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Lioliou E, Fechter P, Caldelari I, Jester BC, Dubrac S, Helfer AC, Boisset S, Vandenesch F, Romby P, Geissmann T. Erratum. RNA Biol 2017; 14:1827. [PMID: 29243975 DOI: 10.1080/15476286.2016.1184436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Efthimia Lioliou
- a Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC , 15 rue René Descartes, F-67084 Strasbourg , France
| | - Pierre Fechter
- a Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC , 15 rue René Descartes, F-67084 Strasbourg , France
| | - Isabelle Caldelari
- a Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC , 15 rue René Descartes, F-67084 Strasbourg , France
| | - Brian C Jester
- a Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC , 15 rue René Descartes, F-67084 Strasbourg , France
| | - Sarah Dubrac
- b Unité de Biologie des Bactéries pathogènes à Gram-positif, Institut Pasteur , 28 rue du Dr Roux, Paris , France
| | - Anne-Catherine Helfer
- a Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC , 15 rue René Descartes, F-67084 Strasbourg , France
| | - Sandrine Boisset
- c CIRI, Center International de Recherche en Infectiologie - Inserm U1111 - Université Lyon 1 - Ecole Normale Supérieure de Lyon - CNRS UMR5308 , 21 Avenue Tony Garnier, LYON cedex 07 , France
| | - François Vandenesch
- c CIRI, Center International de Recherche en Infectiologie - Inserm U1111 - Université Lyon 1 - Ecole Normale Supérieure de Lyon - CNRS UMR5308 , 21 Avenue Tony Garnier, LYON cedex 07 , France
| | - Pascale Romby
- a Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC , 15 rue René Descartes, F-67084 Strasbourg , France
| | - Thomas Geissmann
- c CIRI, Center International de Recherche en Infectiologie - Inserm U1111 - Université Lyon 1 - Ecole Normale Supérieure de Lyon - CNRS UMR5308 , 21 Avenue Tony Garnier, LYON cedex 07 , France
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Durand S, Braun F, Helfer AC, Romby P, Condon C. sRNA-mediated activation of gene expression by inhibition of 5'-3' exonucleolytic mRNA degradation. eLife 2017; 6. [PMID: 28436820 PMCID: PMC5419742 DOI: 10.7554/elife.23602] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 04/23/2017] [Indexed: 12/13/2022] Open
Abstract
Post-transcriptional control by small regulatory RNA (sRNA) is critical for rapid adaptive processes. sRNAs can directly modulate mRNA degradation in Proteobacteria without interfering with translation. However, Firmicutes have a fundamentally different set of ribonucleases for mRNA degradation and whether sRNAs can regulate the activity of these enzymes is an open question. We show that Bacillus subtilis RoxS, a major trans-acting sRNA shared with Staphylococus aureus, prevents degradation of the yflS mRNA, encoding a malate transporter. In the presence of malate, RoxS transiently escapes from repression by the NADH-sensitive transcription factor Rex and binds to the extreme 5'-end of yflS mRNA. This impairs the 5'-3' exoribonuclease activity of RNase J1, increasing the half-life of the primary transcript and concomitantly enhancing ribosome binding to increase expression of the transporter. Globally, the different targets regulated by RoxS suggest that it helps readjust the cellular NAD+/NADH balance when perturbed by different stimuli.
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Affiliation(s)
- Sylvain Durand
- UMR8261 CNRS, Université Paris Diderot (Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris, France
| | - Frédérique Braun
- UMR8261 CNRS, Université Paris Diderot (Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris, France
| | - Anne-Catherine Helfer
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, Strasbourg, France
| | - Pascale Romby
- UMR8261 CNRS, Université Paris Diderot (Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris, France.,Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, Strasbourg, France
| | - Ciarán Condon
- UMR8261 CNRS, Université Paris Diderot (Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris, France
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Morfoisse F, Tatin F, Hantelys F, Adoue A, Helfer AC, Cassant-Sourdy S, Pujol F, Gomez-Brouchet A, Ligat L, Lopez F, Pyronnet S, Courty J, Guillermet-Guibert J, Marzi S, Schneider RJ, Prats AC, Garmy-Susini BH. Nucleolin Promotes Heat Shock-Associated Translation of VEGF-D to Promote Tumor Lymphangiogenesis. Cancer Res 2016; 76:4394-405. [PMID: 27280395 DOI: 10.1158/0008-5472.can-15-3140] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 05/24/2016] [Indexed: 11/16/2022]
Abstract
The vascular endothelial growth factor VEGF-D promotes metastasis by inducing lymphangiogenesis and dilatation of the lymphatic vasculature, facilitating tumor cell extravasion. Here we report a novel level of control for VEGF-D expression at the level of protein translation. In human tumor cells, VEGF-D colocalized with eIF4GI and 4E-BP1, which can program increased initiation at IRES motifs on mRNA by the translational initiation complex. In murine tumors, the steady-state level of VEGF-D protein was increased despite the overexpression and dephosphorylation of 4E-BP1, which downregulates protein synthesis, suggesting the presence of an internal ribosome entry site (IRES) in the 5' UTR of VEGF-D mRNA. We found that nucleolin, a nucleolar protein involved in ribosomal maturation, bound directly to the 5'UTR of VEGF-D mRNA, thereby improving its translation following heat shock stress via IRES activation. Nucleolin blockade by RNAi-mediated silencing or pharmacologic inhibition reduced VEGF-D translation along with a subsequent constriction of lymphatic vessels in tumors. Our results identify nucleolin as a key regulator of VEGF-D expression, deepening understanding of lymphangiogenesis control during tumor formation. Cancer Res; 76(15); 4394-405. ©2016 AACR.
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Affiliation(s)
- Florent Morfoisse
- UMR 1048-1I2MC, Université de Toulouse, Inserm, UPS, Toulouse, France
| | - Florence Tatin
- UMR 1048-1I2MC, Université de Toulouse, Inserm, UPS, Toulouse, France
| | - Fransky Hantelys
- UMR 1048-1I2MC, Université de Toulouse, Inserm, UPS, Toulouse, France
| | - Aurelien Adoue
- UMR 1048-1I2MC, Université de Toulouse, Inserm, UPS, Toulouse, France
| | | | | | - Françoise Pujol
- UMR 1048-1I2MC, Université de Toulouse, Inserm, UPS, Toulouse, France
| | - Anne Gomez-Brouchet
- UMR 5089-IPBS, CNRS, UPS, Toulouse, France. Department of Pathology, IUCT-Oncopole, Toulouse, France
| | - Laetitia Ligat
- Pôle Technologique du CRCT - INSERM-UMR1037, Toulouse, France
| | - Frederic Lopez
- Pôle Technologique du CRCT - INSERM-UMR1037, Toulouse, France
| | | | - Jose Courty
- Laboratoire CRRET Laboratory, Université Paris EST Créteil, Créteil, France
| | | | - Stefano Marzi
- IBMC-CNRS, Université de Strasbourg, Strasbourg, France
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Mollerup MS, Ross JA, Helfer AC, Meistrup K, Romby P, Kallipolitis BH. Two novel members of the LhrC family of small RNAs in Listeria monocytogenes with overlapping regulatory functions but distinctive expression profiles. RNA Biol 2016; 13:895-915. [PMID: 27400116 DOI: 10.1080/15476286.2016.1208332] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Multicopy small RNAs (sRNAs) have gained recognition as an important feature of bacterial gene regulation. In the human pathogen Listeria monocytogenes, 5 homologous sRNAs, called LhrC1-5, control gene expression by base pairing to target mRNAs though 3 conserved UCCC motifs common to all 5 LhrCs. We show here that the sRNAs Rli22 and Rli33-1 are structurally and functionally related to LhrC1-5, expanding the LhrC family to 7 members, which makes it the largest multicopy sRNA family reported so far. Rli22 and Rli33-1 both contain 2 UCCC motifs important for post-transcriptional repression of 3 LhrC target genes. One such target, oppA, encodes a virulence-associated oligo-peptide binding protein. Like LhrC1-5, Rli22 and Rli33-1 employ their UCCC motifs to recognize the Shine-Dalgarno region of oppA mRNA and prevent formation of the ribosomal complex, demonstrating that the 7 sRNAs act in a functionally redundant manner. However, differential expression profiles of the sRNAs under infection-relevant conditions suggest that they might also possess non-overlapping functions. Collectively, this makes the LhrC family a unique case for studying the purpose of sRNA multiplicity in the context of bacterial virulence.
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Affiliation(s)
- Maria Storm Mollerup
- a Department of Biochemistry and Molecular Biology , University of Southern Denmark , Odense , Denmark
| | - Joseph Andrew Ross
- a Department of Biochemistry and Molecular Biology , University of Southern Denmark , Odense , Denmark
| | - Anne-Catherine Helfer
- b Architecture et Réactivité de l´ARN, Université de Strasbourg, CNRS, IBMC , Strasbourg , France
| | - Kristine Meistrup
- a Department of Biochemistry and Molecular Biology , University of Southern Denmark , Odense , Denmark
| | - Pascale Romby
- b Architecture et Réactivité de l´ARN, Université de Strasbourg, CNRS, IBMC , Strasbourg , France
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Lioliou E, Fechter P, Caldelari I, Jester BC, Dubrac S, Helfer AC, Boisset S, Vandenesch F, Romby P, Geissmann T. Various checkpoints prevent the synthesis of Staphylococcus aureus peptidoglycan hydrolase LytM in the stationary growth phase. RNA Biol 2016; 13:427-40. [PMID: 26901414 DOI: 10.1080/15476286.2016.1153209] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
In Staphylococcus aureus, peptidoglycan metabolism plays a role in the host inflammatory response and pathogenesis. Transcription of the peptidoglycan hydrolases is activated by the essential 2-component system WalKR at low cell density. During stationary growth phase, WalKR is not active and transcription of the peptidoglycan hydrolase genes is repressed. In this work, we studied regulation of expression of the glycylglycine endopeptidase LytM. We show that, in addition to the transcriptional regulation mediated by WalKR, the synthesis of LytM is negatively controlled by a unique mechanism at the stationary growth phase. We have identified 2 different mRNAs encoding lytM, which vary in the length of their 5' untranslated (5'UTR) regions. LytM is predominantly produced from the WalKR-regulated mRNA transcript carrying a short 5'UTR. The lytM mRNA is also transcribed as part of a polycistronic operon with the upstream SA0264 gene and is constitutively expressed. Although SA0264 protein can be synthesized from the longer operon transcript, lytM cannot be translated because its ribosome-binding site is sequestered into a translationally inactive secondary structure. In addition, the effector of the agr system, RNAIII, can inhibit translation of lytM present on the operon without altering the transcript level but does not have an effect on the translation of the upstream gene. We propose that this dual regulation of lytM expression, at the transcriptional and post-transcriptional levels, contributes to prevent cell wall damage during the stationary phase of growth.
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Affiliation(s)
- Efthimia Lioliou
- a Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC , 15 rue René Descartes, Strasbourg , France
| | - Pierre Fechter
- a Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC , 15 rue René Descartes, Strasbourg , France
| | - Isabelle Caldelari
- a Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC , 15 rue René Descartes, Strasbourg , France
| | - Brian C Jester
- b Institute of Systems and Synthetic Biology, University of Evry-Val-d'Essonne, CNRS FRE3561 , Evry , France
| | - Sarah Dubrac
- c Unité de Biologie des Bactéries pathogènes à Gram-positif, Institut Pasteur , 28 rue du Dr Roux, Paris , France
| | - Anne-Catherine Helfer
- a Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC , 15 rue René Descartes, Strasbourg , France
| | - Sandrine Boisset
- d CIRI, Center International de Recherche en Infectiologie - Inserm U1111 - Université Lyon 1 - Ecole Normale Supérieure de Lyon - CNRS UMR5308 , 21 Avenue Tony Garnier, LYON cedex 07 , France
| | - François Vandenesch
- d CIRI, Center International de Recherche en Infectiologie - Inserm U1111 - Université Lyon 1 - Ecole Normale Supérieure de Lyon - CNRS UMR5308 , 21 Avenue Tony Garnier, LYON cedex 07 , France
| | - Pascale Romby
- a Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC , 15 rue René Descartes, Strasbourg , France
| | - Thomas Geissmann
- d CIRI, Center International de Recherche en Infectiologie - Inserm U1111 - Université Lyon 1 - Ecole Normale Supérieure de Lyon - CNRS UMR5308 , 21 Avenue Tony Garnier, LYON cedex 07 , France
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Durand S, Braun F, Lioliou E, Romilly C, Helfer AC, 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. PLoS Genet 2015; 11:e1004957. [PMID: 25643072 PMCID: PMC4409812 DOI: 10.1371/journal.pgen.1004957] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 12/15/2014] [Indexed: 11/18/2022] Open
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. Bacteria have evolved various strategies to continually monitor the redox state of the internal and external environments to prevent cell damage and/or to protect them from host defense mechanisms. These signals modify the expression of genes, allowing bacteria to adapt to altered redox environments and to maintain homeostasis. Studies in Enterobacteriaceae have shown that sRNAs play central roles in adaptation to oxidative stress. We show here that the conserved sRNA, RoxS is induced by the presence of nitric oxide (NO) in the medium, through the ResDE and SrrAB two-component systems of Bacillus subtilis and Staphylococcus aureus, respectively. B. subtilis RoxS regulates functions related to oxidation-reduction reactions and acts as an antisense RNA to control translation initiation and the degradation of ppnKB mRNA, encoding an NAD+/NADH kinase. Interestingly, RNase Y processes the 5′ end of the RoxS sRNA leading to a truncated sRNA that in turn interacts more efficiently with a second target, the sucCD mRNA, encoding succinyl-CoA synthase. Taken together this work shows that RoxS is part of a complex regulatory network that allows the cell to sense and respond to redox perturbations, and revealed a novel process that allows an expansion of the repertoire of sRNA targets.
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Affiliation(s)
- Sylvain Durand
- CNRS FRE 3630 (affiliated with Univ. Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris, France
| | - Frédérique Braun
- CNRS FRE 3630 (affiliated with Univ. Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris, France
| | - Efthimia Lioliou
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | - Cédric Romilly
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | - Anne-Catherine Helfer
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | - Laurianne Kuhn
- Plateforme Protéomique Esplanade, IBMC, Strasbourg, France
| | - Noé Quittot
- Mathématique Informatique et Génome, INRA UR1077, Jouy en Josas, France
| | - Pierre Nicolas
- Mathématique Informatique et Génome, INRA UR1077, Jouy en Josas, France
| | - Pascale Romby
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
- * E-mail: (CC); (PR)
| | - Ciarán Condon
- CNRS FRE 3630 (affiliated with Univ. Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris, France
- * E-mail: (CC); (PR)
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Morfoisse F, Kuchnio A, Frainay C, Gomez-Brouchet A, Delisle MB, Marzi S, Helfer AC, Hantelys F, Pujol F, Guillermet-Guibert J, Bousquet C, Dewerchin M, Pyronnet S, Prats AC, Carmeliet P, Garmy-Susini B. Hypoxia induces VEGF-C expression in metastatic tumor cells via a HIF-1α-independent translation-mediated mechanism. Cell Rep 2014; 6:155-67. [PMID: 24388748 DOI: 10.1016/j.celrep.2013.12.011] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 10/28/2013] [Accepted: 12/06/2013] [Indexed: 01/04/2023] Open
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.
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Affiliation(s)
- Florent Morfoisse
- Inserm, U1037, 31432 Toulouse, France; Université de Toulouse, UPS, Cancer Research Center of Toulouse, Equipe Labellisee Ligue Contre le Cancer and Laboratoire d'Excellence Toulouse Cancer, 31432 Toulouse, France
| | - Anna Kuchnio
- Vesalius Research Center, VIB, University of Leuven, 3000 Leuven, Belgium
| | - Clement Frainay
- Inserm, U1037, 31432 Toulouse, France; Université de Toulouse, UPS, Cancer Research Center of Toulouse, Equipe Labellisee Ligue Contre le Cancer and Laboratoire d'Excellence Toulouse Cancer, 31432 Toulouse, France
| | - Anne Gomez-Brouchet
- Inserm, U1037, 31432 Toulouse, France; Université de Toulouse, UPS, Cancer Research Center of Toulouse, Equipe Labellisee Ligue Contre le Cancer and Laboratoire d'Excellence Toulouse Cancer, 31432 Toulouse, France
| | - Marie-Bernadette Delisle
- Inserm, U1037, 31432 Toulouse, France; Université de Toulouse, UPS, Cancer Research Center of Toulouse, Equipe Labellisee Ligue Contre le Cancer and Laboratoire d'Excellence Toulouse Cancer, 31432 Toulouse, France
| | - Stefano Marzi
- UPR 9002 CNRS-ARN, Université De Strasbourg, IBMC, 67084 Strasbourg, France
| | | | - Fransky Hantelys
- Université de Toulouse, UPS, TRADGENE, EA4554, 31432 Toulouse, France
| | - Francoise Pujol
- Université de Toulouse, UPS, TRADGENE, EA4554, 31432 Toulouse, France
| | - Julie Guillermet-Guibert
- Inserm, U1037, 31432 Toulouse, France; Université de Toulouse, UPS, Cancer Research Center of Toulouse, Equipe Labellisee Ligue Contre le Cancer and Laboratoire d'Excellence Toulouse Cancer, 31432 Toulouse, France
| | - Corinne Bousquet
- Inserm, U1037, 31432 Toulouse, France; Université de Toulouse, UPS, Cancer Research Center of Toulouse, Equipe Labellisee Ligue Contre le Cancer and Laboratoire d'Excellence Toulouse Cancer, 31432 Toulouse, France
| | - Mieke Dewerchin
- Vesalius Research Center, VIB, University of Leuven, 3000 Leuven, Belgium
| | - Stephane Pyronnet
- Inserm, U1037, 31432 Toulouse, France; Université de Toulouse, UPS, Cancer Research Center of Toulouse, Equipe Labellisee Ligue Contre le Cancer and Laboratoire d'Excellence Toulouse Cancer, 31432 Toulouse, France
| | | | - Peter Carmeliet
- Vesalius Research Center, VIB, University of Leuven, 3000 Leuven, Belgium
| | - Barbara Garmy-Susini
- Inserm, U1037, 31432 Toulouse, France; Université de Toulouse, UPS, Cancer Research Center of Toulouse, Equipe Labellisee Ligue Contre le Cancer and Laboratoire d'Excellence Toulouse Cancer, 31432 Toulouse, France.
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Lioliou E, Sharma CM, Altuvia Y, Caldelari I, Romilly C, Helfer AC, Margalit H, Romby P. In vivo mapping of RNA-RNA interactions in Staphylococcus aureus using the endoribonuclease III. Methods 2013; 63:135-43. [PMID: 23851283 DOI: 10.1016/j.ymeth.2013.06.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 06/26/2013] [Accepted: 06/27/2013] [Indexed: 01/09/2023] Open
Abstract
Ribonucleases play key roles in gene regulation and in the expression of virulence factors in Staphylococcus aureus. Among these enzymes, the double-strand specific endoribonuclease III (RNase III) is a key mediator of mRNA processing and degradation. Recently, we have defined, direct target sites for RNase III processing on a genome-wide scale in S. aureus. Our approach is based on deep sequencing of cDNA libraries obtained from RNAs isolated by in vivo co-immunoprecipitation with wild-type RNase III and two cleavage-defective mutants. The use of such catalytically inactivated enzymes, which still retain their RNA binding capacity, allows the identification of novel RNA substrates of RNase III. In this report, we will summarize the diversity of RNase III functions, discuss the advantages and the limitations of the approach, and how this strategy identifies novel mRNA targets of small non-coding RNAs in S. aureus.
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Affiliation(s)
- Efthimia Lioliou
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, F-67084 Strasbourg, France
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Lioliou E, Sharma CM, Caldelari I, Helfer AC, Fechter P, Vandenesch F, Vogel J, Romby P. Global regulatory functions of the Staphylococcus aureus endoribonuclease III in gene expression. PLoS Genet 2012; 8:e1002782. [PMID: 22761586 PMCID: PMC3386247 DOI: 10.1371/journal.pgen.1002782] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2011] [Accepted: 05/09/2012] [Indexed: 11/18/2022] Open
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. Control of mRNA stability is crucial for bacteria to survive and rapidly adapt to environmental changes and stress conditions. The molecular players and the degradation pathways involved in these adaptive processes are poorly understood in Staphylococcus aureus. The universally conserved double-strand-specific endoribonuclease III (RNase III) in S. aureus is known to repress the synthesis of several virulence factors and was recently implicated in genome-wide mRNA processing mediated by antisense transcripts. We present here the first global map of direct RNase III targets in S. aureus. Deep sequencing was used to identify RNAs associated with epitope-tagged wild-type RNase III and two catalytically impaired but binding-competent mutant proteins in vivo. Experimental validation revealed an unexpected variety of structured RNA transcripts as novel RNase III substrates. In addition to rRNA operon maturation, autoregulation, degradation of structured RNAs, and antisense regulation, we propose novel mechanisms by which RNase III increases mRNA translation. Overall, this study shows that RNase III has a broad function in gene regulation of S. aureus. We can now address more specifically the roles of this universally conserved enzyme in gene regulation in response to stress and during host infection.
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Affiliation(s)
- Efthimia Lioliou
- Architecture et Réactivité de l′ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | | | - Isabelle Caldelari
- Architecture et Réactivité de l′ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | - Anne-Catherine Helfer
- Architecture et Réactivité de l′ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | - Pierre Fechter
- Architecture et Réactivité de l′ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | - François Vandenesch
- Inserm U851, Centre National de Référence des Staphylocoques, Université de Lyon, Lyon, France
| | - Jörg Vogel
- Institut für Molekulare Infektionsbiologie, Würzburg, Germany
- * E-mail: (JV); (PR)
| | - Pascale Romby
- Architecture et Réactivité de l′ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
- * E-mail: (JV); (PR)
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Namour F, Helfer AC, Quadros EV, Alberto JM, Bibi HM, Orning L, Rosenblatt DS, Jean-Louis G. Transcobalamin deficiency due to activation of an intra exonic cryptic splice site. Br J Haematol 2003; 123:915-20. [PMID: 14632784 DOI: 10.1046/j.1365-2141.2003.04685.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Transcobalamin (TC), a vitamin B12 (cobalamin, Cbl) binding protein in plasma, promotes the cellular uptake of the vitamin by receptor-mediated endocytosis. Inherited TC deficiency is an autosomal recessive disorder characterized by megaloblastic anaemia caused by cellular vitamin B12 depletion. It may be accompanied by neurological complications, including a delay in psychomotor and mental development. This report describes three sisters with inherited TC deficiency resulting from a splicing defect in the TC gene. A point mutation was identified in intron 3 splice site of the TC gene that activates a cryptic splice site in exon 3. The transcript generated has an in-frame deletion of 81 nucleotides and the resulting truncated protein is unstable and not secreted by the cells. Until now, genetic studies have been reported in only five patients with TC deficiency and the molecular defect was different in each of them, which gives evidence for a genetic heterogeneity of the disease.
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Affiliation(s)
- Fares Namour
- Laboratoire de Pathologie Cellulaire et Moléculaire en Nutrition, EMI-INSERM 0014, Faculté de Médecine de Nancy, Cedex, France.
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