Phyletic distribution and diversification of the Phage Shock Protein stress response system in bacteria and archaea

AbstractThe bacterial cell envelope is an essential structure that protects the cell from environmental threats, while simultaneously serving as communication interface and diffusion barrier. Therefore, maintaining cell envelope integrity is of vital importance for all microorganisms. Not surprisingly, evolution has shaped conserved protection networks that connect stress perception, transmembrane signal transduction and mediation of cellular responses upon cell envelope stress. The phage shock protein (PSP) stress response is one of such conserved protection networks. Most of the knowledge about the Psp response comes from studies in the Gram-negative model bacterium, Escherichia coli where the Psp system consists of several well-defined protein components. Homologous systems were identified in representatives of Proteobacteria, Actinobacteria, and Firmicutes; however, the Psp system distribution in the microbial world remains largely unknown. By carrying out a large-scale, unbiased comparative genomics analysis, we found components of the Psp system in many bacterial and archaeal phyla and demonstrated that the PSP system deviates dramatically from the proteobacterial prototype. Two of its core proteins, PspA and PspC, have been integrated in various (often phylum-specifically) conserved protein networks during evolution. Based on protein sequence and gene neighborhood analyses of pspA and pspC homologs, we built a natural classification system of PSP networks in bacteria and archaea. We performed a comprehensive in vivo protein interaction screen for the PSP network newly identified in the Gram-positive model organism Bacillus subtilis and found a strong interconnected PSP response system, illustrating the validity of our approach. Our study highlights the diversity of PSP organization and function across many bacterial and archaeal phyla and will serve as foundation for future studies of this envelope stress response beyond model organisms.

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Alternative Sigma Factor RpoE Is Important for Vibrio parahaemolyticus Cell Envelope Stress Response and Intestinal Colonization

Infection and Immunity ◽

10.1128/iai.01854-14 ◽

2014 ◽

Vol 82 (9) ◽

pp. 3667-3677 ◽

Cited By ~ 20

Author(s):

Brandy Haines-Menges ◽

W. Brian Whitaker ◽

E. Fidelma Boyd

Keyword(s):

Stress Response ◽

Vibrio Parahaemolyticus ◽

Response Regulator ◽

Cell Envelope ◽

Polymyxin B ◽

Content Type ◽

Alternative Sigma Factors ◽

Envelope Stress

ABSTRACTVibrio parahaemolyticusis a halophile that inhabits brackish waters and a wide range of hosts, including crustaceans, fish, mollusks, and humans. In humans, it is the leading cause of bacterial seafood-borne gastroenteritis. The focus of this work was to determine the role of alternative sigma factors in the stress response ofV. parahaemolyticusRIMD2210633, an O3:K6 pandemic isolate. Bioinformatics identified five putative extracytoplasmic function (ECF) family of alternative sigma factors: VP0055, VP2210, VP2358, VP2578, and VPA1690. ECF factors typically respond to cell wall/cell envelope stress, iron levels, and the oxidation state of the cell. We have demonstrated here that one such sigma factor, VP2578, a homologue of RpoE fromEscherichia coli, is important for survival under a number of cell envelope stress conditions and in gastrointestinal colonization of a streptomycin-treated adult mouse. In this study, we determined that anrpoEdeletion mutant strain BHM2578 compared to the wild type (WT) was significantly more sensitive to polymyxin B, ethanol, and high-temperature stresses. We demonstrated that inin vivocompetition assays between therpoEmutant and the WT marked with the β-galactosidase genelacZ(WBWlacZ), the mutant strain was defective in colonization compared to the WT. In contrast, deletion of therpoSstress response regulator did not affectin vivosurvival. In addition, we examined the role of the outer membrane protein, OmpU, which inV. choleraeis proposed to be the sole activator of RpoE. We found that anompUdeletion mutant was sensitive to bile salt stress but resistant to polymyxin B stress, indicating OmpU is not essential for the cell envelope stress responses or RpoE function. Overall, these data demonstrate that RpoE is a key cell envelope stress response regulator and, similar toE. coli, RpoE may have several factors that stimulate its function.

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Phage-shock-protein (Psp) Envelope Stress Response: Evolutionary History & Discovery of Novel Players

10.1101/2020.09.24.301986 ◽

2020 ◽

Author(s):

Janani Ravi ◽

Vivek Anantharaman ◽

Samuel Zorn Chen ◽

Pratik Datta ◽

L Aravind ◽

...

Keyword(s):

Stress Response ◽

Web Application ◽

Cell Envelope ◽

Contextual Information ◽

Specific Cell ◽

Bacterial Phyla ◽

Response System ◽

Envelope Stress ◽

Stress Response System ◽

Conserved Gene

AbstractThe phage shock protein (Psp) stress-response system protects bacteria from envelope stress and stabilizes the cell membrane. Recent work from our group suggests that the psp systems have evolved independently in distinct Gram-positive and Gram-negative bacterial clades to effect similar stress response functions. Despite the prevalence of the key effector, PspA, and the functional Psp system, the various genomic contexts of Psp proteins, as well as their evolution across the kingdoms of life, have not yet been characterized. We have developed a computational pipeline for comparative genomics and protein sequence-structure-function analyses to identify sequence homologs, phyletic patterns, domain architectures, gene neighborhoods, and evolution of the candidates across the tree of life. This integrative pipeline enabled us to make several new discoveries, including the truly universal nature of PspA and the ancestry of the PspA/Snf7 dating all the way back to the Last Universal Common Ancestor. Using contextual information from conserved gene neighborhoods and their domain architectures, we delineated the phyletic patterns of all the Psp members. Next, we systematically identified all possible ‘flavors’ and genomic neighborhoods of the Psp systems. Finally, we traced their evolution, leading us to several interesting findings of their occurrence and co-migration that together point to the functions and roles of Psp in stress-response systems that are often lineage-specific. Conservation of the Psp systems across bacterial phyla emphasizes the established importance of this stress response system in prokaryotes, while the modularity in various lineages is indicative of adaptation to bacteria-specific cell-envelope structures, lifestyles, and adaptation strategies. We also developed an interactive web application that hosts all the data and results in this study that researchers can explore (https://jravilab.shinyapps.io/psp-evolution).

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MIC-Drop: A platform for large-scale in vivo CRISPR screens

Science ◽

10.1126/science.abi8870 ◽

2021 ◽

pp. eabi8870

Author(s):

Saba Parvez ◽

Chelsea Herdman ◽

Manu Beerens ◽

Korak Chakraborti ◽

Zachary P. Harmer ◽

...

Keyword(s):

Large Scale ◽

Cultured Cells ◽

Cardiac Development ◽

Droplet Microfluidics ◽

Model Organisms ◽

Genetic Screens ◽

Large Numbers ◽

And Function ◽

Genome Scale

CRISPR-Cas9 can be scaled up for large-scale screens in cultured cells, but CRISPR screens in animals have been challenging because generating, validating, and keeping track of large numbers of mutant animals is prohibitive. Here, we report Multiplexed Intermixed CRISPR Droplets (MIC-Drop), a platform combining droplet microfluidics, single-needle en masse CRISPR ribonucleoprotein injections, and DNA barcoding to enable large-scale functional genetic screens in zebrafish. The platform can efficiently identify genes responsible for morphological or behavioral phenotypes. In one application, we show MIC-Drop can identify small molecule targets. Furthermore, in a MIC-Drop screen of 188 poorly characterized genes, we discover several genes important for cardiac development and function. With the potential to scale to thousands of genes, MIC-Drop enables genome-scale reverse-genetic screens in model organisms.

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Activity of a Bacterial Cell Envelope Stress Response Is Controlled by the Interaction of a Protein Binding Domain with Different Partners

Journal of Biological Chemistry ◽

10.1074/jbc.m114.614107 ◽

2015 ◽

Vol 290 (18) ◽

pp. 11417-11430 ◽

Cited By ~ 16

Author(s):

Josué Flores-Kim ◽

Andrew J. Darwin

Keyword(s):

Stress Response ◽

Protein Binding ◽

Bacterial Cell ◽

Cell Envelope ◽

Binding Domain ◽

Bacterial Cell Envelope ◽

Envelope Stress

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The Rcs System in Enterobacteriaceae: Envelope Stress Responses and Virulence Regulation

Frontiers in Microbiology ◽

10.3389/fmicb.2021.627104 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jiao Meng ◽

Glenn Young ◽

Jingyu Chen

Keyword(s):

Stress Response ◽

Stress Responses ◽

Bacterial Infections ◽

Pathogenic Bacteria ◽

Cell Envelope ◽

Regulatory System ◽

Virulence Regulation ◽

Bacterial Interaction ◽

Envelope Stress

The bacterial cell envelope is a protective barrier at the frontline of bacterial interaction with the environment, and its integrity is regulated by various stress response systems. The Rcs (regulator of capsule synthesis) system, a non-orthodox two-component regulatory system (TCS) found in many members of the Enterobacteriaceae family, is one of the envelope stress response pathways. The Rcs system can sense envelope damage or defects and regulate the transcriptome to counteract stress, which is particularly important for the survival and virulence of pathogenic bacteria. In this review, we summarize the roles of the Rcs system in envelope stress responses (ESRs) and virulence regulation. We discuss the environmental and intrinsic sources of envelope stress that cause activation of the Rcs system with an emphasis on the role of RcsF in detection of envelope stress and signal transduction. Finally, the different regulation mechanisms governing the Rcs system’s control of virulence in several common pathogens are introduced. This review highlights the important role of the Rcs system in the environmental adaptation of bacteria and provides a theoretical basis for the development of new strategies for control, prevention, and treatment of bacterial infections.

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The three-component system EsrISR regulates a cell envelope stress response inCorynebacterium glutamicum

Molecular Microbiology ◽

10.1111/mmi.13839 ◽

2017 ◽

Vol 106 (5) ◽

pp. 719-741 ◽

Cited By ~ 6

Author(s):

Britta Kleine ◽

Ava Chattopadhyay ◽

Tino Polen ◽

Daniela Pinto ◽

Thorsten Mascher ◽

...

Keyword(s):

Stress Response ◽

Cell Envelope ◽

Component System ◽

Envelope Stress ◽

A Cell

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The Cell Envelope Stress Response of Bacillus subtilis towards Laspartomycin C

Antibiotics ◽

10.3390/antibiotics9110729 ◽

2020 ◽

Vol 9 (11) ◽

pp. 729

Author(s):

Angelika Diehl ◽

Thomas M. Wood ◽

Susanne Gebhard ◽

Nathaniel I. Martin ◽

Georg Fritz

Keyword(s):

Cell Wall ◽

Bacillus Subtilis ◽

Stress Response ◽

Cell Envelope ◽

Resistance Mechanisms ◽

Detailed Knowledge ◽

Knock Out ◽

Lipid Ii ◽

Envelope Stress ◽

The Impact

Cell wall antibiotics are important tools in our fight against Gram-positive pathogens, but many strains become increasingly resistant against existing drugs. Laspartomycin C is a novel antibiotic that targets undecaprenyl phosphate (UP), a key intermediate in the lipid II cycle of cell wall biosynthesis. While laspartomycin C has been thoroughly examined biochemically, detailed knowledge about potential resistance mechanisms in bacteria is lacking. Here, we use reporter strains to monitor the activity of central resistance modules in the Bacillus subtilis cell envelope stress response network during laspartomycin C attack and determine the impact on the resistance of these modules using knock-out strains. In contrast to the closely related UP-binding antibiotic friulimicin B, which only activates ECF σ factor-controlled stress response modules, we find that laspartomycin C additionally triggers activation of stress response systems reacting to membrane perturbation and blockage of other lipid II cycle intermediates. Interestingly, none of the studied resistance genes conferred any kind of protection against laspartomycin C. While this appears promising for therapeutic use of laspartomycin C, it raises concerns that existing cell envelope stress response networks may already be poised for spontaneous development of resistance during prolonged or repeated exposure to this new antibiotic.

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Rcs Phosphorelay Responses to Truncated Lipopolysaccharide-Induced Cell Envelope Stress in Yersinia enterocolitica

Molecules ◽

10.3390/molecules25235718 ◽

2020 ◽

Vol 25 (23) ◽

pp. 5718

Author(s):

Jiao Meng ◽

Junhong Xu ◽

Can Huang ◽

Jingyu Chen

Keyword(s):

Stress Response ◽

Outer Membrane ◽

Yersinia Enterocolitica ◽

Antimicrobial Agents ◽

Cell Envelope ◽

Sodium Dodecyl ◽

Cell Surface Hydrophobicity ◽

Membrane Function ◽

Cell Functions ◽

Envelope Stress

Lipopolysaccharide (LPS) is the major component of the outer membrane of Gram-negative bacteria, and its integrity is monitored by various stress response systems. Although the Rcs system is involved in the envelope stress response and regulates genes controlling numerous bacterial cell functions of Yersinia enterocolitica, whether it can sense the truncated LPS in Y. enterocolitica remains unclear. In this study, the deletion of the Y. enterocolitica waaF gene truncated the structure of LPS and produced a deep rough LPS. The truncated LPS increased the cell surface hydrophobicity and outer membrane permeability, generating cell envelope stress. The truncated LPS also directly exposed the smooth outer membrane to the external environment and attenuated the resistance to adverse conditions, such as impaired survival under polymyxin B and sodium dodecyl sulfate (SDS) exposure. Further phenotypic experiment and gene expression analysis indicated that the truncated LPS was correlated with the activation of the Rcs phosphorelay, thereby repressing cell motility and biofilm formation. Our findings highlight the importance of LPS integrity in maintaining membrane function and broaden the understanding of Rcs phosphorelay signaling in response to cell envelope stress, thus opening new avenues to develop effective antimicrobial agents for combating Y. enterocolitica infections.

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