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Paredes-Martínez F, Eixerés L, Zamora-Caballero S, Casino P. Structural and functional insights underlying recognition of histidine phosphotransfer protein in fungal phosphorelay systems. Commun Biol 2024; 7:814. [PMID: 38965424 PMCID: PMC11224324 DOI: 10.1038/s42003-024-06459-0] [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: 08/17/2023] [Accepted: 06/14/2024] [Indexed: 07/06/2024] Open
Abstract
In human pathogenic fungi, receiver domains from hybrid histidine kinases (hHK) have to recognize one HPt. To understand the recognition mechanism, we have assessed phosphorelay from receiver domains of five hHKs of group III, IV, V, VI, and XI to HPt from Chaetomium thermophilum and obtained the structures of Ct_HPt alone and in complex with the receiver domain of hHK group VI. Our data indicate that receiver domains phosphotransfer to Ct_HPt, show a low affinity for complex formation, and prevent a Leu-Thr switch to stabilize phosphoryl groups, also derived from the structures of the receiver domains of hHK group III and Candida albicans Sln1. Moreover, we have elucidated the envelope structure of C. albicans Ypd1 using small-angle X-ray scattering which reveals an extended flexible conformation of the long loop αD-αE which is not involved in phosphotransfer. Finally, we have analyzed the role of salt bridges in the structure of Ct_HPt alone.
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Affiliation(s)
- Francisco Paredes-Martínez
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Burjassot, Spain
- Instituto Universitario en Biotecnología y Biomedicina (BIOTECMED), Universitat de València, Burjassot, Spain
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Valencia, Spain
| | - Lluís Eixerés
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Burjassot, Spain
- Instituto Universitario en Biotecnología y Biomedicina (BIOTECMED), Universitat de València, Burjassot, Spain
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Valencia, Spain
| | - Sara Zamora-Caballero
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Valencia, Spain
| | - Patricia Casino
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Burjassot, Spain.
- Instituto Universitario en Biotecnología y Biomedicina (BIOTECMED), Universitat de València, Burjassot, Spain.
- CIBER de Enfermedades Raras (CIBERER-ISCIII), Madrid, Spain.
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2
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Kato A. Development of conjugation-mediated versatile site-specific single-copy luciferase fusion system. J GEN APPL MICROBIOL 2024; 69:318-326. [PMID: 37940551 DOI: 10.2323/jgam.2023.10.001] [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] [Indexed: 11/10/2023]
Abstract
There are a number of reporter systems that are useful for gene expression analysis in bacteria. However, at least in Salmonella, a versatile and simple luciferase reporter system that can be integrated precisely behind a promoter or gene of interest on a chromosome is not currently available. The luciferase operon luxCDABE from Photorhabdus luminescens has several advantages, including brightness, wide linear range, absence in most bacteria, stability at high temperature, and no substrate addition required for the assay. Here, a conjugation-mediated site-specific single-copy luciferase fusion system is developed. A reporter plasmid containing the conditional replication origin R6Kgγ, FRT-luxCDABE, and KmR marker was designed to be incorporated into the FRT site behind the promoter or gene of interest on the chromosome in cells expressing FLP. However, when this reporter plasmid was electroporated directly into such a S. enterica strain, no colonies appeared, likely due to the low transformation efficiency of this relatively large plasmid DNA. Meanwhile, the same reporter plasmid was successfully introduced and launched as an insert of an FRT-containing conjugative transfer plasmid from a mating E. coli strain to the same recipient S. enterica strain, as well as Citrobacter koseri. RcsB-dependent inducible luminescence from the constructed wzc-luxCDABE strains was confirmed. This system is feasible for detecting very low levels of transcription, even in Gram-negative bacterial species that are relatively difficult to genetically manipulate.
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Affiliation(s)
- Akinori Kato
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University
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3
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Xie P, Xu Y, Tang J, Wu S, Gao H. Multifaceted regulation of siderophore synthesis by multiple regulatory systems in Shewanella oneidensis. Commun Biol 2024; 7:498. [PMID: 38664541 PMCID: PMC11045786 DOI: 10.1038/s42003-024-06193-7] [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: 01/15/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Siderophore-dependent iron uptake is a mechanism by which microorganisms scavenge and utilize iron for their survival, growth, and many specialized activities, such as pathogenicity. The siderophore biosynthetic system PubABC in Shewanella can synthesize a series of distinct siderophores, yet how it is regulated in response to iron availability remains largely unexplored. Here, by whole genome screening we identify TCS components histidine kinase (HK) BarA and response regulator (RR) SsoR as positive regulators of siderophore biosynthesis. While BarA partners with UvrY to mediate expression of pubABC post-transcriptionally via the Csr regulatory cascade, SsoR is an atypical orphan RR of the OmpR/PhoB subfamily that activates transcription in a phosphorylation-independent manner. By combining structural analysis and molecular dynamics simulations, we observe conformational changes in OmpR/PhoB-like RRs that illustrate the impact of phosphorylation on dynamic properties, and that SsoR is locked in the 'phosphorylated' state found in phosphorylation-dependent counterparts of the same subfamily. Furthermore, we show that iron homeostasis global regulator Fur, in addition to mediating transcription of its own regulon, acts as the sensor of iron starvation to increase SsoR production when needed. Overall, this study delineates an intricate, multi-tiered transcriptional and post-transcriptional regulatory network that governs siderophore biosynthesis.
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Affiliation(s)
- Peilu Xie
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Yuanyou Xu
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jiaxin Tang
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Shihua Wu
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Haichun Gao
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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4
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Grote A, Piscon B, Manson AL, Adani B, Cohen H, Livny J, Earl AM, Gal-Mor O. Persistent Salmonella infections in humans are associated with mutations in the BarA/SirA regulatory pathway. Cell Host Microbe 2024; 32:79-92.e7. [PMID: 38211565 DOI: 10.1016/j.chom.2023.12.001] [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: 07/26/2022] [Revised: 10/04/2023] [Accepted: 12/06/2023] [Indexed: 01/13/2024]
Abstract
Several bacterial pathogens, including Salmonella enterica, can cause persistent infections in humans by mechanisms that are poorly understood. By comparing genomes of isolates longitudinally collected from 256 prolonged salmonellosis patients, we identified repeated mutations in global regulators, including the barA/sirA two-component regulatory system, across multiple patients and Salmonella serovars. Comparative RNA-seq analysis revealed that distinct mutations in barA/sirA led to diminished expression of Salmonella pathogenicity islands 1 and 4 genes, which are required for Salmonella invasion and enteritis. Moreover, barA/sirA mutants were attenuated in an acute salmonellosis mouse model and induced weaker transcription of host immune responses. In contrast, in a persistent infection mouse model, these mutants exhibited long-term colonization and prolonged shedding. Taken together, these findings suggest that selection of mutations in global virulence regulators facilitates persistent Salmonella infection in humans, by attenuating Salmonella virulence and inducing a weaker host inflammatory response.
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Affiliation(s)
- Alexandra Grote
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bar Piscon
- Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel; Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Abigail L Manson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Boaz Adani
- Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
| | - Helit Cohen
- Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
| | - Jonathan Livny
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Ohad Gal-Mor
- Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel; Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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5
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Chen X, Alakavuklar MA, Fiebig A, Crosson S. Cross-regulation in a three-component cell envelope stress signaling system of Brucella. mBio 2023; 14:e0238723. [PMID: 38032291 PMCID: PMC10746171 DOI: 10.1128/mbio.02387-23] [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: 09/06/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE As intracellular pathogens, Brucella must contend with a variety of host-derived stressors when infecting a host cell. The inner membrane, cell wall, and outer membrane, i.e. the cell envelope, of Brucella provide a critical barrier to host assault. A conserved regulatory mechanism known as two-component signaling (TCS) commonly controls transcription of genes that determine the structure and biochemical composition of the cell envelope during stress. We report the identification of previously uncharacterized TCS genes that determine Brucella ovis fitness in the presence of cell envelope disruptors and within infected mammalian host cells. Our study reveals a new molecular mechanism of TCS-dependent gene regulation, and thereby advances fundamental understanding of transcriptional regulatory processes in bacteria.
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Affiliation(s)
- Xingru Chen
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Melene A. Alakavuklar
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Aretha Fiebig
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Sean Crosson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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6
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Chen X, Alakavuklar MA, Fiebig A, Crosson S. Cross regulation in a three-component cell envelope stress signaling system of Brucella. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.15.536747. [PMID: 37873345 PMCID: PMC10592609 DOI: 10.1101/2023.04.15.536747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
A multi-layered structure known as the cell envelope separates the controlled interior of bacterial cells from a fluctuating physical and chemical environment. The transcription of genes that determine cell envelope structure and function is commonly regulated by two-component signaling systems (TCS), comprising a sensor histidine kinase and a cognate response regulator. To identify TCS genes that contribute to cell envelope function in the intracellular mammalian pathogen, Brucella ovis, we subjected a collection of non-essential TCS deletion mutants to compounds that disrupt cell membranes and the peptidoglycan cell wall. Our screen led to the discovery of three TCS proteins that coordinately function to confer resistance to cell envelope stressors and to support B. ovis replication in the intracellular niche. This tripartite regulatory system includes the known cell envelope regulator, CenR, and a previously uncharacterized TCS, EssR-EssS, which is widely conserved in Alphaproteobacteria. The CenR and EssR response regulators bind a shared set of sites on the B. ovis chromosomes to control transcription of an overlapping set of genes with cell envelope functions. CenR directly interacts with EssR and functions to stimulate phosphoryl transfer from the EssS kinase to EssR, while CenR and EssR control the cellular levels of each other via a post-transcriptional mechanism. Our data provide evidence for a new mode of TCS cross-regulation in which a non-cognate response regulator affects both the activity and protein levels of a cognate TCS protein pair.
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Affiliation(s)
- Xingru Chen
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan USA
| | - Melene A Alakavuklar
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan USA
| | - Aretha Fiebig
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan USA
| | - Sean Crosson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan USA
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Pokorzynski ND, Groisman EA. How Bacterial Pathogens Coordinate Appetite with Virulence. Microbiol Mol Biol Rev 2023; 87:e0019822. [PMID: 37358444 PMCID: PMC10521370 DOI: 10.1128/mmbr.00198-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023] Open
Abstract
Cells adjust growth and metabolism to nutrient availability. Having access to a variety of carbon sources during infection of their animal hosts, facultative intracellular pathogens must efficiently prioritize carbon utilization. Here, we discuss how carbon source controls bacterial virulence, with an emphasis on Salmonella enterica serovar Typhimurium, which causes gastroenteritis in immunocompetent humans and a typhoid-like disease in mice, and propose that virulence factors can regulate carbon source prioritization by modifying cellular physiology. On the one hand, bacterial regulators of carbon metabolism control virulence programs, indicating that pathogenic traits appear in response to carbon source availability. On the other hand, signals controlling virulence regulators may impact carbon source utilization, suggesting that stimuli that bacterial pathogens experience within the host can directly impinge on carbon source prioritization. In addition, pathogen-triggered intestinal inflammation can disrupt the gut microbiota and thus the availability of carbon sources. By coordinating virulence factors with carbon utilization determinants, pathogens adopt metabolic pathways that may not be the most energy efficient because such pathways promote resistance to antimicrobial agents and also because host-imposed deprivation of specific nutrients may hinder the operation of certain pathways. We propose that metabolic prioritization by bacteria underlies the pathogenic outcome of an infection.
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Affiliation(s)
- Nick D. Pokorzynski
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Eduardo A. Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Microbial Sciences Institute, West Haven, Connecticut, USA
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8
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Nava-Galeana J, Núñez C, Bustamante VH. Proteomic analysis reveals the global effect of the BarA/SirA-Csr regulatory cascade in Salmonella Typhimurium grown in conditions that favor the expression of invasion genes. J Proteomics 2023; 286:104960. [PMID: 37451358 DOI: 10.1016/j.jprot.2023.104960] [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: 03/29/2023] [Accepted: 06/27/2023] [Indexed: 07/18/2023]
Abstract
In many bacteria, the BarA/SirA and Csr regulatory systems control expression of genes encoding a wide variety of cellular functions. The BarA/SirA two-component system induces the expression of CsrB and CsrC, two small non-coding RNAs that sequester CsrA, a protein that binds to target mRNAs and thus negatively or positively regulates their expression. BarA/SirA and CsrB/C induce expression of the Salmonella Pathogenicity Island 1 (SPI-1) genes required for Salmonella invasion of host cells. To further investigate the regulatory role of the BarA/SirA and Csr systems in Salmonella, we performed LC-MS/MS proteomic analysis using the WT S. Typhimurium strain and its derived ΔsirA and ΔcsrB ΔcsrC mutants grown in SPI-1-inducing conditions. The expression of 164 proteins with a wide diversity, or unknown, functions was significantly affected positively or negatively by the absence of SirA and/or CsrB/C. Interestingly, 19 proteins were identified as new targets for SirA-CsrB/C. Our results support that SirA and CsrB/C act in a cascade fashion to regulate gene expression in S. Typhimurium in the conditions tested. Notably, our results show that SirA-CsrB/C-CsrA controls expression of proteins required for the replication of Salmonella in the intestinal lumen, in an opposite way to its control exerted on the SPI-1 proteins. SIGNIFICANCE: The BarA/SirA and Csr global regulatory systems control a wide range of cellular processes, including the expression of virulence genes. For instance, in Salmonella, BarA/SirA and CsrB/C positively regulate expression of the SPI-1 genes, which are required for Salmonella invasion to host cells. In this study, by performing a proteomic analysis, we identified 164 proteins whose expression was positively or negatively controlled by SirA and CsrB/C in SPI-1-inducing conditions, including 19 new possible targets of these systems. Our results support the action of SirA and CsrB/C in a cascade fashion to control different cellular processes in Salmonella. Interestingly, our data indicate that SirA-CsrB/C-CsrA controls inversely the expression of proteins required for invasion of the intestinal epithelium and for replication in the intestinal lumen, which suggests a role for this regulatory cascade as a molecular switch for Salmonella virulence. Thus, our study further expands the insight into the regulatory mechanisms governing the virulence and physiology of an important pathogen.
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Affiliation(s)
- Jessica Nava-Galeana
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Cinthia Núñez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Víctor H Bustamante
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico.
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9
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Shan S, Hu T, Yang Y. The deletion of HK-1 gene affects the bacterial virulence of Pseudomonas stutzeri LH-42. PLoS One 2022; 17:e0277089. [PMID: 36445858 PMCID: PMC9707753 DOI: 10.1371/journal.pone.0277089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/19/2022] [Indexed: 12/03/2022] Open
Abstract
Two-component systems (TCSs) are widespread regulatory systems in bacteria, which control cellular functions and play an important role in sensing various external stimuli and regulating gene expression in response to environmental changes. Among the nineteen genes for the two-component system found in the whole genome of Pseudomonas stutzeri LH-42, one of the TCS coded by the HK-1 gene, has a structural domain similar to the HAMP domain, which plays an important role in regulating bacterial virulence in other bacteria. In this study, the deletion mutant LH-42△HK-1 was successfully constructed using the lambda Red recombinase system. Compared with the wild-type strain, the mutant strain LH-42△HK-1 showed a significantly slower growth time and a longer stationary phase time. In addition, in the plate bacteriostatic experiment with Escherichia coli DH5α as an indicator strain, the inhibition zone size of the mutant strain showed significantly less than the wild-type strain(P<0.05), indicating that the virulence of the mutant strain was significantly reduced compared with the wild-type strain. Overall, the results indicate that the deletion of the gene HK-1 decreased bacterial virulence in Pseudomonas stutzeri LH-42.
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Affiliation(s)
- Si Shan
- School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, China
| | - Tingting Hu
- The First People’s Hospital of Jingzhou, Jingzhou, Hubei, China
| | - Yu Yang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, China
- Key Laboratory of Biohydrometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, China
- * E-mail:
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10
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Marmion M, Macori G, Whyte P, Scannell AGM. Stress response modulation: the key to survival of pathogenic and spoilage bacteria during poultry processing. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35451951 DOI: 10.1099/mic.0.001184] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The control of bacterial contaminants on meat is a key area of interest in the food industry. Bacteria are exposed to a variety of stresses during broiler processing which challenge bacterial structures and metabolic pathways causing death or sublethal injury. To counter these stresses, bacteria possess robust response systems that can induce shifts in the transcriptome and proteome to enable survival. Effective adaptive responses, such as biofilm formation, shock protein production and metabolic flexibility, require rapid induction and implementation at a cellular and community level to facilitate bacterial survival in adverse conditions. This review aims to provide an overview of the scientific literature pertaining to the regulation of complex adaptive processes used by bacteria to survive the processing environment, with particular focus on species that impact the quality and safety of poultry products like Campylobacter spp., Salmonella enterica and Pseudomonas spp.
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Affiliation(s)
- Maitiú Marmion
- UCD School of Agriculture and Food Science, Belfield, Dublin 4, D04V4W8, Ireland.,UCD Centre for Food Safety, University College Dublin, Belfield, Dublin 4, D04V4W8, Ireland
| | - Guerrino Macori
- UCD School of Agriculture and Food Science, Belfield, Dublin 4, D04V4W8, Ireland.,UCD Centre for Food Safety, University College Dublin, Belfield, Dublin 4, D04V4W8, Ireland
| | - Paul Whyte
- UCD School of Veterinary Medicine, Belfield, Dublin 4, D04V4W8, Ireland
| | - Amalia G M Scannell
- UCD School of Agriculture and Food Science, Belfield, Dublin 4, D04V4W8, Ireland.,UCD Centre for Food Safety, University College Dublin, Belfield, Dublin 4, D04V4W8, Ireland.,UCD Institute of Food and Health, Belfield, Dublin 4, D04V4W8, Ireland
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11
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Marmion M, Macori G, Ferone M, Whyte P, Scannell A. Survive and thrive: Control mechanisms that facilitate bacterial adaptation to survive manufacturing-related stress. Int J Food Microbiol 2022; 368:109612. [DOI: 10.1016/j.ijfoodmicro.2022.109612] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/21/2022] [Accepted: 03/02/2022] [Indexed: 10/18/2022]
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12
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Cheng C, Liu F, Jin H, Xu X, Xu J, Deng S, Xia J, Han Y, Lei L, Zhang X, Song H. The DegU Orphan Response Regulator Contributes to Heat Stress Resistance in Listeria monocytogenes. Front Cell Infect Microbiol 2021; 11:761335. [PMID: 34966695 PMCID: PMC8711649 DOI: 10.3389/fcimb.2021.761335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/25/2021] [Indexed: 11/24/2022] Open
Abstract
Listeria monocytogenes is more heat-resistant than most other non-spore-forming foodborne pathogens, posing a severe threat to food safety and human health, particularly during chilled food processing. The DegU orphan response regulator is known to control heat resistance in L. monocytogenes; however, the underlying regulatory mechanism is poorly understood. Here, we show that DegU contributes to L. monocytogenes exponential growth under mild heat-shock stress. We further demonstrate that DegU directly senses heat stress through autoregulation and upregulates the hrcA-grpE-dnaK-dnaJ operon, leading to increased production of heat-shock proteins. We also show that DegU can directly regulate the expression of the hrcA-grpE-dnaK-dnaJ operon. In conclusion, our results shed light on the regulatory mechanisms underlying how DegU directly activates the hrcA-grpE-dnaK-dnaJ operon, thereby regulating heat resistance in L. monocytogenes.
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Affiliation(s)
- Changyong Cheng
- College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, China-Australia Joint Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Hangzhou, China
| | - Feng Liu
- College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, China-Australia Joint Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Hangzhou, China
| | - Haobo Jin
- College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, China-Australia Joint Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Hangzhou, China
| | - Xiangfei Xu
- College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, China-Australia Joint Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Hangzhou, China
| | - Jiali Xu
- College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, China-Australia Joint Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Hangzhou, China
| | - Simin Deng
- College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, China-Australia Joint Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Hangzhou, China
| | - Jing Xia
- College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, China-Australia Joint Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Hangzhou, China
| | - Yue Han
- College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, China-Australia Joint Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Hangzhou, China
| | - Lei Lei
- College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, China-Australia Joint Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Hangzhou, China
| | - Xian Zhang
- College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, China-Australia Joint Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Hangzhou, China
| | - Houhui Song
- College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, China-Australia Joint Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Hangzhou, China
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13
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Abstract
Mg2+ is the most abundant divalent cation in living cells. It is essential for charge neutralization, macromolecule stabilization, and the assembly and activity of ribosomes and as a cofactor for enzymatic reactions. When experiencing low cytoplasmic Mg2+, bacteria adopt two main strategies: They increase the abundance and activity of Mg2+ importers and decrease the abundance of Mg2+-chelating ATP and rRNA. These changes reduce regulated proteolysis by ATP-dependent proteases and protein synthesis in a systemic fashion. In many bacterial species, the transcriptional regulator PhoP controls expression of proteins mediating these changes. The 5' leader region of some mRNAs responds to low cytoplasmic Mg2+ or to disruptions in translation of open reading frames in the leader regions by furthering expression of the associated coding regions, which specify proteins mediating survival when the cytoplasmic Mg2+ concentration is low. Microbial species often utilize similar adaptation strategies to cope with low cytoplasmic Mg2+ despite relying on different genes to do so.
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Affiliation(s)
- Eduardo A Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, USA; .,Yale Microbial Sciences Institute, West Haven, Connecticut 06516, USA
| | - Carissa Chan
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, USA;
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14
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Campa AR, Smith LM, Hampton HG, Sharma S, Jackson SA, Bischler T, Sharma CM, Fineran PC. The Rsm (Csr) post-transcriptional regulatory pathway coordinately controls multiple CRISPR-Cas immune systems. Nucleic Acids Res 2021; 49:9508-9525. [PMID: 34403463 PMCID: PMC8450108 DOI: 10.1093/nar/gkab704] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/29/2021] [Accepted: 08/03/2021] [Indexed: 12/15/2022] Open
Abstract
CRISPR-Cas systems provide bacteria with adaptive immunity against phages and plasmids; however, pathways regulating their activity are not well defined. We recently developed a high-throughput genome-wide method (SorTn-seq) and used this to uncover CRISPR-Cas regulators. Here, we demonstrate that the widespread Rsm/Csr pathway regulates the expression of multiple CRISPR-Cas systems in Serratia (type I-E, I-F and III-A). The main pathway component, RsmA (CsrA), is an RNA-binding post-transcriptional regulator of carbon utilisation, virulence and motility. RsmA binds cas mRNAs and suppresses type I and III CRISPR-Cas interference in addition to adaptation by type I systems. Coregulation of CRISPR-Cas and flagella by the Rsm pathway allows modulation of adaptive immunity when changes in receptor availability would alter susceptibility to flagella-tropic phages. Furthermore, we show that Rsm controls CRISPR-Cas in other genera, suggesting conservation of this regulatory strategy. Finally, we identify genes encoding RsmA homologues in phages, which have the potential to manipulate the physiology of host bacteria and might provide an anti-CRISPR activity.
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Affiliation(s)
- Aroa Rey Campa
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.,Bio-Protection Research Centre, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Leah M Smith
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Hannah G Hampton
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Sahil Sharma
- Chair of Molecular Infection Biology II, Institute of Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany
| | - Simon A Jackson
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.,Genetics Otago, University of Otago, Dunedin, New Zealand
| | - Thorsten Bischler
- Core Unit Systems Medicine, University of Würzburg, 97080 Würzburg, Germany
| | - Cynthia M Sharma
- Chair of Molecular Infection Biology II, Institute of Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.,Bio-Protection Research Centre, University of Otago, PO Box 56, Dunedin 9054, New Zealand.,Genetics Otago, University of Otago, Dunedin, New Zealand
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15
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Fei K, Chao HJ, Hu Y, Francis MS, Chen S. CpxR regulates the Rcs phosphorelay system in controlling the Ysc-Yop type III secretion system in Yersinia pseudotuberculosis. MICROBIOLOGY-SGM 2021; 167. [PMID: 33295859 DOI: 10.1099/mic.0.000998] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The CpxRA two-component regulatory system and the Rcs phosphorelay system are both employed by the Enterobacteriaceae family to preserve bacterial envelope integrity and function when growing under stress. Although both systems regulate several overlapping physiological processes, evidence demonstrating a molecular connection between Cpx and Rcs signalling outputs is scarce. Here, we show that CpxR negatively regulates the transcription of the rcsB gene in the Rcs phosphorelay system in Yersinia pseudotuberculosis. Interestingly, transcription of rcsB is under the control of three promoters, which were all repressed by CpxR. Critically, synthetic activation of Cpx signalling through mislocalization of the NlpE lipoprotein to the inner membrane resulted in an active form of CpxR that repressed activity of rcsB promoters. On the other hand, a site-directed mutation of the phosphorylation site at residue 51 in CpxR generated an inactive non-phosphorylated variant that was unable to regulate output from these rcsB promoters. Importantly, CpxR-mediated inhibition of rcsB transcription in turn restricted activation of the Ysc-Yop type III secretion system (T3SS). Moreover, active CpxR blocks zinc-mediated activation of Rcs signalling and the subsequent activation of lcrF transcription. Our results demonstrate a novel regulatory cascade linking CpxR-RcsB-LcrF to control production of the Ysc-Yop T3SS.
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Affiliation(s)
- Keke Fei
- University of Chinese Academy of Sciences, Beijing, PR China.,Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, PR China
| | - Hong-Jun Chao
- Present address: School of Biological & pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, PR China.,Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, PR China
| | - Yangbo Hu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, PR China
| | - Matthew S Francis
- Department of Molecular Biology, Umeå University, Umeå, Sweden; Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Shiyun Chen
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, PR China
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16
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de Pina LC, da Silva FSH, Galvão TC, Pauer H, Ferreira RBR, Antunes LCM. The role of two-component regulatory systems in environmental sensing and virulence in Salmonella. Crit Rev Microbiol 2021; 47:397-434. [PMID: 33751923 DOI: 10.1080/1040841x.2021.1895067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Adaptation to environments with constant fluctuations imposes challenges that are only overcome with sophisticated strategies that allow bacteria to perceive environmental conditions and develop an appropriate response. The gastrointestinal environment is a complex ecosystem that is home to trillions of microorganisms. Termed microbiota, this microbial ensemble plays important roles in host health and provides colonization resistance against pathogens, although pathogens have evolved strategies to circumvent this barrier. Among the strategies used by bacteria to monitor their environment, one of the most important are the sensing and signalling machineries of two-component systems (TCSs), which play relevant roles in the behaviour of all bacteria. Salmonella enterica is no exception, and here we present our current understanding of how this important human pathogen uses TCSs as an integral part of its lifestyle. We describe important aspects of these systems, such as the stimuli and responses involved, the processes regulated, and their roles in virulence. We also dissect the genomic organization of histidine kinases and response regulators, as well as the input and output domains for each TCS. Lastly, we explore how these systems may be promising targets for the development of antivirulence therapeutics to combat antibiotic-resistant infections.
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Affiliation(s)
- Lucindo Cardoso de Pina
- Escola Nacional de Saúde Pública Sergio Arouca, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Programa de Pós-Graduação em Biociências, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Programa de Pós-Graduação Ciência para o Desenvolvimento, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Teca Calcagno Galvão
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Heidi Pauer
- Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas, Rio de Janeiro, Brazil
| | | | - L Caetano M Antunes
- Escola Nacional de Saúde Pública Sergio Arouca, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas, Rio de Janeiro, Brazil.,Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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17
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Huesa J, Giner-Lamia J, Pucciarelli MG, Paredes-Martínez F, García-del Portillo F, Marina A, Casino P. Structure-based analyses of Salmonella RcsB variants unravel new features of the Rcs regulon. Nucleic Acids Res 2021; 49:2357-2374. [PMID: 33638994 PMCID: PMC7913699 DOI: 10.1093/nar/gkab060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/13/2021] [Accepted: 01/26/2021] [Indexed: 12/13/2022] Open
Abstract
RcsB is a transcriptional regulator that controls expression of numerous genes in enteric bacteria. RcsB accomplishes this role alone or in combination with auxiliary transcriptional factors independently or dependently of phosphorylation. To understand the mechanisms by which RcsB regulates such large number of genes, we performed structural studies as well as in vitro and in vivo functional studies with different RcsB variants. Our structural data reveal that RcsB binds promoters of target genes such as rprA and flhDC in a dimeric active conformation. In this state, the RcsB homodimer docks the DNA-binding domains into the major groove of the DNA, facilitating an initial weak read-out of the target sequence. Interestingly, comparative structural analyses also show that DNA binding may stabilize an active conformation in unphosphorylated RcsB. Furthermore, RNAseq performed in strains expressing wild-type or several RcsB variants provided new insights into the contribution of phosphorylation to gene regulation and assign a potential role of RcsB in controlling iron metabolism. Finally, we delimited the RcsB box for homodimeric active binding to DNA as the sequence TN(G/A)GAN4TC(T/C)NA. This RcsB box was found in promoter, intergenic and intragenic regions, facilitating both increased or decreased gene transcription.
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Affiliation(s)
- Juanjo Huesa
- Departamento de Bioquímica y Biología Molecular, Universitat de València. Dr Moliner 50, 46100 Burjassot, Spain.,Instituto universitario de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València. Dr Moliner 50, 46100 Burjassot, Spain
| | - Joaquín Giner-Lamia
- Laboratorio de Patógenos Bacterianos Intracelulares. Centro Nacional de Biotecnología (CNB)-CSIC. Darwin 3, 28049 Madrid. Spain.,Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Campus Montegancedo, E-28223 Pozuelo de Alarcón, Madrid, Spain.,Departamento de Biotecnología y Biología Vegetal, ETSI Agronómica, Alimentaria y de Biosistemas, Universidad Politócnica de Madrid, 28040 Madrid, Spain
| | - M Graciela Pucciarelli
- Laboratorio de Patógenos Bacterianos Intracelulares. Centro Nacional de Biotecnología (CNB)-CSIC. Darwin 3, 28049 Madrid. Spain.,Centro de Biología Molecular 'Severo Ochoa' (CBMSO)-CSIC. Departamento de Biología Molecular. Universidad Autónoma de Madrid, Madrid, Spain
| | - Francisco Paredes-Martínez
- Departamento de Bioquímica y Biología Molecular, Universitat de València. Dr Moliner 50, 46100 Burjassot, Spain.,Instituto universitario de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València. Dr Moliner 50, 46100 Burjassot, Spain
| | - Francisco García-del Portillo
- Laboratorio de Patógenos Bacterianos Intracelulares. Centro Nacional de Biotecnología (CNB)-CSIC. Darwin 3, 28049 Madrid. Spain
| | - Alberto Marina
- Department of Genomic and Proteomic, Instituto de Biomedicina de Valencia (IBV-CSIC), Jaume Roig 11, 46010 Valencia, Spain.,Group 739 of the Centro de Investigación Biomédica en Red sobre Enfermedades Raras (CIBERER) del Instituto de Salud Carlos III, Spain
| | - Patricia Casino
- Departamento de Bioquímica y Biología Molecular, Universitat de València. Dr Moliner 50, 46100 Burjassot, Spain.,Instituto universitario de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València. Dr Moliner 50, 46100 Burjassot, Spain.,Group 739 of the Centro de Investigación Biomédica en Red sobre Enfermedades Raras (CIBERER) del Instituto de Salud Carlos III, Spain
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18
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Hamed S, Shawky RM, Emara M, Slauch JM, Rao CV. HilE is required for synergistic activation of SPI-1 gene expression in Salmonella enterica serovar Typhimurium. BMC Microbiol 2021; 21:49. [PMID: 33593291 PMCID: PMC7887791 DOI: 10.1186/s12866-021-02110-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Salmonella enterica serovar Typhimurium is an intestinal pathogen capable of infecting a wide range of animals. It initiates infection by invading intestinal epithelial cells using a type III secretion system encoded within Salmonella pathogenicity island 1 (SPI-1). The SPI-1 genes are regulated by multiple interacting transcription factors. The master regulator is HilD. HilE represses SPI-1 gene expression by binding HilD and preventing it from activating its target promoters. Previous work found that acetate and nutrients synergistically induce SPI-1 gene expression. In the present study, we investigated the role of HilE, nominally a repressor of SPI-1 gene expression, in mediating this response to acetate and nutrients. RESULTS HilE is necessary for activation of SPI-1 gene expression by acetate and nutrients. In mutants lacking hilE, acetate and nutrients no longer increase SPI-1 gene expression but rather repress it. This puzzling response is not due to the BarA/SirA two component system, which governs the response to acetate. To identify the mechanism, we profiled gene expression using RNAseq in the wild type and a ΔhilE mutant under different growth conditions. Analysis of these data suggested that the Rcs system, which regulates gene expression in response to envelope stress, is involved. Consistent with this hypothesis, acetate and nutrients were able to induce SPI-1 gene expression in mutants lacking hilE and the Rcs system. CONCLUSIONS While the exact mechanism is unknown, these results demonstrate the HilE, nominally a repressor of SPI-1 gene expression, can also function as an activator under the growth conditions investigated. Collectively, these results provide new insights regarding SPI-1 gene regulation and demonstrate that HilE is more complex than initially envisioned.
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Affiliation(s)
- Selwan Hamed
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL, 61801, USA. .,Department of Microbiology and Immunology, Faculty of Pharmacy, Helwan University - Ain Helwan, Helwan, 11795, Egypt.
| | - Riham M Shawky
- Department of Microbiology and Immunology, Faculty of Pharmacy, Helwan University - Ain Helwan, Helwan, 11795, Egypt
| | - Mohamed Emara
- Department of Microbiology and Immunology, Faculty of Pharmacy, Helwan University - Ain Helwan, Helwan, 11795, Egypt
| | - James M Slauch
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Christopher V Rao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL, 61801, USA.
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19
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Smith LM, Jackson SA, Malone LM, Ussher JE, Gardner PP, Fineran PC. The Rcs stress response inversely controls surface and CRISPR-Cas adaptive immunity to discriminate plasmids and phages. Nat Microbiol 2021; 6:162-172. [PMID: 33398095 DOI: 10.1038/s41564-020-00822-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 10/23/2020] [Indexed: 12/16/2022]
Abstract
Bacteria harbour multiple innate defences and adaptive CRISPR-Cas systems that provide immunity against bacteriophages and mobile genetic elements. Although some bacteria modulate defences in response to population density, stress and metabolic state, a lack of high-throughput methods to systematically reveal regulators has hampered efforts to understand when and how immune strategies are deployed. We developed a robust approach called SorTn-seq, which combines saturation transposon mutagenesis, fluorescence-activated cell sorting and deep sequencing to characterize regulatory networks controlling CRISPR-Cas immunity in Serratia sp. ATCC 39006. We applied our technology to assess csm gene expression for ~300,000 mutants and uncovered multiple pathways regulating type III-A CRISPR-Cas expression. Mutation of igaA or mdoG activated the Rcs outer-membrane stress response, eliciting cell-surface-based innate immunity against diverse phages via the transcriptional regulators RcsB and RcsA. Activation of this Rcs phosphorelay concomitantly attenuated adaptive immunity by three distinct type I and III CRISPR-Cas systems. Rcs-mediated repression of CRISPR-Cas defence enabled increased acquisition and retention of plasmids. Dual downregulation of cell-surface receptors and adaptive immunity in response to stress by the Rcs pathway enables protection from phage infection without preventing the uptake of plasmids that may harbour beneficial traits.
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Affiliation(s)
- Leah M Smith
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Simon A Jackson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.,Genetics Otago, University of Otago, Dunedin, New Zealand
| | - Lucia M Malone
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - James E Ussher
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Paul P Gardner
- Genetics Otago, University of Otago, Dunedin, New Zealand.,Department of Biochemistry, University of Otago, Dunedin, New Zealand.,Bio-Protection Research Centre, University of Otago, Dunedin, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand. .,Genetics Otago, University of Otago, Dunedin, New Zealand. .,Bio-Protection Research Centre, University of Otago, Dunedin, New Zealand.
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