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets},
author = { P. Mandin and F. Repoila and M. Vergassola and T. Geissmann and P. Cossart},
year = {2007},
date = {2007-01-01},
journal = {Nucleic Acids Res},
volume = {35},
number = {3},
pages = {962-74},
abstract = {To identify noncoding RNAs (ncRNAs) in the pathogenic bacterium Listeria monocytogenes, we analyzed the intergenic regions (IGRs) of strain EGD-e by in silico-based approaches. Among the twelve ncRNAs found, nine are novel and specific to the Listeria genus, and two of these ncRNAs are expressed in a growth-dependent manner. Three of the ncRNAs are transcribed in opposite direction to overlapping open reading frames (ORFs), suggesting that they act as antisense on the corresponding mRNAs. The other ncRNA genes appear as single transcription units. One of them displays five repeats of 29 nucleotides. Five of these new ncRNAs are absent from the non-pathogenic species L. innocua, raising the possibility that they might be involved in virulence. To predict mRNA targets of the ncRNAs, we developed a computational method based on thermodynamic pairing energies and known ncRNA-mRNA hybrids. Three ncRNAs, including one of the putative antisense ncRNAs, were predicted to have more than one mRNA targets. Several of them were shown to bind efficiently to the ncRNAs suggesting that our in silico approach could be used as a general tool to search for mRNA targets of ncRNAs.},
note = {1362-4962 (Electronic)
Journal Article
Research Support, Non-U.S. Gov't},
keywords = {5', Assay, Bacterial, Base, Biology, Computational, Data, DNA, Electrophoretic, Flanking, Genes, Genomics, Intergenic/chemistry, Listeria, Messenger/chemistry/*metabolism, Mobility, Molecular, monocytogenes/*genetics/metabolism, Region, RNA, ROMBY, Sequence, Shift, Untranslated/analysis/*genetics/metabolism},
pubstate = {published},
tppubtype = {article}
}
To identify noncoding RNAs (ncRNAs) in the pathogenic bacterium Listeria monocytogenes, we analyzed the intergenic regions (IGRs) of strain EGD-e by in silico-based approaches. Among the twelve ncRNAs found, nine are novel and specific to the Listeria genus, and two of these ncRNAs are expressed in a growth-dependent manner. Three of the ncRNAs are transcribed in opposite direction to overlapping open reading frames (ORFs), suggesting that they act as antisense on the corresponding mRNAs. The other ncRNA genes appear as single transcription units. One of them displays five repeats of 29 nucleotides. Five of these new ncRNAs are absent from the non-pathogenic species L. innocua, raising the possibility that they might be involved in virulence. To predict mRNA targets of the ncRNAs, we developed a computational method based on thermodynamic pairing energies and known ncRNA-mRNA hybrids. Three ncRNAs, including one of the putative antisense ncRNAs, were predicted to have more than one mRNA targets. Several of them were shown to bind efficiently to the ncRNAs suggesting that our in silico approach could be used as a general tool to search for mRNA targets of ncRNAs.
Marzi S, Romby P, Klaholz B P
[Twisting of mRNA reversibly blocks its translation by the ribosome] Journal Article
In: Med Sci (Paris), vol. 23, no. 10, pp. 881-3, 2007, ISBN: 17937901, (0767-0974 (Print) News).
Links | BibTeX | Tags: ROMBY, Unité ARN
@article{,
title = {[Twisting of mRNA reversibly blocks its translation by the ribosome]},
author = {S Marzi and P Romby and B P Klaholz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17937901},
isbn = {17937901},
year = {2007},
date = {2007-01-01},
journal = {Med Sci (Paris)},
volume = {23},
number = {10},
pages = {881-3},
note = {0767-0974 (Print)
News},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Marzi S, Myasnikov A G, Serganov A, Ehresmann C, Romby P, Yusupov M, Klaholz B P
Structured mRNAs regulate translation initiation by binding to the platform of the ribosome Journal Article
In: Cell, vol. 130, no. 6, pp. 1019-31, 2007, ISBN: 17889647, (0092-8674 (Print) Comparative Study Journal Article Research Support, Non-U.S. Gov't).
Abstract | Links | BibTeX | Tags: 5' Untranslated Regions Amino Acid Sequence Base Sequence Binding Sites Cryoelectron Microscopy Escherichia coli/*genetics/metabolism Escherichia coli Proteins/chemistry/genetics/*metabolism *Gene Expression Regulation, Amino Acid Sequence Homology, Bacterial Models, Bacterial/chemistry/*metabolism RNA, Messenger/*metabolism RNA, Molecular Molecular Sequence Data Mutation Nucleic Acid Conformation *Peptide Chain Initiation, Nucleic Acid Structural Homology, Protein Time Factors, Ribonucleic Acid Ribosomal Proteins/chemistry/genetics/*metabolism Ribosomes/chemistry/*metabolism/ultrastructure Sequence Homology, ROMBY, Transfer/metabolism Regulatory Sequences, Translational Protein Binding Protein Conformation RNA, Unité ARN
@article{,
title = {Structured mRNAs regulate translation initiation by binding to the platform of the ribosome},
author = {S Marzi and A G Myasnikov and A Serganov and C Ehresmann and P Romby and M Yusupov and B P Klaholz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17889647},
isbn = {17889647},
year = {2007},
date = {2007-01-01},
journal = {Cell},
volume = {130},
number = {6},
pages = {1019-31},
abstract = {Gene expression can be regulated at the level of initiation of protein biosynthesis via structural elements present at the 5' untranslated region of mRNAs. These folded mRNA segments may bind to the ribosome, thus blocking translation until the mRNA unfolds. Here, we report a series of cryo-electron microscopy snapshots of ribosomal complexes directly visualizing either the mRNA structure blocked by repressor protein S15 or the unfolded, active mRNA. In the stalled state, the folded mRNA prevents the start codon from reaching the peptidyl-tRNA (P) site inside the ribosome. Upon repressor release, the mRNA unfolds and moves into the mRNA channel allowing translation initiation. A comparative structure and sequence analysis suggests the existence of a universal stand-by site on the ribosome (the 30S platform) dedicated for binding regulatory 5' mRNA elements. Different types of mRNA structures may be accommodated during translation preinitiation and regulate gene expression by transiently stalling the ribosome.},
note = {0092-8674 (Print)
Comparative Study
Journal Article
Research Support, Non-U.S. Gov't},
keywords = {5' Untranslated Regions Amino Acid Sequence Base Sequence Binding Sites Cryoelectron Microscopy Escherichia coli/*genetics/metabolism Escherichia coli Proteins/chemistry/genetics/*metabolism *Gene Expression Regulation, Amino Acid Sequence Homology, Bacterial Models, Bacterial/chemistry/*metabolism RNA, Messenger/*metabolism RNA, Molecular Molecular Sequence Data Mutation Nucleic Acid Conformation *Peptide Chain Initiation, Nucleic Acid Structural Homology, Protein Time Factors, Ribonucleic Acid Ribosomal Proteins/chemistry/genetics/*metabolism Ribosomes/chemistry/*metabolism/ultrastructure Sequence Homology, ROMBY, Transfer/metabolism Regulatory Sequences, Translational Protein Binding Protein Conformation RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Gene expression can be regulated at the level of initiation of protein biosynthesis via structural elements present at the 5' untranslated region of mRNAs. These folded mRNA segments may bind to the ribosome, thus blocking translation until the mRNA unfolds. Here, we report a series of cryo-electron microscopy snapshots of ribosomal complexes directly visualizing either the mRNA structure blocked by repressor protein S15 or the unfolded, active mRNA. In the stalled state, the folded mRNA prevents the start codon from reaching the peptidyl-tRNA (P) site inside the ribosome. Upon repressor release, the mRNA unfolds and moves into the mRNA channel allowing translation initiation. A comparative structure and sequence analysis suggests the existence of a universal stand-by site on the ribosome (the 30S platform) dedicated for binding regulatory 5' mRNA elements. Different types of mRNA structures may be accommodated during translation preinitiation and regulate gene expression by transiently stalling the ribosome.
Maone E, Stefano M Di, Berardi A, Benelli D, Marzi S, Teana A La, Londei P
Functional analysis of the translation factor aIF2/5B in the thermophilic archaeon Sulfolobus solfataricus Journal Article
In: Mol Microbiol, vol. 65, no. 3, pp. 700-13, 2007, ISBN: 17608795, (0950-382X (Print) 0950-382X (Linking) Journal Article Research Support, Non-U.S. Gov't).
Abstract | Links | BibTeX | Tags: Archaeal Hydrolysis Peptide Chain Initiation, Met/metabolism Recombinant Fusion Proteins/metabolism Ribosomes/metabolism Sulfolobus solfataricus/genetics/*metabolism, Molecular Conserved Sequence GTP Phosphohydrolases/metabolism Gene Expression Genes, ROMBY, Secondary RNA, Transfer, Translational Peptide Initiation Factors/chemistry/isolation & purification/*metabolism Protein Binding *Protein Biosynthesis Protein Structure, Unité ARN
@article{,
title = {Functional analysis of the translation factor aIF2/5B in the thermophilic archaeon Sulfolobus solfataricus},
author = {E Maone and M Di Stefano and A Berardi and D Benelli and S Marzi and A La Teana and P Londei},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17608795},
doi = {10.1111/j.1365-2958.2007.05820.x},
isbn = {17608795},
year = {2007},
date = {2007-01-01},
journal = {Mol Microbiol},
volume = {65},
number = {3},
pages = {700-13},
abstract = {The protein IF2/eIF5B is one of the few translation initiation factors shared by all three primary domains of life (bacteria, archaea, eukarya). Despite its phylogenetic conservation, the factor is known to present marked functional divergences in the bacteria and the eukarya. In this work, the function in translation of the archaeal homologue (aIF2/5B) has been analysed in detail for the first time using a variety of in vitro assays. The results revealed that the protein is a ribosome-dependent GTPase which strongly stimulates the binding of initiator tRNA to the ribosomes even in the absence of other factors. In agreement with this finding, aIF2/5B enhances the translation of both leadered and leaderless mRNAs when expressed in a cell-free protein-synthesizing system. Moreover, the degree of functional conservation of the IF2-like factors in the archaeal and bacterial lineages was investigated by analysing the behaviour of 'chimeric' proteins produced by swapping domains between the Sulfolobus solfataricus aIF2/5B factor and the IF2 protein of the thermophilic bacterium Bacillus stearothermophilus. Beside evidencing similarities and differences between the archaeal and bacterial factors, these experiments have provided insight into the common role played by the IF2/5B proteins in all extant cells.},
note = {0950-382X (Print)
0950-382X (Linking)
Journal Article
Research Support, Non-U.S. Gov't},
keywords = {Archaeal Hydrolysis Peptide Chain Initiation, Met/metabolism Recombinant Fusion Proteins/metabolism Ribosomes/metabolism Sulfolobus solfataricus/genetics/*metabolism, Molecular Conserved Sequence GTP Phosphohydrolases/metabolism Gene Expression Genes, ROMBY, Secondary RNA, Transfer, Translational Peptide Initiation Factors/chemistry/isolation & purification/*metabolism Protein Binding *Protein Biosynthesis Protein Structure, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The protein IF2/eIF5B is one of the few translation initiation factors shared by all three primary domains of life (bacteria, archaea, eukarya). Despite its phylogenetic conservation, the factor is known to present marked functional divergences in the bacteria and the eukarya. In this work, the function in translation of the archaeal homologue (aIF2/5B) has been analysed in detail for the first time using a variety of in vitro assays. The results revealed that the protein is a ribosome-dependent GTPase which strongly stimulates the binding of initiator tRNA to the ribosomes even in the absence of other factors. In agreement with this finding, aIF2/5B enhances the translation of both leadered and leaderless mRNAs when expressed in a cell-free protein-synthesizing system. Moreover, the degree of functional conservation of the IF2-like factors in the archaeal and bacterial lineages was investigated by analysing the behaviour of 'chimeric' proteins produced by swapping domains between the Sulfolobus solfataricus aIF2/5B factor and the IF2 protein of the thermophilic bacterium Bacillus stearothermophilus. Beside evidencing similarities and differences between the archaeal and bacterial factors, these experiments have provided insight into the common role played by the IF2/5B proteins in all extant cells.
2006
Romby P, Vandenesch F, Wagner E G
The role of RNAs in the regulation of virulence-gene expression Journal Article
In: Curr Opin Microbiol, vol. 9, no. 2, pp. 229-236, 2006, ISBN: 16529986, (1369-5274 (Print) Journal Article).
Abstract | Links | BibTeX | Tags: ROMBY, Unité ARN
@article{,
title = {The role of RNAs in the regulation of virulence-gene expression},
author = {P Romby and F Vandenesch and E G Wagner},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16529986},
isbn = {16529986},
year = {2006},
date = {2006-01-01},
journal = {Curr Opin Microbiol},
volume = {9},
number = {2},
pages = {229-236},
abstract = {Bacterial pathogens sense their environment, and in response, virulence genes are induced or repressed through spatial and temporal regulation. They are also subjected to stress conditions, which require appropriate responses. Recent research has revealed that RNAs are key regulators in pathogens. Small RNAs regulate the translation and/or stability of mRNAs that encode virulence proteins, or proteins with roles in adaptive responses, which are triggered by environmental cues and stresses. In most cases, these small RNAs act directly on target RNAs by an antisense mechanism. Other small RNAs act indirectly, by sequestration of regulatory proteins. Direct sensing of environmental signals can occur through induced structural changes in mRNAs.},
note = {1369-5274 (Print)
Journal Article},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Bacterial pathogens sense their environment, and in response, virulence genes are induced or repressed through spatial and temporal regulation. They are also subjected to stress conditions, which require appropriate responses. Recent research has revealed that RNAs are key regulators in pathogens. Small RNAs regulate the translation and/or stability of mRNAs that encode virulence proteins, or proteins with roles in adaptive responses, which are triggered by environmental cues and stresses. In most cases, these small RNAs act directly on target RNAs by an antisense mechanism. Other small RNAs act indirectly, by sequestration of regulatory proteins. Direct sensing of environmental signals can occur through induced structural changes in mRNAs.
Geissmann T, Possedko M, Huntzinger E, Fechter P, Ehresmann C, Romby P
Regulatory RNAs as mediators of virulence gene expression in bacteria Book Chapter
In: Hofmann, F B (Ed.): Handbook of Experimental Pharmacology, vol. 173, pp. 9-43, Springer, 2006, ISBN: 16594609.
Abstract | Links | BibTeX | Tags: ROMBY, Unité ARN
@inbook{,
title = {Regulatory RNAs as mediators of virulence gene expression in bacteria},
author = {T Geissmann and M Possedko and E Huntzinger and P Fechter and C Ehresmann and P Romby},
editor = {F B Hofmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16594609},
isbn = {16594609},
year = {2006},
date = {2006-01-01},
booktitle = {Handbook of Experimental Pharmacology},
volume = {173},
pages = {9-43},
publisher = {Springer},
abstract = {Bacteria exploit functional diversity of RNAs in a wide range of regulatory mechanisms to control gene expression. In last few years, small RNA molecules have been discovered at a staggering rate in bacteria, mainly in Escherichia coli. While functions of many of these RNA molecules are still not known, several of them behave as key effectors of adaptive responses, such as environmental cue recognition, stress response, and virulence control. Most fascinating, perhaps, is the discovery that mRNAs behave as direct sensors of small molecules or of environmental cues. The astonishing diversity of RNA-dependent regulatory mechanisms is linked to the dynamic properties and versatility of the RNA structure. In this review, we relate several recent studies in different bacterial pathogens that illustrate the diverse roles of RNA to control virulence gene expression.},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Bacteria exploit functional diversity of RNAs in a wide range of regulatory mechanisms to control gene expression. In last few years, small RNA molecules have been discovered at a staggering rate in bacteria, mainly in Escherichia coli. While functions of many of these RNA molecules are still not known, several of them behave as key effectors of adaptive responses, such as environmental cue recognition, stress response, and virulence control. Most fascinating, perhaps, is the discovery that mRNAs behave as direct sensors of small molecules or of environmental cues. The astonishing diversity of RNA-dependent regulatory mechanisms is linked to the dynamic properties and versatility of the RNA structure. In this review, we relate several recent studies in different bacterial pathogens that illustrate the diverse roles of RNA to control virulence gene expression.
2005
Myasnikov A G, Marzi S, Simonetti A, Giuliodori A M, Gualerzi C O, Yusupova G, Yusupov M, Klaholz B P
Conformational transition of initiation factor 2 from the GTP- to GDP-bound state visualized on the ribosome Journal Article
In: Nat Struct Mol Biol, vol. 12, no. 12, pp. 1145-1149, 2005, ISBN: 16284619, (1545-9993 Journal article).
Abstract | Links | BibTeX | Tags: ROMBY, Unité ARN
@article{,
title = {Conformational transition of initiation factor 2 from the GTP- to GDP-bound state visualized on the ribosome},
author = {A G Myasnikov and S Marzi and A Simonetti and A M Giuliodori and C O Gualerzi and G Yusupova and M Yusupov and B P Klaholz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16284619},
isbn = {16284619},
year = {2005},
date = {2005-01-01},
journal = {Nat Struct Mol Biol},
volume = {12},
number = {12},
pages = {1145-1149},
abstract = {Initiation of protein synthesis is a universally conserved event that requires initiation factors IF1, IF2 and IF3 in prokaryotes. IF2 is a GTPase essential for binding initiator transfer RNA to the 30S ribosomal subunit and recruiting the 50S subunit into the 70S initiation complex. We present two cryo-EM structures of the assembled 70S initiation complex comprising mRNA, fMet-tRNA(fMet) and IF2 with either a non-hydrolyzable GTP analog or GDP. Transition from the GTP-bound to the GDP-bound state involves substantial conformational changes of IF2 and of the entire ribosome. In the GTP analog-bound state, IF2 interacts mostly with the 30S subunit and extends to the initiator tRNA in the peptidyl (P) site, whereas in the GDP-bound state IF2 steps back and adopts a 'ready-to-leave' conformation. Our data also provide insights into the molecular mechanism guiding release of IF1 and IF3.},
note = {1545-9993
Journal article},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Initiation of protein synthesis is a universally conserved event that requires initiation factors IF1, IF2 and IF3 in prokaryotes. IF2 is a GTPase essential for binding initiator transfer RNA to the 30S ribosomal subunit and recruiting the 50S subunit into the 70S initiation complex. We present two cryo-EM structures of the assembled 70S initiation complex comprising mRNA, fMet-tRNA(fMet) and IF2 with either a non-hydrolyzable GTP analog or GDP. Transition from the GTP-bound to the GDP-bound state involves substantial conformational changes of IF2 and of the entire ribosome. In the GTP analog-bound state, IF2 interacts mostly with the 30S subunit and extends to the initiator tRNA in the peptidyl (P) site, whereas in the GDP-bound state IF2 steps back and adopts a 'ready-to-leave' conformation. Our data also provide insights into the molecular mechanism guiding release of IF1 and IF3.
Huntzinger E, Winter F, Moine H, Ehresmann C, Romby P
Probing RNA structures with enzymes and chemicals in vitro and in vivo Book Chapter
In: Hartmann, R K; Bindereif, A; Schon, A; Westhof, E (Ed.): Handbook of RNA biochemistry, vol. 1, pp. 151-171, Wiley-Vch Verlag, 2005.
Links | BibTeX | Tags: ROMBY, ROMBY thiouridine 6-thioguanosine structures relationships variants, Unité ARN
@inbook{,
title = {Probing RNA structures with enzymes and chemicals in vitro and in vivo},
author = {E Huntzinger and F Winter and H Moine and C Ehresmann and P Romby},
editor = {R K Hartmann and A Bindereif and A Schon and E Westhof},
url = {http://onlinelibrary.wiley.com/doi/10.1002/9783527619504.ch10/summary},
year = {2005},
date = {2005-01-01},
booktitle = {Handbook of RNA biochemistry},
volume = {1},
pages = {151-171},
publisher = {Wiley-Vch Verlag},
keywords = {ROMBY, ROMBY thiouridine 6-thioguanosine structures relationships variants, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Huntzinger E, Boisset S, Saveanu C, Benito Y, Geissmann T, Namane A, Lina G, Etienne J, Ehresmann B, Ehresmann C, Jacquier A, Vandenesch F, Romby P
Staphylococcus aureus RNAIII and the endoribonuclease III coordinately regulate spa gene expression Journal Article
In: EMBO J, vol. 24, no. 4, pp. 824-835, 2005, ISBN: 15678100, (0261-4189 Journal Article).
Abstract | Links | BibTeX | Tags: ROMBY, Unité ARN
@article{,
title = {Staphylococcus aureus RNAIII and the endoribonuclease III coordinately regulate spa gene expression},
author = {E Huntzinger and S Boisset and C Saveanu and Y Benito and T Geissmann and A Namane and G Lina and J Etienne and B Ehresmann and C Ehresmann and A Jacquier and F Vandenesch and P Romby},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15678100},
isbn = {15678100},
year = {2005},
date = {2005-01-01},
journal = {EMBO J},
volume = {24},
number = {4},
pages = {824-835},
abstract = {Staphylococcus aureus RNAIII is one of the largest regulatory RNAs, which controls several virulence genes encoding exoproteins and cell-wall-associated proteins. One of the RNAIII effects is the repression of spa gene (coding for the surface protein A) expression. Here, we show that spa repression occurs not only at the transcriptional level but also by RNAIII-mediated inhibition of translation and degradation of the stable spa mRNA by the double-strand-specific endoribonuclease III (RNase III). The 3' end domain of RNAIII, partially complementary to the 5' part of spa mRNA, efficiently anneals to spa mRNA through an initial loop-loop interaction. Although this annealing is sufficient to inhibit in vitro the formation of the translation initiation complex, the coordinated action of RNase III is essential in vivo to degrade the mRNA and irreversibly arrest translation. Our results further suggest that RNase III is recruited for targeting the paired RNAs. These findings add further complexity to the expression of the S. aureus virulon.},
note = {0261-4189
Journal Article},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Staphylococcus aureus RNAIII is one of the largest regulatory RNAs, which controls several virulence genes encoding exoproteins and cell-wall-associated proteins. One of the RNAIII effects is the repression of spa gene (coding for the surface protein A) expression. Here, we show that spa repression occurs not only at the transcriptional level but also by RNAIII-mediated inhibition of translation and degradation of the stable spa mRNA by the double-strand-specific endoribonuclease III (RNase III). The 3' end domain of RNAIII, partially complementary to the 5' part of spa mRNA, efficiently anneals to spa mRNA through an initial loop-loop interaction. Although this annealing is sufficient to inhibit in vitro the formation of the translation initiation complex, the coordinated action of RNase III is essential in vivo to degrade the mRNA and irreversibly arrest translation. Our results further suggest that RNase III is recruited for targeting the paired RNAs. These findings add further complexity to the expression of the S. aureus virulon.
