1
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Wulff T, Hahnke K, Lécrivain AL, Schmidt K, Ahmed-Begrich R, Finstermeier K, Charpentier E. Dynamics of diversified A-to-I editing in Streptococcus pyogenes is governed by changes in mRNA stability. Nucleic Acids Res 2024; 52:11234-11253. [PMID: 39087550 PMCID: PMC11472039 DOI: 10.1093/nar/gkae629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 07/01/2024] [Accepted: 07/23/2024] [Indexed: 08/02/2024] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing plays an important role in the post-transcriptional regulation of eukaryotic cell physiology. However, our understanding of the occurrence, function and regulation of A-to-I editing in bacteria remains limited. Bacterial mRNA editing is catalysed by the deaminase TadA, which was originally described to modify a single tRNA in Escherichia coli. Intriguingly, several bacterial species appear to perform A-to-I editing on more than one tRNA. Here, we provide evidence that in the human pathogen Streptococcus pyogenes, tRNA editing has expanded to an additional tRNA substrate. Using RNA sequencing, we identified more than 27 editing sites in the transcriptome of S. pyogenes SF370 and demonstrate that the adaptation of S. pyogenes TadA to a second tRNA substrate has also diversified the sequence context and recoding scope of mRNA editing. Based on the observation that editing is dynamically regulated in response to several infection-relevant stimuli, such as oxidative stress, we further investigated the underlying determinants of editing dynamics and identified mRNA stability as a key modulator of A-to-I editing. Overall, our findings reveal the presence and diversification of A-to-I editing in S. pyogenes and provide novel insights into the plasticity of the editome and its regulation in bacteria.
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Affiliation(s)
- Thomas F Wulff
- Max Planck Unit for the Science of Pathogens, 10117 Berlin, Germany
| | - Karin Hahnke
- Max Planck Unit for the Science of Pathogens, 10117 Berlin, Germany
| | | | - Katja Schmidt
- Max Planck Unit for the Science of Pathogens, 10117 Berlin, Germany
| | | | | | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, 10117 Berlin, Germany
- Institute for Biology, Humboldt University Berlin, 10115 Berlin, Germany
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2
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Le Scornet A, Jousselin A, Baumas K, Kostova G, Durand S, Poljak L, Barriot R, Coutant E, Pigearias R, Tejero G, Lootvoet J, Péllisier C, Munoz G, Condon C, Redder P. Critical factors for precise and efficient RNA cleavage by RNase Y in Staphylococcus aureus. PLoS Genet 2024; 20:e1011349. [PMID: 39088561 PMCID: PMC11321564 DOI: 10.1371/journal.pgen.1011349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 08/13/2024] [Accepted: 06/23/2024] [Indexed: 08/03/2024] Open
Abstract
Cellular processes require precise and specific gene regulation, in which continuous mRNA degradation is a major element. The mRNA degradation mechanisms should be able to degrade a wide range of different RNA substrates with high efficiency, but should at the same time be limited, to avoid killing the cell by elimination of all cellular RNA. RNase Y is a major endoribonuclease found in most Firmicutes, including Bacillus subtilis and Staphylococcus aureus. However, the molecular interactions that direct RNase Y to cleave the correct RNA molecules at the correct position remain unknown. In this work we have identified transcripts that are homologs in S. aureus and B. subtilis, and are RNase Y targets in both bacteria. Two such transcript pairs were used as models to show a functional overlap between the S. aureus and the B. subtilis RNase Y, which highlighted the importance of the nucleotide sequence of the RNA molecule itself in the RNase Y targeting process. Cleavage efficiency is driven by the primary nucleotide sequence immediately downstream of the cleavage site and base-pairing in a secondary structure a few nucleotides downstream. Cleavage positioning is roughly localised by the downstream secondary structure and fine-tuned by the nucleotide immediately upstream of the cleavage. The identified elements were sufficient for RNase Y-dependent cleavage, since the sequence elements from one of the model transcripts were able to convert an exogenous non-target transcript into a target for RNase Y.
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Affiliation(s)
- Alexandre Le Scornet
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Toulouse III–Paul Sabatier, Toulouse, France
| | - Ambre Jousselin
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Toulouse III–Paul Sabatier, Toulouse, France
| | - Kamila Baumas
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Toulouse III–Paul Sabatier, Toulouse, France
| | - Gergana Kostova
- UMR8261 CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Sylvain Durand
- UMR8261 CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Leonora Poljak
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Toulouse III–Paul Sabatier, Toulouse, France
| | - Roland Barriot
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Toulouse III–Paul Sabatier, Toulouse, France
| | - Eve Coutant
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Toulouse III–Paul Sabatier, Toulouse, France
| | - Romain Pigearias
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Toulouse III–Paul Sabatier, Toulouse, France
| | - Gabriel Tejero
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Toulouse III–Paul Sabatier, Toulouse, France
| | - Jonas Lootvoet
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Toulouse III–Paul Sabatier, Toulouse, France
| | - Céline Péllisier
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Toulouse III–Paul Sabatier, Toulouse, France
| | - Gladys Munoz
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Toulouse III–Paul Sabatier, Toulouse, France
| | - Ciarán Condon
- UMR8261 CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Peter Redder
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Toulouse III–Paul Sabatier, Toulouse, France
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3
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Meyer I, Volk M, Salto I, Moesser T, Chaoprasid P, Herbrüggen AS, Rohde M, Beckstette M, Heroven AK, Dersch P. RNase-mediated reprogramming of Yersinia virulence. PLoS Pathog 2024; 20:e1011965. [PMID: 39159284 PMCID: PMC11361751 DOI: 10.1371/journal.ppat.1011965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 08/29/2024] [Accepted: 07/15/2024] [Indexed: 08/21/2024] Open
Abstract
RNA degradation is an essential process that allows bacteria to regulate gene expression and has emerged as an important mechanism for controlling virulence. However, the individual contributions of RNases in this process are mostly unknown. Here, we tested the influence of 11 potential RNases in the intestinal pathogen Yersinia pseudotuberculosis on the expression of its type III secretion system (T3SS) and associated effectors (Yops) that are encoded on the Yersinia virulence plasmid. We found that exoribonuclease PNPase and endoribonuclease RNase III inhibit T3SS and yop gene transcription by repressing the synthesis of LcrF, the master activator of Yop-T3SS. Loss of both RNases led to an increase in lcrF mRNA levels. Our work indicates that PNPase exerts its influence via YopD, which accelerates lcrF mRNA degradation. Loss of RNase III, on the other hand, results in the downregulation of the CsrB and CsrC RNAs, thereby increasing the availability of active CsrA, which has been shown previously to enhance lcrF mRNA translation and stability. This CsrA-promoted increase of lcrF mRNA translation could be supported by other factors promoting the protein translation efficiency (e.g. IF-3, RimM, RsmG) that were also found to be repressed by RNase III. Transcriptomic profiling further revealed that Ysc-T3SS-mediated Yop secretion leads to global reprogramming of the Yersinia transcriptome with a massive shift of the expression from chromosomal to virulence plasmid-encoded genes. A similar reprogramming was also observed in the RNase III-deficient mutant under non-secretion conditions. Overall, our work revealed a complex control system where RNases orchestrate the expression of the T3SS/Yop machinery on multiple levels to antagonize phagocytic uptake and elimination by innate immune cells.
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Affiliation(s)
- Ines Meyer
- Institute for Infectiology, Center for Molecular Biology of Inflammation (ZMBE), University of Münster, Münster, Germany
| | - Marcel Volk
- Institute for Infectiology, Center for Molecular Biology of Inflammation (ZMBE), University of Münster, Münster, Germany
| | - Ileana Salto
- Institute for Infectiology, Center for Molecular Biology of Inflammation (ZMBE), University of Münster, Münster, Germany
| | - Theresa Moesser
- Institute for Infectiology, Center for Molecular Biology of Inflammation (ZMBE), University of Münster, Münster, Germany
| | - Paweena Chaoprasid
- Institute for Infectiology, Center for Molecular Biology of Inflammation (ZMBE), University of Münster, Münster, Germany
| | - Anne-Sophie Herbrüggen
- Institute for Infectiology, Center for Molecular Biology of Inflammation (ZMBE), University of Münster, Münster, Germany
| | - Manfred Rohde
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Michael Beckstette
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ann Kathrin Heroven
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Petra Dersch
- Institute for Infectiology, Center for Molecular Biology of Inflammation (ZMBE), University of Münster, Münster, Germany
- German Center for Infection Research (DZIF), Partner site HZI Braunschweig and associated site University of Münster, Münster, Germany
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4
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Broglia L, Le Rhun A, Charpentier E. Methodologies for bacterial ribonuclease characterization using RNA-seq. FEMS Microbiol Rev 2023; 47:fuad049. [PMID: 37656885 PMCID: PMC10503654 DOI: 10.1093/femsre/fuad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/06/2023] [Accepted: 08/23/2023] [Indexed: 09/03/2023] Open
Abstract
Bacteria adjust gene expression at the post-transcriptional level through an intricate network of small regulatory RNAs and RNA-binding proteins, including ribonucleases (RNases). RNases play an essential role in RNA metabolism, regulating RNA stability, decay, and activation. These enzymes exhibit species-specific effects on gene expression, bacterial physiology, and different strategies of target recognition. Recent advances in high-throughput RNA sequencing (RNA-seq) approaches have provided a better understanding of the roles and modes of action of bacterial RNases. Global studies aiming to identify direct targets of RNases have highlighted the diversity of RNase activity and RNA-based mechanisms of gene expression regulation. Here, we review recent RNA-seq approaches used to study bacterial RNases, with a focus on the methods for identifying direct RNase targets.
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Affiliation(s)
- Laura Broglia
- Max Planck Unit for the Science of Pathogens, D-10117 Berlin, Germany
- Center for Human Technologies, Istituto Italiano di Tecnologia, 16152 Genova, Italy
| | - Anaïs Le Rhun
- Max Planck Unit for the Science of Pathogens, D-10117 Berlin, Germany
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, D-10117 Berlin, Germany
- Institute for Biology, Humboldt University, D-10115 Berlin, Germany
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5
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Wang N, Li P, Cheng Y, Song H, Xu C. Stem-loop structures control mRNA processing of the cellulosomal cip-cel operon in Ruminiclostridium cellulolyticum. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:106. [PMID: 37386549 DOI: 10.1186/s13068-023-02357-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 06/11/2023] [Indexed: 07/01/2023]
Abstract
BACKGROUND Anaerobic, mesophilic, and cellulolytic Ruminiclostridium cellulolyticum produces an efficient cellulolytic extracellular complex named cellulosome, which consist of a non-catalytic multi-functional integrating subunit, organizing the various catalytic subunits into the complex. Main components of cellulosome were encoded by the cip-cel operon in R. cellulolyticum, and their stoichiometry is controlled by the mechanism of selective RNA processing and stabilization, which allows to confer each processed RNA portion from the cip-cel mRNA on different fates due to their stability and resolve the potential contradiction between the equimolar stoichiometry of transcripts with a within a transcription unit and the non-equimolar stoichiometry of subunits. RESULTS In this work, RNA processing events were found to occur at six intergenic regions (IRs) harboring stem-loop structures in cip-cel operon. These stem-loops not only stabilize processed transcripts at their both ends, but also act as cleavage signals specifically recognized by endoribonucleases. We further demonstrated that cleavage sites were often located downstream or 3' end of their associated stem-loops that could be classified into two types, with distinct GC-rich stems being required for RNA cleavage. However, the cleavage site in IR4 was found to be located upstream of the stem-loop, as determined by the bottom AT-pair region of this stem-loop, together with its upstream structure. Thus, our findings reveal the structural requirements for processing of cip-cel transcripts, which can be potentially used to control the stoichiometry of gene expression in an operon. CONCLUSIONS Our findings reveal that stem-loop structures acting as RNA cleavage signals not only can be recognized by endoribonucleases and determine the location of cleavage sites but also determine the stoichiometry of their flanking processed transcripts by controlling stability in cip-cel operon. These features represent a complexed regulation of cellulosome in the post-transcriptional level, which can be exploited for designing synthetic elements to control gene expression.
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Affiliation(s)
- Na Wang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, China-Australia Joint Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Ping Li
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Ying Cheng
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Houhui Song
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, China-Australia Joint Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.
| | - Chenggang Xu
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, China-Australia Joint Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006, Shanxi, China.
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6
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Abstract
The nasopharynx and the skin are the major oxygen-rich anatomical sites for colonization by the human pathogen Streptococcus pyogenes (group A Streptococcus [GAS]). To establish infection, GAS must survive oxidative stress generated during aerobic metabolism and the release of reactive oxygen species (ROS) by host innate immune cells. Glutathione is the major host antioxidant molecule, while GAS is glutathione auxotrophic. Here, we report the molecular characterization of the ABC transporter substrate binding protein GshT in the GAS glutathione salvage pathway. We demonstrate that glutathione uptake is critical for aerobic growth of GAS and that impaired import of glutathione induces oxidative stress that triggers enhanced production of the reducing equivalent NADPH. Our results highlight the interrelationship between glutathione assimilation, carbohydrate metabolism, virulence factor production, and innate immune evasion. Together, these findings suggest an adaptive strategy employed by extracellular bacterial pathogens to exploit host glutathione stores for their own benefit.
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7
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Chhabra S, Mandell ZF, Liu B, Babitzke P, Bechhofer DH. Analysis of mRNA Decay Intermediates in Bacillus subtilis 3' Exoribonuclease and RNA Helicase Mutant Strains. mBio 2022; 13:e0040022. [PMID: 35311531 PMCID: PMC9040804 DOI: 10.1128/mbio.00400-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 02/28/2022] [Indexed: 12/22/2022] Open
Abstract
The Bacillus subtilis genome encodes four 3' exoribonucleases: polynucleotide phosphorylase (PNPase), RNase R, RNase PH, and YhaM. Previous work showed that PNPase, encoded by the pnpA gene, is the major 3' exonuclease involved in mRNA turnover; in a pnpA deletion strain, numerous mRNA decay intermediates accumulate. Whether B. subtilis mRNA decay occurs in the context of a degradosome complex is controversial. In this study, global mapping of mRNA decay intermediate 3' ends within coding sequences was performed in strains that were either deleted for or had an inactivating point mutation in the pnpA gene. The patterns of 3'-end accumulation in these strains were highly similar, which may have implications for the role of a degradosome in mRNA decay. A comparison with mapped 3' ends in a strain lacking CshA, the major RNA helicase, indicated that many mRNAs require both PNPase and CshA for efficient decay. Transcriptome sequencing (RNA-seq) analysis of strains lacking RNase R suggested that this enzyme did not play a major role in mRNA turnover in the wild-type strain. Strains were constructed that contained only one of the four known 3' exoribonucleases. When RNase R was the only 3' exonuclease present, it was able to degrade a model mRNA efficiently, showing processive decay even through a strong stem-loop structure that inhibits PNPase processivity. Strains containing only RNase PH or only YhaM were also insensitive to this RNA secondary structure, suggesting the existence of another, as-yet-unidentified, 3' exoribonuclease. IMPORTANCE The ability to rapidly change bacterial gene expression programs in response to environmental conditions is highly dependent on the efficient turnover of mRNA. While much is known about the regulation of gene expression at the transcriptional and translational levels, much less is known about the intermediate step of mRNA decay. Here, we mapped the 3' ends of mRNA decay intermediates in strains that were missing the major 3' exoribonuclease PNPase or the RNA helicase CshA. We also assessed the roles of three other B. subtilis 3' exonucleases in the mRNA decay process. The data confirm the primary role of PNPase in mRNA turnover and suggest the involvement of one or more unknown RNases.
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Affiliation(s)
- Shivani Chhabra
- Icahn School of Medicine at Mount Sinai, Department of Pharmacological Sciences, New York, New York, USA
| | - Zachary F. Mandell
- The Pennsylvania State University, Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, University Park, Pennsylvania, USA
| | - Bo Liu
- Icahn School of Medicine at Mount Sinai, Department of Pharmacological Sciences, New York, New York, USA
| | - Paul Babitzke
- The Pennsylvania State University, Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, University Park, Pennsylvania, USA
| | - David H. Bechhofer
- Icahn School of Medicine at Mount Sinai, Department of Pharmacological Sciences, New York, New York, USA
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8
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Broglia L, Lécrivain AL, Renault TT, Hahnke K, Ahmed-Begrich R, Le Rhun A, Charpentier E. An RNA-seq based comparative approach reveals the transcriptome-wide interplay between 3'-to-5' exoRNases and RNase Y. Nat Commun 2020; 11:1587. [PMID: 32221293 PMCID: PMC7101322 DOI: 10.1038/s41467-020-15387-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 02/29/2020] [Indexed: 11/29/2022] Open
Abstract
RNA degradation is an essential process that allows bacteria to control gene expression and adapt to various environmental conditions. It is usually initiated by endoribonucleases (endoRNases), which produce intermediate fragments that are subsequently degraded by exoribonucleases (exoRNases). However, global studies of the coordinated action of these enzymes are lacking. Here, we compare the targetome of endoRNase Y with the targetomes of 3′-to-5′ exoRNases from Streptococcus pyogenes, namely, PNPase, YhaM, and RNase R. We observe that RNase Y preferentially cleaves after guanosine, generating substrate RNAs for the 3′-to-5′ exoRNases. We demonstrate that RNase Y processing is followed by trimming of the newly generated 3′ ends by PNPase and YhaM. Conversely, the RNA 5′ ends produced by RNase Y are rarely further trimmed. Our strategy enables the identification of processing events that are otherwise undetectable. Importantly, this approach allows investigation of the intricate interplay between endo- and exoRNases on a genome-wide scale. Bacterial RNA degradation is typically initiated by endoribonucleases and followed by exoribonucleases. Here the authors report the targetome of endoRNase Y in Streptococcus pyogenes, revealing the interplay between RNase Y and 3′-to-5′ exoribonuclease PNPase and YhaM.
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Affiliation(s)
- Laura Broglia
- Max Planck Unit for the Science of Pathogens, D-10117, Berlin, Germany.,Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, D-10117, Berlin, Germany.,Institute for Biology, Humboldt University, D-10115, Berlin, Germany
| | - Anne-Laure Lécrivain
- Max Planck Unit for the Science of Pathogens, D-10117, Berlin, Germany.,Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, D-10117, Berlin, Germany.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, S-90187, Umeå, Sweden
| | - Thibaud T Renault
- Max Planck Unit for the Science of Pathogens, D-10117, Berlin, Germany.,Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, D-10117, Berlin, Germany.,Institute for Biology, Humboldt University, D-10115, Berlin, Germany
| | - Karin Hahnke
- Max Planck Unit for the Science of Pathogens, D-10117, Berlin, Germany.,Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, D-10117, Berlin, Germany
| | - Rina Ahmed-Begrich
- Max Planck Unit for the Science of Pathogens, D-10117, Berlin, Germany.,Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, D-10117, Berlin, Germany
| | - Anaïs Le Rhun
- Max Planck Unit for the Science of Pathogens, D-10117, Berlin, Germany. .,Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, D-10117, Berlin, Germany.
| | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, D-10117, Berlin, Germany. .,Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, D-10117, Berlin, Germany. .,Institute for Biology, Humboldt University, D-10115, Berlin, Germany. .,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, S-90187, Umeå, Sweden.
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9
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Salze M, Muller C, Bernay B, Hartke A, Clamens T, Lesouhaitier O, Rincé A. Study of key RNA metabolism proteins in Enterococcus faecalis. RNA Biol 2020; 17:794-804. [PMID: 32070211 DOI: 10.1080/15476286.2020.1728103] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
The control of mRNA turnover is essential in bacteria to allow rapid adaptation, especially in opportunistic pathogen like Enterococcus faecalis. This mechanism involves RNase and DEAD-box helicases that are key elements in RNA processing and their associations form the degradosome with accessory proteins. In this study, we investigated the function of four RNases (J1, J2, Y and III) and three DEAD-box helicases (CshA, CshB, CshC) present in most Enterococci. The interactions of all these RNA metabolism actors were investigated in vitro, and the results are in accordance with a degradosome structure close to the one of Bacillus subtilis. At the physiological level, we showed that RNase J1 is essential, whereas RNases J2 and III have a role in cold, oxidative and bile salts stress response, and RNase Y in general fitness. Furthermore, RNases J2, Y and III mutants are affected in virulence in the Galleria mellonella infection model. Concerning DEAD-box helicases, all of them are involved in cold shock response. Since the ΔcshA mutant was the most stress impacted strain, we studied this DEAD-box helicase CshA in more detail. This showed that CshA autoregulates its own expression by binding to its mRNA 5'Unstranslated Region. Interestingly, CshC is also involved in the expression control of CshA by a hitherto unprecedented mechanism.
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Affiliation(s)
- Marine Salze
- Normandie Univ, UNICAEN, Unité De Recherche Risques Microbiens U2RM , Caen, France
| | - Cécile Muller
- Normandie Univ, UNICAEN, Unité De Recherche Risques Microbiens U2RM , Caen, France
| | - Benoit Bernay
- Proteogen Platform, Normandie Univ, UNICAEN, SFR ICORE , Caen, France
| | - Axel Hartke
- Normandie Univ, UNICAEN, Unité De Recherche Risques Microbiens U2RM , Caen, France
| | - Thomas Clamens
- Laboratoire de Microbiologie Signaux et Microenvironnement LMSM, Normandie Univ, University of Rouen , Evreux, France
| | - Olivier Lesouhaitier
- Laboratoire de Microbiologie Signaux et Microenvironnement LMSM, Normandie Univ, University of Rouen , Evreux, France
| | - Alain Rincé
- Normandie Univ, UNICAEN, Unité De Recherche Risques Microbiens U2RM , Caen, France
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10
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Rosinski-Chupin I, Sauvage E, Fouet A, Poyart C, Glaser P. Conserved and specific features of Streptococcus pyogenes and Streptococcus agalactiae transcriptional landscapes. BMC Genomics 2019; 20:236. [PMID: 30902048 PMCID: PMC6431027 DOI: 10.1186/s12864-019-5613-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 03/14/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The human pathogen Streptococcus pyogenes, or group A Streptococcus, is responsible for mild infections to life-threatening diseases. To facilitate the characterization of regulatory networks involved in the adaptation of this pathogen to its different environments and their evolution, we have determined the primary transcriptome of a serotype M1 S. pyogenes strain at single-nucleotide resolution and compared it with that of Streptococcus agalactiae, also from the pyogenic group of streptococci. RESULTS By using a combination of differential RNA-sequencing and oriented RNA-sequencing we have identified 892 transcription start sites (TSS) and 885 promoters in the S. pyogenes M1 strain S119. 8.6% of S. pyogenes mRNAs were leaderless, among which 81% were also classified as leaderless in S. agalactiae. 26% of S. pyogenes transcript 5' untranslated regions (UTRs) were longer than 60 nt. Conservation of long 5' UTRs with S. agalactiae allowed us to predict new potential regulatory sequences. In addition, based on the mapping of 643 transcript ends in the S. pyogenes strain S119, we constructed an operon map of 401 monocistrons and 349 operons covering 81.5% of the genome. One hundred fifty-six operons and 254 monocistrons retained the same organization, despite multiple genomic reorganizations between S. pyogenes and S. agalactiae. Genomic reorganization was found to more often go along with variable promoter sequences and 5' UTR lengths. Finally, we identified 117 putative regulatory RNAs, among which nine were regulated in response to magnesium concentration. CONCLUSIONS Our data provide insights into transcriptome evolution in pyogenic streptococci and will facilitate the analysis of genetic polymorphisms identified by comparative genomics in S. pyogenes.
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Affiliation(s)
- Isabelle Rosinski-Chupin
- Ecology and Evolution of Resistance to Antibiotics, Institut Pasteur-APHP-Université Paris Saclay, UMR3525 CNRS, Paris, France
| | - Elisabeth Sauvage
- Ecology and Evolution of Resistance to Antibiotics, Institut Pasteur-APHP-Université Paris Saclay, UMR3525 CNRS, Paris, France
| | - Agnès Fouet
- INSERM U1016, Institut Cochin, CNRS UMR 8104, Université Paris Descartes (UMR-S1016), Paris, France
- Centre Nationale de Référence des Streptocoques, Hôpitaux Universitaires Paris Centre, Cochin, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Claire Poyart
- INSERM U1016, Institut Cochin, CNRS UMR 8104, Université Paris Descartes (UMR-S1016), Paris, France
- Centre Nationale de Référence des Streptocoques, Hôpitaux Universitaires Paris Centre, Cochin, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Philippe Glaser
- Ecology and Evolution of Resistance to Antibiotics, Institut Pasteur-APHP-Université Paris Saclay, UMR3525 CNRS, Paris, France
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