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Bouillet S, Bauer TS, Gottesman S. RpoS and the bacterial general stress response. Microbiol Mol Biol Rev 2024; 88:e0015122. [PMID: 38411096 PMCID: PMC10966952 DOI: 10.1128/mmbr.00151-22] [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] [Indexed: 02/28/2024] Open
Abstract
SUMMARYThe general stress response (GSR) is a widespread strategy developed by bacteria to adapt and respond to their changing environments. The GSR is induced by one or multiple simultaneous stresses, as well as during entry into stationary phase and leads to a global response that protects cells against multiple stresses. The alternative sigma factor RpoS is the central GSR regulator in E. coli and conserved in most γ-proteobacteria. In E. coli, RpoS is induced under conditions of nutrient deprivation and other stresses, primarily via the activation of RpoS translation and inhibition of RpoS proteolysis. This review includes recent advances in our understanding of how stresses lead to RpoS induction and a summary of the recent studies attempting to define RpoS-dependent genes and pathways.
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Affiliation(s)
- Sophie Bouillet
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland, USA
| | - Taran S. Bauer
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland, USA
| | - Susan Gottesman
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland, USA
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Lee SM, Le HT, Taizhanova A, Nong LK, Park JY, Lee EJ, Palsson BO, Kim D. Experimental promoter identification of a foodborne pathogen Salmonella enterica subsp. enterica serovar Typhimurium with near single base-pair resolution. Front Microbiol 2024; 14:1271121. [PMID: 38239730 PMCID: PMC10794520 DOI: 10.3389/fmicb.2023.1271121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 12/01/2023] [Indexed: 01/22/2024] Open
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) is a common foodborne pathogen which is frequently used as the reference strain for Salmonella. Investigating the sigma factor network and protomers is crucial to understand the genomic and transcriptomic properties of the bacterium. Its promoters were identified using various methods such as dRNA-seq, ChIP-chip, or ChIP-Seq. However, validation using ChIP-exo, which exhibits higher-resolution performance compared to conventional ChIP, has not been conducted to date. In this study, using the representative strain S. Typhimurium LT2 (LT2), the ChIP-exo experiment was conducted to accurately determine the binding sites of catalytic RNA polymerase subunit RpoB and major sigma factors (RpoD, RpoN, RpoS, and RpoE) during exponential phase. Integrated with the results of RNA-Seq, promoters and sigmulons for the sigma factors and their association with RpoB have been discovered. Notably, the overlapping regions among binding sites of each alternative sigma factor were found. Furthermore, comparative analysis with Escherichia coli str. K-12 substr. MG1655 (MG1655) revealed conserved binding sites of RpoD and RpoN across different species. In the case of small RNAs (sRNAs), 50 sRNAs observed their expression during the exponential growth of LT2. Collectively, the integration of ChIP-exo and RNA-Seq enables genome-scale promoter mapping with high resolution and facilitates the characterization of binding events of alternative sigma factors, enabling a comprehensive understanding of the bacterial sigma factor network and condition-specific active promoters.
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Affiliation(s)
- Sang-Mok Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Hoa Thi Le
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Assiya Taizhanova
- Department of Genetic Engineering and Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, Republic of Korea
| | - Linh Khanh Nong
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Joon Young Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Eun-Jin Lee
- Department of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA, United States
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
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Petrova O, Semenova E, Parfirova O, Tsers I, Gogoleva N, Gogolev Y, Nikolaichik Y, Gorshkov V. RpoS-Regulated Genes and Phenotypes in the Phytopathogenic Bacterium Pectobacterium atrosepticum. Int J Mol Sci 2023; 24:17348. [PMID: 38139177 PMCID: PMC10743746 DOI: 10.3390/ijms242417348] [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: 11/07/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
The alternative sigma factor RpoS is considered to be one of the major regulators providing stress resistance and cross-protection in bacteria. In phytopathogenic bacteria, the effects of RpoS have not been analyzed with regard to cross-protection, and genes whose expression is directly or indirectly controlled by RpoS have not been determined at the whole-transcriptome level. Our study aimed to determine RpoS-regulated genes and phenotypes in the phytopathogenic bacterium Pectobacterium atrosepticum. Knockout of the rpoS gene in P. atrosepticum affected the long-term starvation response, cross-protection, and virulence toward plants with enhanced immune status. The whole-transcriptome profiles of the wild-type P. atrosepticum strain and its ΔrpoS mutant were compared under different experimental conditions, and functional gene groups whose expression was affected by RpoS were determined. The RpoS promoter motif was inferred within the promoter regions of the genes affected by rpoS deletion, and the P. atrosepticum RpoS regulon was predicted. Based on RpoS-controlled phenotypes, transcriptome profiles, and RpoS regulon composition, the regulatory role of RpoS in P. atrosepticum is discussed.
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Affiliation(s)
- Olga Petrova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
| | - Elizaveta Semenova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
| | - Olga Parfirova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
| | - Ivan Tsers
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
| | - Natalia Gogoleva
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
| | - Yuri Gogolev
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Yevgeny Nikolaichik
- Department of Molecular Biology, Belarusian State University, 220030 Minsk, Belarus;
| | - Vladimir Gorshkov
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
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Metaane S, Monteil V, Douché T, Giai Gianetto Q, Matondo M, Maufrais C, Norel F. Loss of CorA, the primary magnesium transporter of Salmonella, is alleviated by MgtA and PhoP-dependent compensatory mechanisms. PLoS One 2023; 18:e0291736. [PMID: 37713445 PMCID: PMC10503707 DOI: 10.1371/journal.pone.0291736] [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: 06/09/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023] Open
Abstract
In many Gram-negative bacteria, the stress sigma factor of RNA polymerase, σS/RpoS, remodels global gene expression to reshape the physiology of stationary phase cells and ensure their survival under non-optimal growth conditions. In the foodborne pathogen Salmonella enterica serovar Typhimurium, σS is also required for biofilm formation and virulence. We have recently shown that a ΔrpoS mutation decreases the magnesium content and expression level of the housekeeping Mg2+-transporter CorA in stationary phase Salmonella. The other two Mg2+-transporters of Salmonella are encoded by the PhoP-activated mgtA and mgtB genes and are expressed under magnesium starvation. The σS control of corA prompted us to evaluate the impact of CorA in stationary phase Salmonella cells, by using global and analytical proteomic analyses and physiological assays. The ΔcorA mutation conferred a competitive disadvantage to exit from stationary phase, and slightly impaired motility, but had no effect on total and free cellular magnesium contents. In contrast to the wild-type strain, the ΔcorA mutant produced MgtA, but not MgtB, in the presence of high extracellular magnesium concentration. Under these conditions, MgtA production in the ΔcorA mutant did not require PhoP. Consistently, a ΔmgtA, but not a ΔphoP, mutation slightly reduced the magnesium content of the ΔcorA mutant. Synthetic phenotypes were observed when the ΔphoP and ΔcorA mutations were combined, including a strong reduction in growth and motility, independently of the extracellular magnesium concentration. The abundance of several proteins involved in flagella formation, chemotaxis and secretion was lowered by the ΔcorA and ΔphoP mutations in combination, but not alone. These findings unravel the importance of PhoP-dependent functions in the absence of CorA when magnesium is sufficient. Altogether, our data pinpoint a regulatory network, where the absence of CorA is sensed by the cell and compensated by MgtA and PhoP- dependent mechanisms.
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Affiliation(s)
- Selma Metaane
- Biochimie des Interactions Macromoléculaires, Institut Pasteur, CNRS UMR3528, Université Paris Cité, Paris, France
| | - Véronique Monteil
- Biochimie des Interactions Macromoléculaires, Institut Pasteur, CNRS UMR3528, Université Paris Cité, Paris, France
| | - Thibaut Douché
- Proteomic Platform, Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS UAR 2024, Université Paris Cité, Paris, France
| | - Quentin Giai Gianetto
- Proteomic Platform, Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS UAR 2024, Université Paris Cité, Paris, France
| | - Mariette Matondo
- Proteomic Platform, Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS UAR 2024, Université Paris Cité, Paris, France
| | - Corinne Maufrais
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, Paris, France
| | - Françoise Norel
- Biochimie des Interactions Macromoléculaires, Institut Pasteur, CNRS UMR3528, Université Paris Cité, Paris, France
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da Silva MR, Alves de Almeida F, Coelho AÍM, da Silva FL, Vanetti MCD. Enhancing cell resistance for production of mixed microbiological reference materials with Salmonella and coliforms by freeze-drying. Braz J Microbiol 2022; 53:2107-2119. [PMID: 35962856 PMCID: PMC9679061 DOI: 10.1007/s42770-022-00808-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/29/2022] [Indexed: 01/13/2023] Open
Abstract
The reference material (RM) is a technical requirement for the quality assurance of analytical results and proficiency tests or interlaboratory comparisons. Microbiological RMs are most available in the dehydrated form, mainly by freeze-drying, and maintaining bacterial survival after preparation is a challenge. Thus, obtaining the most resistant cells is essential. Considering that bacteria present cross-response to dehydration after being submitted to an array of stress conditions, this study aimed to evaluate the influence of growth conditions on enterobacteria for the production of mixed microbiological RMs by freeze-drying in skim milk powder. Salmonella enterica serovar Enteritidis, Cronobacter sakazakii, Escherichia coli, and Citrobacter freundii were grown in a minimal medium with 0.5 M NaCl and 0 to 5.0 mM of manganese sulfate (MnSO4) until stationary phase. Salmonella Enteritidis presented an increased resistance to dehydration in the presence of Mn, while C. sakazakii was the most resistant to freeze-drying and further storage for 90 days. Mixed microbiological RMs were produced by freeze-drying and containing Salmonella Enteritidis and coliforms in skim milk powder with 100 mM of trehalose and the Salmonella survival rate was 91.2 to 93.6%. The mixed RM was stable after 30 days at -20 °C, and Salmonella and coliforms were detected by different methods being, the Rambach Agar the best for the bacterial differentiation. The results showed that the culture conditions applied in this study resulted in bacterial cells being more resistant to dehydration, freeze-drying, and stabilization for the production of mixed microbiological RMs more stable and homogeneous.
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Affiliation(s)
- Maria Roméria da Silva
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Felipe Alves de Almeida
- Department of Nutrition, Universidade Federal de Juiz de Fora, Governador Valadares, MG, 35032-620, Brazil
| | | | - Fernanda Lopes da Silva
- Department of Food Technology, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
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Cellier MFM. Nramp: Deprive and conquer? Front Cell Dev Biol 2022; 10:988866. [PMID: 36313567 PMCID: PMC9606685 DOI: 10.3389/fcell.2022.988866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Solute carriers 11 (Slc11) evolved from bacterial permease (MntH) to eukaryotic antibacterial defense (Nramp) while continuously mediating proton (H+)-dependent manganese (Mn2+) import. Also, Nramp horizontal gene transfer (HGT) toward bacteria led to mntH polyphyly. Prior demonstration that evolutionary rate-shifts distinguishing Slc11 from outgroup carriers dictate catalytic specificity suggested that resolving Slc11 family tree may provide a function-aware phylogenetic framework. Hence, MntH C (MC) subgroups resulted from HGTs of prototype Nramp (pNs) parologs while archetype Nramp (aNs) correlated with phagocytosis. PHI-Blast based taxonomic profiling confirmed MntH B phylogroup is confined to anaerobic bacteria vs. MntH A (MA)’s broad distribution; suggested niche-related spread of MC subgroups; established that MA-variant MH, which carries ‘eukaryotic signature’ marks, predominates in archaea. Slc11 phylogeny shows MH is sister to Nramp. Site-specific analysis of Slc11 charge network known to interact with the protonmotive force demonstrates sequential rate-shifts that recapitulate Slc11 evolution. 3D mapping of similarly coevolved sites across Slc11 hydrophobic core revealed successive targeting of discrete areas. The data imply that pN HGT could advantage recipient bacteria for H+-dependent Mn2+ acquisition and Alphafold 3D models suggest conformational divergence among MC subgroups. It is proposed that Slc11 originated as a bacterial stress resistance function allowing Mn2+-dependent persistence in conditions adverse for growth, and that archaeal MH could contribute to eukaryogenesis as a Mn2+ sequestering defense perhaps favoring intracellular growth-competent bacteria.
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