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Muriel-Millán LF, Montelongo-Martínez LF, González-Valdez A, Bedoya-Pérez LP, Cocotl-Yañez M, Soberón-Chávez G. The alternative sigma factor RpoS regulates Pseudomonas aeruginosa quorum sensing response by repressing the pqsABCDE operon and activating vfr. Mol Microbiol 2024; 121:291-303. [PMID: 38169053 DOI: 10.1111/mmi.15224] [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: 08/11/2023] [Revised: 12/02/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024]
Abstract
Pseudomonas aeruginosa is an important opportunistic pathogen. Several of its virulence-related processes, including the synthesis of pyocyanin (PYO) and biofilm formation, are controlled by quorum sensing (QS). It has been shown that the alternative sigma factor RpoS regulates QS through the reduction of lasR and rhlR transcription (encoding QS regulators). However, paradoxically, the absence of RpoS increases PYO production and biofilm development (that are RhlR dependent) by unknown mechanisms. Here, we show that RpoS represses pqsE transcription, which impacts the stability and activity of RhlR. In the absence of RpoS, rhlR transcript levels are reduced but not the RhlR protein concentration, presumably by its stabilization by PqsE, whose expression is increased. We also report that PYO synthesis and the expression of pqsE and phzA1B1C1D1E1F1G1 operon exhibit the same pattern at different RpoS concentrations, suggesting that the RpoS-dependent PYO production is due to its ability to modify PqsE concentration, which in turn modulates the activation of the phzA1 promoter by RhlR. Finally, we demonstrate that RpoS favors the expression of Vfr, which activates the transcription of lasR and rhlR. Our study contributes to the understanding of how RpoS modulates the QS response in P. aeruginosa, exerting both negative and positive regulation.
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Affiliation(s)
- Luis Felipe Muriel-Millán
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
| | - Luis Fernando Montelongo-Martínez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
| | - Abigail González-Valdez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
| | - Leidy Patricia Bedoya-Pérez
- Programa de Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Miguel Cocotl-Yañez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
| | - Gloria Soberón-Chávez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
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2
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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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3
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Zhang QX, Xiong ZW, Li SY, Yin Y, Xing CL, Wen DY, Xu J, Liu Q. Regulatory roles of RpoS in the biosynthesis of antibiotics 2,4-diacetyphloroglucinol and pyoluteorin of Pseudomonas protegens FD6. Front Microbiol 2022; 13:993732. [PMID: 36583049 PMCID: PMC9793710 DOI: 10.3389/fmicb.2022.993732] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/21/2022] [Indexed: 12/14/2022] Open
Abstract
The rhizosphere microbe Pseudomonas protegens FD6 possesses beneficial traits such as the production of antibiotics like pyoluteorin (Plt) and 2,4-diacetylphloroglucinol (2,4-DAPG). The alternative RpoS (σ38 factor), as a master regulator, activates or inhibits the transcription of stationary phase genes in several biocontrol organisms. Here, we investigated the complicated function and regulatory mechanism of RpoS in the biosynthesis of 2,4-DAPG and Plt in strain FD6. Phenotypic assays suggested that ΔrpoS was impaired in biofilm formation, swimming motility, swarming motility, and resistance to stress, such as heat, H2O2 and 12% ethanol. The RpoS mutation significantly increased both 2,4-DAPG and Plt production and altered the transcription and translation of the biosynthetic genes phlA and pltL, indicating that RpoS inhibited antibiotic production by FD6 at both the transcriptional and translational levels. RpoS negatively controlled 2,4-DAPG biosynthesis and transcription of the 2,4-DAPG operon phlACBD by directly interacting with the promoter sequences of phlG and phlA. In addition, RpoS significantly inhibited Plt production and the expression of its operon pltLABCDEFG by directly binding to the promoter regions of pltR, pltL and pltF. Further analyzes demonstrated that a putative R147 mutation in the RpoS binding domain abolished its inhibitory activity on the expression of pltL and phlA. Overall, our results reveal the pleiotropic regulatory function of RpoS in P. protegens FD6 and provide the basis for improving antibiotic biosynthesis by genetic engineering in biocontrol organisms.
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Affiliation(s)
- Qing Xia Zhang
- College of Plant Protection, Yangzhou University, Yangzhou, China,*Correspondence: Qing Xia Zhang,
| | - Zheng Wen Xiong
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Shen Yu Li
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Yue Yin
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Cheng Lin Xing
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - De Yu Wen
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Jian Xu
- Jiangsu Lixiahe District Institute of Agricultural Sciences, Yangzhou, China
| | - Qin Liu
- Jiangsu Lixiahe District Institute of Agricultural Sciences, Yangzhou, China,Qin Liu,
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4
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Role of RpoS in Regulating Stationary Phase Salmonella Typhimurium Pathogenesis-Related Stress Responses under Physiological Low Fluid Shear Force Conditions. mSphere 2022; 7:e0021022. [PMID: 35913142 PMCID: PMC9429890 DOI: 10.1128/msphere.00210-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The discovery that biomechanical forces regulate microbial virulence was established with the finding that physiological low fluid shear (LFS) forces altered gene expression, stress responses, and virulence of the enteric pathogen Salmonella enterica serovar Typhimurium during the log phase. These log phase LFS-induced phenotypes were independent of the master stress response regulator, RpoS (σS). Given the central importance of RpoS in regulating stationary-phase stress responses of S. Typhimurium cultured under conventional shake flask and static conditions, we examined its role in stationary-phase cultures grown under physiological LFS. We constructed an isogenic rpoS mutant derivative of wild-type S. Typhimurium and compared the ability of these strains to survive in vitro pathogenesis-related stresses that mimic those encountered in the infected host and environment. We also compared the ability of these strains to colonize (adhere, invade, and survive within) human intestinal epithelial cell cultures. Unexpectedly, LFS-induced resistance of stationary-phase S. Typhimurium cultures to acid and bile salts stresses did not rely on RpoS. Likewise, RpoS was dispensable for stationary-phase LFS cultures to adhere to and survive within intestinal epithelial cells. In contrast, the resistance of these cultures to challenges of oxidative and thermal stresses, and their invasion into intestinal epithelial cells was influenced by RpoS. These findings expand our mechanistic understanding of how physiological fluid shear forces modulate stationary-phase S. Typhimurium physiology in unexpected ways and provide clues into microbial mechanobiology and nuances of Salmonella responses to microenvironmental niches in the infected host. IMPORTANCE Bacterial pathogens respond dynamically to a variety of stresses in the infected host, including physical forces of fluid flow (fluid shear) across their surfaces. While pathogens experience wide fluctuations in fluid shear during infection, little is known about how these forces regulate microbial pathogenesis. This is especially important for stationary-phase bacterial growth, which is a critical period to understand microbial resistance, survival, and infection potential, and is regulated in many bacteria by the general stationary-phase stress response protein RpoS. Here, we showed that, unlike conventional culture conditions, several stationary-phase Salmonella pathogenic stress responses were not impacted by RpoS when bacteria were cultured under fluid shear conditions relevant to those encountered in the intestine of the infected host. These findings offer new insight into how physiological fluid shear forces encountered by Salmonella during infection might impact pathogenic responses in unexpected ways that are relevant to their disease-causing ability.
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The stress sigma factor σS/RpoS counteracts Fur repression of genes involved in iron and manganese metabolism and modulates the ionome of Salmonella enterica serovar Typhimurium. PLoS One 2022; 17:e0265511. [PMID: 35358211 PMCID: PMC8970401 DOI: 10.1371/journal.pone.0265511] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/02/2022] [Indexed: 11/24/2022] 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 quiescent 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 previously identified sRNAs genes positively controlled by σS in Salmonella, including the two paralogous sRNA genes, ryhB1 and ryhB2/isrE. Expression of ryhB1 and ryhB2 is repressed by the ferric uptake regulator Fur when iron is available. In this study, we show that σS alleviates Fur-mediated repression of the ryhB genes and of additional Fur target genes. Moreover, σS induces transcription of the manganese transporter genes mntH and sitABCD and prevents their repression, not only by Fur, but also by the manganese-responsive regulator MntR. These findings prompted us to evaluate the impact of a ΔrpoS mutation on the Salmonella ionome. Inductively coupled plasma mass spectrometry analyses revealed a significant effect of the ΔrpoS mutation on the cellular concentration of manganese, magnesium, cobalt and potassium. In addition, transcriptional fusions in several genes involved in the transport of these ions were regulated by σS. This study suggests that σS controls fluxes of ions that might be important for the fitness of quiescent cells. Consistent with this hypothesis, the ΔrpoS mutation extended the lag phase of Salmonella grown in rich medium supplemented with the metal ion chelator EDTA, and this effect was abolished when magnesium, but not manganese or iron, was added back. These findings unravel the importance of σS and magnesium in the regrowth potential of quiescent cells.
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Kim SI, Kim E, Yoon H. σ S-Mediated Stress Response Induced by Outer Membrane Perturbation Dampens Virulence in Salmonella enterica serovar Typhimurium. Front Microbiol 2021; 12:750940. [PMID: 34659184 PMCID: PMC8516096 DOI: 10.3389/fmicb.2021.750940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 08/30/2021] [Indexed: 12/13/2022] Open
Abstract
Salmonella alters cellular processes as a strategy to improve its intracellular fitness during host infection. Alternative σ factors are known to rewire cellular transcriptional regulation in response to environmental stressors. σs factor encoded by the rpoS gene is a key regulator required for eliciting the general stress response in many proteobacteria. In this study, Salmonella Typhimurium deprived of an outer membrane protein YcfR was attenuated in intracellular survival and exhibited downregulation in Salmonella pathogenicity island-2 (SPI-2) genes. This decreased SPI-2 expression caused by the outer membrane perturbation was abolished in the absence of rpoS. Interestingly, regardless of the defects in the outer membrane integrity, RpoS overproduction decreased transcription from the common promoter of ssrA and ssrB, which encode a two-component regulatory system for SPI-2. RpoS was found to compete with RpoD for binding to the PssrA region, and its binding activity with RNA polymerase (RNAP) to form Eσs holoenzyme was stimulated by the small regulatory protein Crl. This study demonstrates that Salmonella undergoing RpoS-associated stress responses due to impaired envelope integrity may reciprocally downregulate the expression of SPI-2 genes to reduce its virulence.
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Affiliation(s)
- Seul I Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Eunsuk Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Hyunjin Yoon
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea.,Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, South Korea
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7
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Feng Z, El Hag M, Qin T, Du Y, Chen S, Peng D. Residue L193P Mutant of RpoS Affects Its Activity During Biofilm Formation in Salmonella Pullorum. Front Vet Sci 2020; 7:571361. [PMID: 33251260 PMCID: PMC7674402 DOI: 10.3389/fvets.2020.571361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/16/2020] [Indexed: 11/21/2022] Open
Abstract
The role of alternative sigma factor RpoS in regulating biofilm formation may differ in various Salmonella Pullorum strains. In this study, the biofilm-forming ability of two Salmonella Pullorum strains S6702 and S11923-3 were compared. The biofilm forming ability of S11923-3 was much stronger than that of S6702. After knocking out the rpoS gene, S11923-3ΔrpoS had significantly reduced biofilm while S6702ΔrpoS demonstrated similar biofilm compared with each parent strain. The analysis of RpoS sequences indicated two amino acid substitutions (L193P and R293C) between S6702 and S11923-3 RpoS. A complementation study confirmed that the expression of S11923-3 RpoS rather than S6702 RpoS could restore the biofilm-forming ability of ΔrpoS strains and the L193P mutation contributed to the restoration of the biofilm-forming ability. Further study indicated that RpoS with the L193P mutant had significantly improved expression level and binding activity to RNAP and csgD gene promoter, which increased the efficacy of the csgD gene promoter and biofilm-forming ability. Therefore, the L193P mutation of RpoS is critical for stronger biofilm formation of Salmonella Pullorum.
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Affiliation(s)
- Zheng Feng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, Yangzhou, China.,Joint Laboratory Safety of International Cooperation of Agriculture and Agricultural-Products, Yangzhou University, Yangzhou, China
| | - Muhanad El Hag
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, Yangzhou, China.,Joint Laboratory Safety of International Cooperation of Agriculture and Agricultural-Products, Yangzhou University, Yangzhou, China
| | - Tao Qin
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, Yangzhou, China.,Joint Laboratory Safety of International Cooperation of Agriculture and Agricultural-Products, Yangzhou University, Yangzhou, China
| | - Yinping Du
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, Yangzhou, China.,Joint Laboratory Safety of International Cooperation of Agriculture and Agricultural-Products, Yangzhou University, Yangzhou, China
| | - Sujuan Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, Yangzhou, China.,Joint Laboratory Safety of International Cooperation of Agriculture and Agricultural-Products, Yangzhou University, Yangzhou, China
| | - Daxin Peng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, Yangzhou, China.,Joint Laboratory Safety of International Cooperation of Agriculture and Agricultural-Products, Yangzhou University, Yangzhou, China
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8
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Schellhorn HE. Function, Evolution, and Composition of the RpoS Regulon in Escherichia coli. Front Microbiol 2020; 11:560099. [PMID: 33042067 PMCID: PMC7527412 DOI: 10.3389/fmicb.2020.560099] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 08/25/2020] [Indexed: 11/13/2022] Open
Abstract
For many bacteria, successful growth and survival depends on efficient adaptation to rapidly changing conditions. In Escherichia coli, the RpoS alternative sigma factor plays a central role in the adaptation to many suboptimal growth conditions by controlling the expression of many genes that protect the cell from stress and help the cell scavenge nutrients. Neither RpoS or the genes it controls are essential for growth and, as a result, the composition of the regulon and the nature of RpoS control in E. coli strains can be variable. RpoS controls many genetic systems, including those affecting pathogenesis, phenotypic traits including metabolic pathways and biofilm formation, and the expression of genes needed to survive nutrient deprivation. In this review, I review the origin of RpoS and assess recent transcriptomic and proteomic studies to identify features of the RpoS regulon in specific clades of E. coli to identify core functions of the regulon and to identify more specialized potential roles for the regulon in E. coli subgroups.
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9
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Cross Talk between SigB and PrfA in Listeria monocytogenes Facilitates Transitions between Extra- and Intracellular Environments. Microbiol Mol Biol Rev 2019; 83:83/4/e00034-19. [PMID: 31484692 DOI: 10.1128/mmbr.00034-19] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The foodborne pathogen Listeria monocytogenes can modulate its transcriptome and proteome to ensure its survival during transmission through vastly differing environmental conditions. While L. monocytogenes utilizes a large array of regulators to achieve survival and growth in different intra- and extrahost environments, the alternative sigma factor σB and the transcriptional activator of virulence genes protein PrfA are two key transcriptional regulators essential for responding to environmental stress conditions and for host infection. Importantly, emerging evidence suggests that the shift from extrahost environments to the host gastrointestinal tract and, subsequently, to intracellular environments requires regulatory interplay between σB and PrfA at transcriptional, posttranscriptional, and protein activity levels. Here, we review the current evidence for cross talk and interplay between σB and PrfA and their respective regulons and highlight the plasticity of σB and PrfA cross talk and the role of this cross talk in facilitating successful transition of L. monocytogenes from diverse extrahost to diverse extra- and intracellular host environments.
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Miyakoshi M, Matera G, Maki K, Sone Y, Vogel J. Functional expansion of a TCA cycle operon mRNA by a 3' end-derived small RNA. Nucleic Acids Res 2019; 47:2075-2088. [PMID: 30541135 PMCID: PMC6393394 DOI: 10.1093/nar/gky1243] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/13/2018] [Accepted: 12/01/2018] [Indexed: 01/24/2023] Open
Abstract
Global RNA profiling studies in bacteria have predicted the existence of many of small noncoding RNAs (sRNAs) that are processed off mRNA 3′ ends to regulate other mRNAs via the RNA chaperones Hfq and ProQ. Here, we present targets of SdhX (RybD), an Hfq-dependent sRNA that is generated by RNase E mediated 3′ processing of the ∼10 000-nt mRNA of the TCA cycle operon sdhCDAB-sucABCD in enteric bacteria. An in silico search predicted ackA mRNA, which encodes acetate kinase, as a conserved primary target of SdhX. Through base pairing, SdhX represses AckA synthesis during growth of Salmonella on acetate. Repression can be achieved by a naturally occurring 38-nucleotide SdhX variant, revealing the shortest functional Hfq-associated sRNA yet. Salmonella SdhX also targets the mRNAs of fumB (anaerobic fumarase) and yfbV, a gene of unknown function adjacent to ackA. Instead, through a slightly different seed sequence, SdhX can repress other targets in Escherichia coli, namely katG (catalase) and fdoG (aerobic formate dehydrogenase). This study illustrates how a key operon from central metabolism is functionally connected to other metabolic pathways through a 3′ appended sRNA, and supports the notion that mRNA 3′UTRs are a playground for the evolution of regulatory RNA networks in bacteria.
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Affiliation(s)
- Masatoshi Miyakoshi
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 305-8575 Tsukuba, Japan.,Department of Biotechnology, Akita Prefectural University, 010-0195 Akita, Japan.,Center for Food Science and Wellness, Gunma University, 371-8510 Maebashi, Japan.,RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Gianluca Matera
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Kanako Maki
- Department of Biotechnology, Akita Prefectural University, 010-0195 Akita, Japan
| | - Yasuhiro Sone
- Department of Biotechnology, Akita Prefectural University, 010-0195 Akita, Japan
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research, D-97080 Würzburg, Germany
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11
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Caimano MJ, Groshong AM, Belperron A, Mao J, Hawley KL, Luthra A, Graham DE, Earnhart CG, Marconi RT, Bockenstedt LK, Blevins JS, Radolf JD. The RpoS Gatekeeper in Borrelia burgdorferi: An Invariant Regulatory Scheme That Promotes Spirochete Persistence in Reservoir Hosts and Niche Diversity. Front Microbiol 2019; 10:1923. [PMID: 31507550 PMCID: PMC6719511 DOI: 10.3389/fmicb.2019.01923] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 08/05/2019] [Indexed: 11/28/2022] Open
Abstract
Maintenance of Borrelia burgdorferi within its enzootic cycle requires a complex regulatory pathway involving the alternative σ factors RpoN and RpoS and two ancillary trans-acting factors, BosR and Rrp2. Activation of this pathway occurs within ticks during the nymphal blood meal when RpoS, the effector σ factor, transcribes genes required for tick transmission and mammalian infection. RpoS also exerts a 'gatekeeper' function by repressing σ70-dependent tick phase genes (e.g., ospA, lp6.6). Herein, we undertook a broad examination of RpoS functionality throughout the enzootic cycle, beginning with modeling to confirm that this alternative σ factor is a 'genuine' RpoS homolog. Using a novel dual color reporter system, we established at the single spirochete level that ospA is expressed in nymphal midguts throughout transmission and is not downregulated until spirochetes have been transmitted to a naïve host. Although it is well established that rpoS/RpoS is expressed throughout infection, its requirement for persistent infection has not been demonstrated. Plasmid retention studies using a trans-complemented ΔrpoS mutant demonstrated that (i) RpoS is required for maximal fitness throughout the mammalian phase and (ii) RpoS represses tick phase genes until spirochetes are acquired by a naïve vector. By transposon mutant screening, we established that bba34/oppA5, the only OppA oligopeptide-binding protein controlled by RpoS, is a bona fide persistence gene. Lastly, comparison of the strain 297 and B31 RpoS DMC regulons identified two cohorts of RpoS-regulated genes. The first consists of highly conserved syntenic genes that are similarly regulated by RpoS in both strains and likely required for maintenance of B. burgdorferi sensu stricto strains in the wild. The second includes RpoS-regulated plasmid-encoded variable surface lipoproteins ospC, dbpA and members of the ospE/ospF/elp, mlp, revA, and Pfam54 paralogous gene families, all of which have evolved via inter- and intra-strain recombination. Thus, while the RpoN/RpoS pathway regulates a 'core' group of orthologous genes, diversity within RpoS regulons of different strains could be an important determinant of reservoir host range as well as spirochete virulence.
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Affiliation(s)
- Melissa J. Caimano
- Department of Medicine, UConn Health, Farmington, CT, United States,Department of Pediatrics, UConn Health, Farmington, CT, United States,Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States,*Correspondence: Melissa J. Caimano,
| | | | - Alexia Belperron
- Department of Internal Medicine, Section of Rheumatology, Allergy and Immunology, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Jialing Mao
- Department of Internal Medicine, Section of Rheumatology, Allergy and Immunology, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Kelly L. Hawley
- Department of Pediatrics, UConn Health, Farmington, CT, United States,Division of Infectious Diseases and Immunology, Connecticut Children’s Medical Center, Hartford, CT, United States
| | - Amit Luthra
- Department of Medicine, UConn Health, Farmington, CT, United States
| | - Danielle E. Graham
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Christopher G. Earnhart
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, Richmond, VA, United States
| | - Richard T. Marconi
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, Richmond, VA, United States
| | - Linda K. Bockenstedt
- Department of Internal Medicine, Section of Rheumatology, Allergy and Immunology, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Jon S. Blevins
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Justin D. Radolf
- Department of Medicine, UConn Health, Farmington, CT, United States,Department of Pediatrics, UConn Health, Farmington, CT, United States,Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States,Department of Genetics and Genome Science, UConn Health, Farmington, CT, United States,Department of Immunology, UConn Health, Farmington, CT, United States
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12
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Wahl A, Battesti A, Ansaldi M. Prophages in Salmonella enterica: a driving force in reshaping the genome and physiology of their bacterial host? Mol Microbiol 2018; 111:303-316. [PMID: 30466179 PMCID: PMC7380047 DOI: 10.1111/mmi.14167] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2018] [Indexed: 12/11/2022]
Abstract
Thanks to the exponentially increasing number of publicly available bacterial genome sequences, one can now estimate the important contribution of integrated viral sequences to the diversity of bacterial genomes. Indeed, temperate bacteriophages are able to stably integrate the genome of their host through site‐specific recombination and transmit vertically to the host siblings. Lysogenic conversion has been long acknowledged to provide additional functions to the host, and particularly to bacterial pathogen genomes where prophages contribute important virulence factors. This review aims particularly at highlighting the current knowledge and questions about lysogeny in Salmonella genomes where functional prophages are abundant, and where genetic interactions between host and prophages are of particular importance for human health considerations.
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Affiliation(s)
- Astrid Wahl
- Laboratoire de Chimie Bactérienne, UMR7283, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | - Aurélia Battesti
- Laboratoire de Chimie Bactérienne, UMR7283, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | - Mireille Ansaldi
- Laboratoire de Chimie Bactérienne, UMR7283, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
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13
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Yin K, Guan Y, Ma R, Wei L, Liu B, Liu X, Zhou X, Ma Y, Zhang Y, Waldor MK, Wang Q. Critical role for a promoter discriminator in RpoS control of virulence in Edwardsiella piscicida. PLoS Pathog 2018; 14:e1007272. [PMID: 30169545 PMCID: PMC6136808 DOI: 10.1371/journal.ppat.1007272] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 09/13/2018] [Accepted: 08/09/2018] [Indexed: 12/11/2022] Open
Abstract
Edwardsiella piscicida is a leading fish pathogen that causes significant economic loses in the aquaculture industry. The pathogen depends on type III and type VI secretion systems (T3/T6SS) for growth and virulence in fish and the expression of both systems is controlled by the EsrB transcription activator. Here, we performed a Tn-seq-based screen to uncover factors that govern esrB expression. Unexpectedly, we discovered that RpoS antagonizes esrB expression and thereby inhibits production of E. piscicida’s T3/T6SS. Using in vitro transcription assays, we showed that RpoS can block RpoD-mediated transcription of esrB. ChIP-seq- and RNA-seq-based profiling, as well as mutational and biochemical analyses revealed that RpoS-repressed promoters contain a -6G in their respective discriminator sequences; moreover, this -6G proved critical for RpoS to inhibit esrB expression. Mutation of the RpoS R99 residue, an amino acid that molecular modeling predicts interacts with -6G in the esrB discriminator, abolished RpoS’ capacity for repression. In a turbot model, an rpoS deletion mutant was attenuated early but not late in infection, whereas a mutant expressing RpoSR99A exhibited elevated fitness throughout the infection period. Collectively, these findings deepen our understanding of how RpoS can inhibit gene expression and demonstrate the temporal variation in the requirement for this sigma factor during infection. Edwardsiella piscicida, a major fish pathogen, relies on T3/T6SSs for virulence and the EsrB transcription activator promotes the expression of these secretion systems and many other genes that enable growth in fish. Here, we found that the alternative sigma factor RpoS inhibits expression of esrB thereby diminishing expression of virulence-associated genes. Transcriptome profiling revealed that, as in many other organisms, RpoS enables expression of hundreds of genes, many of which are linked to stress responses, suggesting that RpoS may mediate a trade-off between stress adaptation and virulence. Consistent with this idea, we found that an rpoS mutant was attenuated early, but not late in infection of turbot, whereas an esrB mutant was attenuated late and not early in infection. Molecular analyses demonstrated that RpoS inhibition of esrB expression involves a direct interaction between RpoS and the esrB promoter; in particular, interactions between RpoS residue R99 and the -6G nucleotide in the esrB promoter discriminator appear to be critical for repression of esrB expression. These findings provide new insight into how a sigma factor can impede transcription and demonstrate the temporal dynamics of the requirement for a sigma factor during the course of infection.
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Affiliation(s)
- Kaiyu Yin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, East China University of Science and Technology, Shanghai, China
| | - Yunpeng Guan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Ruiqing Ma
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Lifan Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Bing Liu
- Institut de Biotecnologia i Biomedicina, Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Xiaohong Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xiangshan Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yue Ma
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, East China University of Science and Technology, Shanghai, China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, East China University of Science and Technology, Shanghai, China
| | - Matthew K. Waldor
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Division of Infectious Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, East China University of Science and Technology, Shanghai, China
- * E-mail:
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14
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Two Distinct Mechanisms Govern RpoS-Mediated Repression of Tick-Phase Genes during Mammalian Host Adaptation by Borrelia burgdorferi, the Lyme Disease Spirochete. mBio 2017; 8:mBio.01204-17. [PMID: 28830947 PMCID: PMC5565969 DOI: 10.1128/mbio.01204-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The alternative sigma factor RpoS plays a key role modulating gene expression in Borrelia burgdorferi, the Lyme disease spirochete, by transcribing mammalian host-phase genes and repressing σ70-dependent genes required within the arthropod vector. To identify cis regulatory elements involved in RpoS-dependent repression, we analyzed green fluorescent protein (GFP) transcriptional reporters containing portions of the upstream regions of the prototypical tick-phase genes ospAB, the glp operon, and bba74. As RpoS-mediated repression occurs only following mammalian host adaptation, strains containing the reporters were grown in dialysis membrane chambers (DMCs) implanted into the peritoneal cavities of rats. Wild-type spirochetes harboring ospAB- and glp-gfp constructs containing only the minimal (−35/−10) σ70 promoter elements had significantly lower expression in DMCs relative to growth in vitro at 37°C; no reduction in expression occurred in a DMC-cultivated RpoS mutant harboring these constructs. In contrast, RpoS-mediated repression of bba74 required a stretch of DNA located between −165 and −82 relative to its transcriptional start site. Electrophoretic mobility shift assays employing extracts of DMC-cultivated B. burgdorferi produced a gel shift, whereas extracts from RpoS mutant spirochetes did not. Collectively, these data demonstrate that RpoS-mediated repression of tick-phase borrelial genes occurs by at least two distinct mechanisms. One (e.g., ospAB and the glp operon) involves primarily sequence elements near the core promoter, while the other (e.g., bba74) involves an RpoS-induced transacting repressor. Our results provide a genetic framework for further dissection of the essential “gatekeeper” role of RpoS throughout the B. burgdorferi enzootic cycle. Borrelia burgdorferi, the Lyme disease spirochete, modulates gene expression to adapt to the distinctive environments of its mammalian host and arthropod vector during its enzootic cycle. The alternative sigma factor RpoS has been referred to as a “gatekeeper” due to its central role in regulating the reciprocal expression of mammalian host- and tick-phase genes. While RpoS-dependent transcription has been studied extensively, little is known regarding the mechanism(s) of RpoS-mediated repression. We employed a combination of green fluorescent protein transcriptional reporters along with an in vivo model to define cis regulatory sequences responsible for RpoS-mediated repression of prototypical tick-phase genes. Repression of ospAB and the glp operon requires only sequences near their core promoters, whereas modulation of bba74 expression involves a putative RpoS-dependent repressor that binds upstream of the core promoter. Thus, Lyme disease spirochetes employ at least two different RpoS-dependent mechanisms to repress tick-phase genes within the mammal.
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15
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Lago M, Monteil V, Douche T, Guglielmini J, Criscuolo A, Maufrais C, Matondo M, Norel F. Proteome remodelling by the stress sigma factor RpoS/σ S in Salmonella: identification of small proteins and evidence for post-transcriptional regulation. Sci Rep 2017; 7:2127. [PMID: 28522802 PMCID: PMC5437024 DOI: 10.1038/s41598-017-02362-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 04/10/2017] [Indexed: 12/17/2022] Open
Abstract
The RpoS/σS sigma subunit of RNA polymerase is the master regulator of the general stress response in many Gram-negative bacteria. Extensive studies have been conducted on σS-regulated gene expression at the transcriptional level. In contrast, very limited information regarding the impact of σS on global protein production is available. In this study, we used a mass spectrometry-based proteomics approach to explore the wide σS-dependent proteome of the human pathogen Salmonella enterica serovar Typhimurium. Our present goals were twofold: (1) to survey the protein changes associated with the ΔrpoS mutation and (2) to assess the coding capacity of σS-dependent small RNAs. Our proteomics data, and complementary assays, unravelled the large impact of σS on the Salmonella proteome, and validated expression and σS regulation of twenty uncharacterized small proteins of 27 to 96 amino acids. Furthermore, a large number of genes regulated at the protein level only were identified, suggesting that post-transcriptional regulation is an important component of the σS response. Novel aspects of σS in the control of important catabolic pathways such as myo-inositol, L-fucose, propanediol, and ethanolamine were illuminated by this work, providing new insights into the physiological remodelling involved in bacterial adaptation to a non-actively growing state.
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Affiliation(s)
- Magali Lago
- Institut Pasteur, Laboratoire Systèmes Macromoléculaires et Signalisation, Département de Microbiologie, rue du Dr. Roux, 75015, Paris, France
- CNRS ERL6002, rue du Docteur Roux, 75015, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, rue du Dr. Roux, 75015, Paris, France
| | - Véronique Monteil
- Institut Pasteur, Laboratoire Systèmes Macromoléculaires et Signalisation, Département de Microbiologie, rue du Dr. Roux, 75015, Paris, France
- CNRS ERL6002, rue du Docteur Roux, 75015, Paris, France
- Institut Pasteur, Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie structurale et Chimie, rue du Dr. Roux, 75015, Paris, France
| | - Thibaut Douche
- Institut Pasteur, Unité de Spectrométrie de Masse Structurale et Protéomique, Département de Biologie Structurale et Chimie, UMR3528, rue du Dr. Roux, 75015, Paris, France
| | - Julien Guglielmini
- Institut Pasteur, Bioinformatics and Biostatistics Hub, C3BI, USR 3756 IP CNRS, rue du Dr. Roux, 75015, Paris, France
| | - Alexis Criscuolo
- Institut Pasteur, Bioinformatics and Biostatistics Hub, C3BI, USR 3756 IP CNRS, rue du Dr. Roux, 75015, Paris, France
| | - Corinne Maufrais
- Institut Pasteur, Bioinformatics and Biostatistics Hub, C3BI, USR 3756 IP CNRS, rue du Dr. Roux, 75015, Paris, France
| | - Mariette Matondo
- Institut Pasteur, Unité de Spectrométrie de Masse Structurale et Protéomique, Département de Biologie Structurale et Chimie, UMR3528, rue du Dr. Roux, 75015, Paris, France
| | - Françoise Norel
- Institut Pasteur, Laboratoire Systèmes Macromoléculaires et Signalisation, Département de Microbiologie, rue du Dr. Roux, 75015, Paris, France.
- CNRS ERL6002, rue du Docteur Roux, 75015, Paris, France.
- Institut Pasteur, Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie structurale et Chimie, rue du Dr. Roux, 75015, Paris, France.
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Genome-Wide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12. J Bacteriol 2017; 199:JB.00755-16. [PMID: 28115545 DOI: 10.1128/jb.00755-16] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/12/2017] [Indexed: 01/31/2023] Open
Abstract
The alternative sigma factor RpoS is a central regulator of many stress responses in Escherichia coli The level of functional RpoS differs depending on the stress. The effect of these differing concentrations of RpoS on global transcriptional responses remains unclear. We investigated the effect of RpoS concentration on the transcriptome during stationary phase in rich media. We found that 23% of genes in the E. coli genome are regulated by RpoS, and we identified many RpoS-transcribed genes and promoters. We observed three distinct classes of response to RpoS by genes in the regulon: genes whose expression changes linearly with increasing RpoS level, genes whose expression changes dramatically with the production of only a little RpoS ("sensitive" genes), and genes whose expression changes very little with the production of a little RpoS ("insensitive"). We show that sequences outside the core promoter region determine whether an RpoS-regulated gene is sensitive or insensitive. Moreover, we show that sensitive and insensitive genes are enriched for specific functional classes and that the sensitivity of a gene to RpoS corresponds to the timing of induction as cells enter stationary phase. Thus, promoter sensitivity to RpoS is a mechanism to coordinate specific cellular processes with growth phase and may also contribute to the diversity of stress responses directed by RpoS.IMPORTANCE The sigma factor RpoS is a global regulator that controls the response to many stresses in Escherichia coli Different stresses result in different levels of RpoS production, but the consequences of this variation are unknown. We describe how changing the level of RpoS does not influence all RpoS-regulated genes equally. The cause of this variation is likely the action of transcription factors that bind the promoters of the genes. We show that the sensitivity of a gene to RpoS levels explains the timing of expression as cells enter stationary phase and that genes with different RpoS sensitivities are enriched for specific functional groups. Thus, promoter sensitivity to RpoS is a mechanism that coordinates specific cellular processes in response to stresses.
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Cavaliere P, Norel F. Recent advances in the characterization of Crl, the unconventional activator of the stress sigma factor σS/RpoS. Biomol Concepts 2017; 7:197-204. [PMID: 27180360 DOI: 10.1515/bmc-2016-0006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 03/29/2016] [Indexed: 11/15/2022] Open
Abstract
The bacterial RNA polymerase (RNAP) holoenzyme is a multisubunit core enzyme associated with a σ factor that is required for promoter-specific transcription initiation. Besides a primary σ responsible for most of the gene expression during active growth, bacteria contain alternative σ factors that control adaptive responses. A recurring strategy in the control of σ factor activity is their sequestration by anti-sigma factors that occlude the RNAP binding determinants, reducing their activity. In contrast, the unconventional transcription factor Crl binds specifically to the alternative σ factor σS/RpoS, and favors its association with the core RNAP, thereby increasing its activity. σS is the master regulator of the general stress response that protects many Gram-negative bacteria from several harmful environmental conditions. It is also required for biofilm formation and virulence of Salmonella enterica serovar Typhimurium. In this report, we discuss current knowledge on the regulation and function of Crl in Salmonella and Escherichia coli, two bacterial species in which Crl has been studied. We review recent advances in the structural characterization of the Crl-σS interaction that have led to a better understanding of this unusual mechanism of σ regulation.
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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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Binding interface between the Salmonella σ(S)/RpoS subunit of RNA polymerase and Crl: hints from bacterial species lacking crl. Sci Rep 2015; 5:13564. [PMID: 26338235 PMCID: PMC4559669 DOI: 10.1038/srep13564] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/30/2015] [Indexed: 01/30/2023] Open
Abstract
In many Gram-negative bacteria, including Salmonella enterica serovar Typhimurium (S. Typhimurium), the sigma factor RpoS/σS accumulates during stationary phase of growth, and associates with the core RNA polymerase enzyme (E) to promote transcription initiation of genes involved in general stress resistance and starvation survival. Whereas σ factors are usually inactivated upon interaction with anti-σ proteins, σS binding to the Crl protein increases σS activity by favouring its association to E. Taking advantage of evolution of the σS sequence in bacterial species that do not contain a crl gene, like Pseudomonas aeruginosa, we identified and assigned a critical arginine residue in σS to the S. Typhimurium σS-Crl binding interface. We solved the solution structure of S. Typhimurium Crl by NMR and used it for NMR binding assays with σS and to generate in silico models of the σS-Crl complex constrained by mutational analysis. The σS-Crl models suggest that the identified arginine in σS interacts with an aspartate of Crl that is required for σS binding and is located inside a cavity enclosed by flexible loops, which also contribute to the interface. This study provides the basis for further structural investigation of the σS-Crl complex.
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Schaefer J, Engl C, Zhang N, Lawton E, Buck M. Genome wide interactions of wild-type and activator bypass forms of σ54. Nucleic Acids Res 2015; 43:7280-91. [PMID: 26082500 PMCID: PMC4551910 DOI: 10.1093/nar/gkv597] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 05/25/2015] [Indexed: 01/05/2023] Open
Abstract
Enhancer-dependent transcription involving the promoter specificity factor σ54 is widely distributed amongst bacteria and commonly associated with cell envelope function. For transcription initiation, σ54-RNA polymerase yields open promoter complexes through its remodelling by cognate AAA+ ATPase activators. Since activators can be bypassed in vitro, bypass transcription in vivo could be a source of emergent gene expression along evolutionary pathways yielding new control networks and transcription patterns. At a single test promoter in vivo bypass transcription was not observed. We now use genome-wide transcription profiling, genome-wide mutagenesis and gene over-expression strategies in Escherichia coli, to (i) scope the range of bypass transcription in vivo and (ii) identify genes which might alter bypass transcription in vivo. We find little evidence for pervasive bypass transcription in vivo with only a small subset of σ54 promoters functioning without activators. Results also suggest no one gene limits bypass transcription in vivo, arguing bypass transcription is strongly kept in check. Promoter sequences subject to repression by σ54 were evident, indicating loss of rpoN (encoding σ54) rather than creating rpoN bypass alleles would be one evolutionary route for new gene expression patterns. Finally, cold-shock promoters showed unusual σ54-dependence in vivo not readily correlated with conventional σ54 binding-sites.
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Affiliation(s)
- Jorrit Schaefer
- Faculty of Natural Sciences, Division of Cell & Molecular Biology, Imperial College London, London SW7 2AZ, UK
| | - Christoph Engl
- Faculty of Natural Sciences, Division of Cell & Molecular Biology, Imperial College London, London SW7 2AZ, UK Institute for Global Food Security, Queen's University Belfast, Belfast BT9 5BN, UK
| | - Nan Zhang
- Faculty of Natural Sciences, Division of Cell & Molecular Biology, Imperial College London, London SW7 2AZ, UK
| | - Edward Lawton
- Faculty of Natural Sciences, Division of Cell & Molecular Biology, Imperial College London, London SW7 2AZ, UK
| | - Martin Buck
- Faculty of Natural Sciences, Division of Cell & Molecular Biology, Imperial College London, London SW7 2AZ, UK
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21
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Awale M, Jin X, Reymond JL. Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints. J Cheminform 2015; 7:3. [PMID: 25750664 PMCID: PMC4352573 DOI: 10.1186/s13321-014-0051-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 12/19/2014] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Tools to explore large compound databases in search for analogs of query molecules provide a strategically important support in drug discovery to help identify available analogs of any given reference or hit compound by ligand based virtual screening (LBVS). We recently showed that large databases can be formatted for very fast searching with various 2D-fingerprints using the city-block distance as similarity measure, in particular a 2D-atom pair fingerprint (APfp) and the related category extended atom pair fingerprint (Xfp) which efficiently encode molecular shape and pharmacophores, but do not perceive stereochemistry. Here we investigated related 3D-atom pair fingerprints to enable rapid stereoselective searches in the ZINC database (23.2 million 3D structures). RESULTS Molecular fingerprints counting atom pairs at increasing through-space distance intervals were designed using either all atoms (16-bit 3DAPfp) or different atom categories (80-bit 3DXfp). These 3D-fingerprints retrieved molecular shape and pharmacophore analogs (defined by OpenEye ROCS scoring functions) of 110,000 compounds from the Cambridge Structural Database with equal or better accuracy than the 2D-fingerprints APfp and Xfp, and showed comparable performance in recovering actives from decoys in the DUD database. LBVS by 3DXfp or 3DAPfp similarity was stereoselective and gave very different analogs when starting from different diastereomers of the same chiral drug. Results were also different from LBVS with the parent 2D-fingerprints Xfp or APfp. 3D- and 2D-fingerprints also gave very different results in LBVS of folded molecules where through-space distances between atom pairs are much shorter than topological distances. CONCLUSIONS 3DAPfp and 3DXfp are suitable for stereoselective searches for shape and pharmacophore analogs of query molecules in large databases. Web-browsers for searching ZINC by 3DAPfp and 3DXfp similarity are accessible at www.gdb.unibe.ch and should provide useful assistance to drug discovery projects. Graphical abstractAtom pair fingerprints based on through-space distances (3DAPfp) provide better shape encoding than atom pair fingerprints based on topological distances (APfp) as measured by the recovery of ROCS shape analogs by fp similarity.
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Affiliation(s)
- Mahendra Awale
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Xian Jin
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
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