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McQuail J, Matera G, Gräfenhan T, Bischler T, Haberkant P, Stein F, Vogel J, Wigneshweraraj S. Global Hfq-mediated RNA interactome of nitrogen starved Escherichia coli uncovers a conserved post-transcriptional regulatory axis required for optimal growth recovery. Nucleic Acids Res 2024; 52:2323-2339. [PMID: 38142457 PMCID: PMC10954441 DOI: 10.1093/nar/gkad1211] [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: 10/02/2023] [Revised: 11/17/2023] [Accepted: 12/20/2023] [Indexed: 12/26/2023] Open
Abstract
The RNA binding protein Hfq has a central role in the post-transcription control of gene expression in many bacteria. Numerous studies have mapped the transcriptome-wide Hfq-mediated RNA-RNA interactions in growing bacteria or bacteria that have entered short-term growth-arrest. To what extent post-transcriptional regulation underpins gene expression in growth-arrested bacteria remains unknown. Here, we used nitrogen (N) starvation as a model to study the Hfq-mediated RNA interactome as Escherichia coli enter, experience, and exit long-term growth arrest. We observe that the Hfq-mediated RNA interactome undergoes extensive changes during N starvation, with the conserved SdsR sRNA making the most interactions with different mRNA targets exclusively in long-term N-starved E. coli. Taking a proteomics approach, we reveal that in growth-arrested cells SdsR influences gene expression far beyond its direct mRNA targets. We demonstrate that the absence of SdsR significantly compromises the ability of the mutant bacteria to recover growth competitively from the long-term N-starved state and uncover a conserved post-transcriptional regulatory axis which underpins this process.
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Affiliation(s)
- Josh McQuail
- Section of Molecular Microbiology and Centre for Bacterial Resistance Biology, Faculty of Medicine, Imperial College London, UK
| | - Gianluca Matera
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
| | - Tom Gräfenhan
- Core Unit Systems Medicine, University of Würzburg, D-97080 Würzburg, Germany
| | - Thorsten Bischler
- Core Unit Systems Medicine, University of Würzburg, D-97080 Würzburg, Germany
| | - Per Haberkant
- Proteomics Core Facility, EMBL Heidelberg, D-69117,Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, D-69117,Heidelberg, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
- Institute for Molecular Infection Biology (IMIB), Faculty of Medicine, University of Würzburg, D-97080 Würzburg, Germany
| | - Sivaramesh Wigneshweraraj
- Section of Molecular Microbiology and Centre for Bacterial Resistance Biology, Faculty of Medicine, Imperial College London, UK
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2
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Identification of serine/threonine kinases that regulate metabolism and sporulation in Clostridium beijerinckii. Appl Microbiol Biotechnol 2022; 106:7563-7575. [DOI: 10.1007/s00253-022-12234-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 09/17/2022] [Accepted: 10/07/2022] [Indexed: 11/02/2022]
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Zhang A, Lebrun R, Espinosa L, Galinier A, Pompeo F. PrkA is an ATP-dependent protease that regulates sporulation in Bacillus subtilis. J Biol Chem 2022; 298:102436. [PMID: 36041628 PMCID: PMC9512850 DOI: 10.1016/j.jbc.2022.102436] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 11/18/2022] Open
Abstract
In Bacillus subtilis, sporulation is a sequential and highly regulated process. Phosphorylation events by histidine kinases are key points in the phosphorelay that initiates sporulation, but serine/threonine protein kinases also play important auxiliary roles in this regulation. PrkA has been proposed to be a serine protein kinase expressed during the initiation of sporulation and involved in this differentiation process. Additionally, the role of PrkA in sporulation has been previously proposed to be mediated via the transition phase regulator ScoC, which in turn regulates the transcriptional factor σK and its regulon. However, the kinase activity of PrkA has not been clearly demonstrated, and neither its autophosphorylation nor phosphorylated substrates have been unambiguously established in B. subtilis. We demonstrated here that PrkA regulation of ScoC is likely indirect. Following bioinformatic homology searches, we revealed sequence similarities of PrkA with the ATPases associated with diverse cellular activities ATP-dependent Lon protease family. Here, we showed that PrkA is indeed able to hydrolyze α-casein, an exogenous substrate of Lon proteases, in an ATP-dependent manner. We also showed that this ATP-dependent protease activity is essential for PrkA function in sporulation since mutation in the Walker A motif leads to a sporulation defect. Furthermore, we found that PrkA protease activity is tightly regulated by phosphorylation events involving one of the Ser/Thr protein kinases of B. subtilis, PrkC. Taken together, our results clarify the key role of PrkA in the complex process of B. subtilis sporulation.
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Affiliation(s)
- Ao Zhang
- Laboratoire de Chimie Bactérienne, UMR 7283, IMM, CNRS, Aix-Marseille Université, Marseille, France
| | - Régine Lebrun
- Plateforme Protéomique de l'IMM, Marseille Protéomique (MaP), CNRS FR 3479, Aix-Marseille Université, Marseille, France
| | - Leon Espinosa
- Laboratoire de Chimie Bactérienne, UMR 7283, IMM, CNRS, Aix-Marseille Université, Marseille, France
| | - Anne Galinier
- Laboratoire de Chimie Bactérienne, UMR 7283, IMM, CNRS, Aix-Marseille Université, Marseille, France
| | - Frédérique Pompeo
- Laboratoire de Chimie Bactérienne, UMR 7283, IMM, CNRS, Aix-Marseille Université, Marseille, France.
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4
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Overview of protein phosphorylation in bacteria with a main focus on unusual protein kinases in Bacillus subtilis. Res Microbiol 2021; 172:103871. [PMID: 34500011 DOI: 10.1016/j.resmic.2021.103871] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/12/2021] [Accepted: 07/22/2021] [Indexed: 12/21/2022]
Abstract
Protein phosphorylation is a post-translational modification that affects protein activity through the addition of a phosphate moiety by protein kinases or phosphotransferases. It occurs in all life forms. In addition to Hanks kinases found also in eukaryotes, bacteria encode membrane histidine kinases that, with their cognate response regulator, constitute two-component systems and phosphotransferases that phosphorylate proteins involved in sugar utilization on histidine and cysteine residues. In addition, they encode BY-kinases and arginine kinases that phosphorylate protein specifically on tyrosine and arginine residues respectively. They also possess unusual bacterial protein kinases illustrated here by examples from Bacillus subtilis.
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5
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Ye C, Lin H, Zhang M, Chen S, Yu X. Characterization and potential mechanisms of highly antibiotic tolerant VBNC Escherichia coli induced by low level chlorination. Sci Rep 2020; 10:1957. [PMID: 32029755 PMCID: PMC7005040 DOI: 10.1038/s41598-020-58106-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 01/08/2020] [Indexed: 12/29/2022] Open
Abstract
Escherichia coli is an important pathogenic indicator in drinking water. Viable but non-culturable (VBNC) E. coli induced by low level chlorination was found to have higher antibiotic tolerance. The emerging of VBNC bacteria in drinking water systems is posing challenges to the control of bio-safety. It is necessary to study the underlying mechanisms of VBNC state E. coli under actual residual chlorine condition of drinking water pipe network. In this study, we investigated the changes of morphology and gene expressions that might present such state. The results indicated that the size of VBNC E. coli was not remarkably changed or recovered culturability under favorable environmental conditions. Results from transcriptomic analysis revealed that the regulated genes related to fimbrial-like adhesin protein, putative periplasmic pilin chaperone, regulators of the transcriptional regulation, antibiotic resistance genes and stress-induced genes, rendering VBNC cells more tolerant to adverse environmental conditions. In total of 16 genes were significantly up-regulated under the VBNC state, including three genes encoding toxic protein (ygeG, ibsD, shoB), indicating that VBNC E. coil was still a threat to human. The work is of great relevance in the context of better understanding this poorly understood physiological state.
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Affiliation(s)
- Chengsong Ye
- College of the Environment&Ecology, Xiamen University, Xiamen, 361005, China
| | - Huirong Lin
- Department of Environmental Science and Engineering, College of Chemical Engineering, Huaqiao University, Xiamen, Fujian, 361021, China
| | - Menglu Zhang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Sheng Chen
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xin Yu
- College of the Environment&Ecology, Xiamen University, Xiamen, 361005, China. .,Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China.
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New insights into the adaptive transcriptional response to nitrogen starvation in Escherichia coli. Biochem Soc Trans 2018; 46:1721-1728. [PMID: 30514772 PMCID: PMC6299236 DOI: 10.1042/bst20180502] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/14/2018] [Accepted: 10/17/2018] [Indexed: 12/11/2022]
Abstract
Bacterial adaptive responses to biotic and abiotic stresses often involve large-scale reprogramming of the transcriptome. Since nitrogen is an essential component of the bacterial cell, the transcriptional basis of the adaptive response to nitrogen starvation has been well studied. The adaptive response to N starvation in Escherichia coli is primarily a 'scavenging response', which results in the transcription of genes required for the transport and catabolism of nitrogenous compounds. However, recent genome-scale studies have begun to uncover and expand some of the intricate regulatory complexities that underpin the adaptive transcriptional response to nitrogen starvation in E. coli The purpose of this review is to highlight some of these new developments.
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7
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Switzer A, Evangelopoulos D, Figueira R, de Carvalho LPS, Brown DR, Wigneshweraraj S. A novel regulatory factor affecting the transcription of methionine biosynthesis genes in Escherichia coli experiencing sustained nitrogen starvation. Microbiology (Reading) 2018; 164:1457-1470. [DOI: 10.1099/mic.0.000683] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Amy Switzer
- 1MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK
| | - Dimitrios Evangelopoulos
- 2Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Rita Figueira
- 1MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK
| | - Luiz Pedro S. de Carvalho
- 2Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Daniel R. Brown
- 1MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK
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8
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Price MN, Wetmore KM, Waters RJ, Callaghan M, Ray J, Liu H, Kuehl JV, Melnyk RA, Lamson JS, Suh Y, Carlson HK, Esquivel Z, Sadeeshkumar H, Chakraborty R, Zane GM, Rubin BE, Wall JD, Visel A, Bristow J, Blow MJ, Arkin AP, Deutschbauer AM. Mutant phenotypes for thousands of bacterial genes of unknown function. Nature 2018; 557:503-509. [PMID: 29769716 DOI: 10.1038/s41586-018-0124-0] [Citation(s) in RCA: 291] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 04/09/2018] [Indexed: 01/25/2023]
Abstract
One-third of all protein-coding genes from bacterial genomes cannot be annotated with a function. Here, to investigate the functions of these genes, we present genome-wide mutant fitness data from 32 diverse bacteria across dozens of growth conditions. We identified mutant phenotypes for 11,779 protein-coding genes that had not been annotated with a specific function. Many genes could be associated with a specific condition because the gene affected fitness only in that condition, or with another gene in the same bacterium because they had similar mutant phenotypes. Of the poorly annotated genes, 2,316 had associations that have high confidence because they are conserved in other bacteria. By combining these conserved associations with comparative genomics, we identified putative DNA repair proteins; in addition, we propose specific functions for poorly annotated enzymes and transporters and for uncharacterized protein families. Our study demonstrates the scalability of microbial genetics and its utility for improving gene annotations.
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Affiliation(s)
- Morgan N Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kelly M Wetmore
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - R Jordan Waters
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mark Callaghan
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jayashree Ray
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hualan Liu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jennifer V Kuehl
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ryan A Melnyk
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jacob S Lamson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yumi Suh
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hans K Carlson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Zuelma Esquivel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Harini Sadeeshkumar
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Romy Chakraborty
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Grant M Zane
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Benjamin E Rubin
- Division of Biological Sciences, University of California, San Diego, CA, USA
| | - Judy D Wall
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Axel Visel
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,School of Natural Sciences, University of California, Merced, CA, USA
| | - James Bristow
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matthew J Blow
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Department of Bioengineering, University of California, Berkeley, CA, USA.
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
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9
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Richarme G, Liu C, Mihoub M, Abdallah J, Leger T, Joly N, Liebart JC, Jurkunas UV, Nadal M, Bouloc P, Dairou J, Lamouri A. Guanine glycation repair by DJ-1/Park7 and its bacterial homologs. Science 2017; 357:208-211. [DOI: 10.1126/science.aag1095] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 05/17/2017] [Indexed: 01/05/2023]
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10
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Abdallah J, Mihoub M, Gautier V, Richarme G. The DJ-1 superfamily members YhbO and YajL from Escherichia coli repair proteins from glycation by methylglyoxal and glyoxal. Biochem Biophys Res Commun 2016; 470:282-286. [PMID: 26774339 DOI: 10.1016/j.bbrc.2016.01.068] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 01/10/2016] [Indexed: 11/28/2022]
Abstract
YhbO and YajL belong to the PfpI/Hsp31/DJ-1 superfamily. Both proteins are involved in protection against environmental stresses. Here, we show that, like DJ-1 and Hsp31, they repair glyoxal- and methylglyoxal-glycated proteins. YhbO and YajL repair glycated serum albumin, collagen, glyceraldehyde-3-phosphate dehydrogenase, and fructose biphosphate aldolase. Bacterial extracts from deglycase mutants display increased glycation levels, whereas deglycase overexpression decreases protein glycation. Moreover, yhbO and yajL mutants display decreased viability in methylglyoxal- or glucose-containing media. Finally, the apparent glyoxalase activities of YhbO and YajL reflect their deglycase activities.
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Affiliation(s)
- Jad Abdallah
- Stress Molecules, Institut Jacques Monod, Université Paris 7, CNRS UMR 7592, 15 rue Hélène Brion, 75013 Paris, France; Lebanese American University, School of Pharmacy, Byblos, Lebanon
| | - Mouadh Mihoub
- Stress Molecules, Institut Jacques Monod, Université Paris 7, CNRS UMR 7592, 15 rue Hélène Brion, 75013 Paris, France
| | - Valérie Gautier
- Stress Molecules, Institut Jacques Monod, Université Paris 7, CNRS UMR 7592, 15 rue Hélène Brion, 75013 Paris, France
| | - Gilbert Richarme
- Stress Molecules, Institut Jacques Monod, Université Paris 7, CNRS UMR 7592, 15 rue Hélène Brion, 75013 Paris, France.
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11
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Figueira R, Brown DR, Ferreira D, Eldridge MJG, Burchell L, Pan Z, Helaine S, Wigneshweraraj S. Adaptation to sustained nitrogen starvation by Escherichia coli requires the eukaryote-like serine/threonine kinase YeaG. Sci Rep 2015; 5:17524. [PMID: 26621053 PMCID: PMC4664914 DOI: 10.1038/srep17524] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/30/2015] [Indexed: 12/13/2022] Open
Abstract
The Escherichia coli eukaryote-like serine/threonine kinase, encoded by yeaG, is expressed in response to diverse stresses, including nitrogen (N) starvation. A role for yeaG in bacterial stress response is unknown. Here we reveal for the first time that wild-type E. coli displays metabolic heterogeneity following sustained periods of N starvation, with the metabolically active population displaying compromised viability. In contrast, such heterogeneity in metabolic activity is not observed in an E. coli ∆yeaG mutant, which continues to exist as a single and metabolically active population and thus displays an overall compromised ability to survive sustained periods of N starvation. The mechanism by which yeaG acts, involves the transcriptional repression of two toxin/antitoxin modules, mqsR/mqsA and dinJ/yafQ. This, consequently, has a positive effect on the expression of rpoS, the master regulator of the general bacterial stress response. Overall, results indicate that yeaG is required to fully execute the rpoS-dependent gene expression program to allow E. coli to adapt to sustained N starvation and unravels a novel facet to the regulatory basis that underpins adaptive response to N stress.
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Affiliation(s)
- Rita Figueira
- MRC Centre for Molecular Microbiology and Infection, Imperial College London, UK
| | - Daniel R Brown
- MRC Centre for Molecular Microbiology and Infection, Imperial College London, UK
| | - Delfim Ferreira
- MRC Centre for Molecular Microbiology and Infection, Imperial College London, UK
| | - Matthew J G Eldridge
- MRC Centre for Molecular Microbiology and Infection, Imperial College London, UK
| | - Lynn Burchell
- MRC Centre for Molecular Microbiology and Infection, Imperial College London, UK
| | - Zhensheng Pan
- MRC Centre for Molecular Microbiology and Infection, Imperial College London, UK
| | - Sophie Helaine
- MRC Centre for Molecular Microbiology and Infection, Imperial College London, UK
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12
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Vercruysse M, Fauvart M, Jans A, Beullens S, Braeken K, Cloots L, Engelen K, Marchal K, Michiels J. Stress response regulators identified through genome-wide transcriptome analysis of the (p)ppGpp-dependent response in Rhizobium etli. Genome Biol 2011; 12:R17. [PMID: 21324192 PMCID: PMC3188799 DOI: 10.1186/gb-2011-12-2-r17] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 02/01/2011] [Accepted: 02/16/2011] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The alarmone (p)ppGpp mediates a global reprogramming of gene expression upon nutrient limitation and other stresses to cope with these unfavorable conditions. Synthesis of (p)ppGpp is, in most bacteria, controlled by RelA/SpoT (Rsh) proteins. The role of (p)ppGpp has been characterized primarily in Escherichia coli and several Gram-positive bacteria. Here, we report the first in-depth analysis of the (p)ppGpp-regulon in an α-proteobacterium using a high-resolution tiling array to better understand the pleiotropic stress phenotype of a relA/rsh mutant. RESULTS We compared gene expression of the Rhizobium etli wild type and rsh (previously rel) mutant during exponential and stationary phase, identifying numerous (p)ppGpp targets, including small non-coding RNAs. The majority of the 834 (p)ppGpp-dependent genes were detected during stationary phase. Unexpectedly, 223 genes were expressed (p)ppGpp-dependently during early exponential phase, indicating the hitherto unrecognized importance of (p)ppGpp during active growth. Furthermore, we identified two (p)ppGpp-dependent key regulators for survival during heat and oxidative stress and one regulator putatively involved in metabolic adaptation, namely extracytoplasmic function sigma factor EcfG2/PF00052, transcription factor CH00371, and serine protein kinase PrkA. CONCLUSIONS The regulatory role of (p)ppGpp in R. etli stress adaptation is far-reaching in redirecting gene expression during all growth phases. Genome-wide transcriptome analysis of a strain deficient in a global regulator, and exhibiting a pleiotropic phenotype, enables the identification of more specific regulators that control genes associated with a subset of stress phenotypes. This work is an important step toward a full understanding of the regulatory network underlying stress responses in α-proteobacteria.
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Affiliation(s)
- Maarten Vercruysse
- Centre of Microbial and Plant Genetics, Katholiek Universiteit Leuven, Kasteelpark Arenberg 20, 3001 Heverlee, Belgium
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13
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Tagourti J, Gautier V, Beaujouan JC, Gauchy C, Landoulsi A, Richarme G. Phosphorylation of a 65 kDa cytoplasmic protein by the Escherichia coli YeaG kinase. ANN MICROBIOL 2010. [DOI: 10.1007/s13213-010-0164-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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14
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Evolution of the RpoS regulon: origin of RpoS and the conservation of RpoS-dependent regulation in bacteria. J Mol Evol 2010; 70:557-71. [PMID: 20506020 DOI: 10.1007/s00239-010-9352-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Accepted: 05/03/2010] [Indexed: 10/19/2022]
Abstract
The RpoS sigma factor in proteobacteria regulates genes in stationary phase and in response to stress. Although of conserved function, the RpoS regulon may have different gene composition across species due to high genomic diversity and to known environmental conditions that select for RpoS mutants. In this study, the distribution of RpoS homologs in prokaryotes and the differential dependence of regulon members on RpoS for expression in two gamma-proteobacteria (Escherichia coli and Pseudomonas aeruginosa) were examined. Using a maximum-likelihood phylogeny and reciprocal best hits analysis, we show that the RpoS sigma factor is conserved within gamma-, beta-, and delta-proteobacteria. Annotated RpoS of Borrelia and the enteric RpoS are postulated to have separate evolutionary origins. To determine the conservation of RpoS-dependent gene expression across species, reciprocal best hits analysis was used to identify orthologs of the E. coli RpoS regulon in the RpoS regulon of P. aeruginosa. Of the 186 RpoS-dependent genes of E. coli, 50 proteins have an ortholog within the P. aeruginosa genome. Twelve genes of the 50 orthologs are RpoS-dependent in both species, and at least four genes are regulated by RpoS in other gamma-proteobacteria. Despite RpoS conservation in gamma-, beta-, and delta-proteobacteria, RpoS regulon composition is subject to modification between species. Environmental selection for RpoS mutants likely contributes to the evolutionary divergence and specialization of the RpoS regulon within different bacterial genomes.
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15
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Tagourti J, Malki A, Kern R, d'Alençon E, Richarme G. Membrane docking of an aggregation-prone protein improves its solubilization. Gene 2008; 426:32-8. [PMID: 18809475 DOI: 10.1016/j.gene.2008.08.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2008] [Revised: 07/31/2008] [Accepted: 08/26/2008] [Indexed: 11/29/2022]
Abstract
We used preS2-S'-beta-galactosidase, a three domain fusion protein that aggregates extensively at 43 degrees C in the cytoplasm of Escherichia coli to search for multicopy suppressors of protein aggregation and inclusion bodies formation, and took advantage of the known differential solubility of preS2-S'-beta-galactosidase at 37 and 43 degrees C to develop a selection procedure for the gene products that would prevent its aggregation in vivo at 43 degrees C. First, we demonstrate that the differential solubility of preS2-S'-beta-galactosidase results in a lactose-positive phenotype at 37 degrees C as opposed to a lactose-negative phenotype at 43 degrees C. We searched for multicopy suppressors of preS2-S'-beta-galactosidase aggregation at 43 degrees C by selecting pink lactose-positive colonies on a background of white lactose-negative colonies after transformation of bacteria with an E. coli gene bank. We found only two multicopy suppressors of preS2-S'-beta-galactosidase aggregation at 43 degrees C, protein isoaspartate methyltransferase (PIMT) and the membrane components ChbBC of the N,N'-diacetylchitobiose phosphotransferase transporter. We have previously shown that PIMT overexpression reduces the level of isoaspartate in preS2-S'-beta-galactosidase, increases its thermal stability and consequently helps in its solubilization at 43 degrees C (Kern et al., J. Bacteriol. 187, 1377-1383). In the present work, we show that ChbBC overexpression targets a fraction of preS2-S'-beta-galactosidase to the membrane, and decreases its amount in inclusion bodies, which results in its decreased thermodenaturation and in a lactose-positive phenotype at 43 degrees C. Cross-linking experiments show that the inner membrane protein ChbC interacts with preS2-S'-beta-galactosidase. Our results suggest that membrane docking of aggregation-prone proteins might be a useful method for their solubilization.
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Affiliation(s)
- Jihen Tagourti
- Molecules de stress, Institut Jacques Monod, Université Paris 7, 2, place Jussieu, 75005 Paris, France
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