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Kristensen SS, Diep DB, Kjos M, Mathiesen G. The role of site-2-proteases in bacteria: a review on physiology, virulence, and therapeutic potential. MICROLIFE 2023; 4:uqad025. [PMID: 37223736 PMCID: PMC10202637 DOI: 10.1093/femsml/uqad025] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/21/2023] [Accepted: 05/02/2023] [Indexed: 05/25/2023]
Abstract
Site-2-proteases are a class of intramembrane proteases involved in regulated intramembrane proteolysis. Regulated intramembrane proteolysis is a highly conserved signaling mechanism that commonly involves sequential digestion of an anti-sigma factor by a site-1- and site-2-protease in response to external stimuli, resulting in an adaptive transcriptional response. Variation of this signaling cascade continues to emerge as the role of site-2-proteases in bacteria continues to be explored. Site-2-proteases are highly conserved among bacteria and play a key role in multiple processes, including iron uptake, stress response, and pheromone production. Additionally, an increasing number of site-2-proteases have been found to play a pivotal role in the virulence properties of multiple human pathogens, such as alginate production in Pseudomonas aeruginosa, toxin production in Vibrio cholerae, resistance to lysozyme in enterococci and antimicrobials in several Bacillus spp, and cell-envelope lipid composition in Mycobacterium tuberculosis. The prominent role of site-2-proteases in bacterial pathogenicity highlights the potential of site-2-proteases as novel targets for therapeutic intervention. In this review, we summarize the role of site-2-proteases in bacterial physiology and virulence, as well as evaluate the therapeutic potential of site-2-proteases.
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Affiliation(s)
- Sofie S Kristensen
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), 1433 Ås, Norway
| | | | - Morten Kjos
- Corresponding author. NMBU, P.O. Box 5003, 1433 Ås, Norway. E-mail:
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Activation of the Extracytoplasmic Function σ Factor σ V in Clostridioides difficile Requires Regulated Intramembrane Proteolysis of the Anti-σ Factor RsiV. mSphere 2022; 7:e0009222. [PMID: 35317618 PMCID: PMC9044953 DOI: 10.1128/msphere.00092-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Clostridioides (Clostridium) difficile is one of the leading causes of nosocomial diarrhea. Lysozyme is a common host defense against many pathogenic bacteria. C. difficile exhibits high levels of lysozyme resistance, which is due in part to the extracytoplasmic functioning (ECF) σ factor, σV. It has been previously demonstrated that genes regulated by σV are responsible for peptidoglycan modifications that provide C. difficile with high lysozyme resistance. σV is not unique to C. difficile however, and its role in lysozyme resistance and its mechanism of activation has been well characterized in Bacillus subtilis where the anti-σ, RsiV, sequesters σV until lysozyme directly binds to RsiV, activating σV. However, it remains unclear if the mechanism of σV activation is similar in C. difficile. Here, we investigated how activation of σV is controlled in C. difficile by lysozyme. We found that C. difficile RsiV was degraded in the presence of lysozyme. We also found that disruption of a predicted signal peptidase cleavage site blocked RsiV degradation and σV activation, indicating that the site-1 protease is likely a signal peptidase. We also identified a conserved site-2 protease, RasP, that was required for site-2 cleavage of RsiV and σV activation in response to lysozyme. Combined with previous work showing RsiV directly binds lysozyme, these data suggested that RsiV directly binds lysozyme in C. difficile, which leads to RsiV destruction via cleavage at site-1 by signal peptidase and then at site-2 by RasP, ultimately resulting in σV activation and increased resistance to lysozyme. IMPORTANCE Clostridioides difficile is a major cause of hospital-acquired diarrhea and represents an urgent concern due to the prevalence of antibiotic resistance and the rate of recurrent infections. We previously showed that σV and the regulon under its control were involved in lysozyme resistance. We have also shown in B. subtilis that the anti-σ RsiV acts as a direct sensor for lysozyme. which results in the destruction of RsiV and activation of σV. Here, we described the proteases required for degradation of RsiV in C. difficile in response to lysozyme. Our data indicated that the mechanism is highly conserved between B. subtilis and C. difficile.
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The Cationic Antimicrobial Peptide Activity of Lysozyme Reduces Viable Enterococcus faecalis Cells in Biofilms. Antimicrob Agents Chemother 2022; 66:e0233921. [PMID: 35446133 DOI: 10.1128/aac.02339-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Enterococcus faecalis, a leading cause of health care-associated infections, forms biofilms and is resistant to many antimicrobial agents. Planktonic-phase E. faecalis is resistant to high concentrations of the enzyme lysozyme, which catalyzes the hydrolysis of N-acetylmuramic acid and N-acetylglucosamine linkages in peptidoglycan and is also a cationic antimicrobial peptide (CAMP). E. faecalis lysozyme resistance in planktonic cells is stimulated upon activation of the extracytoplasmic function sigma factor SigV via cleavage of the anti-sigma factor RsiV by the transmembrane protease Eep. Planktonically grown E. faecalis lacking eep is more sensitive than wild-type strains to growth inhibition by lysozyme. This study was initiated to determine whether E. faecalis OG1RFΔeep biofilms would be protected from lysozyme. Serendipitously, we discovered that exposure of both E. faecalis OG1RF and OG1RFΔeep biofilms to chicken egg white lysozyme resulted in decreases in biofilm cell viability of 3.7 and 3.8 log10 CFU/mL, respectively. Treatment of biofilms of both strains with recombinant purified human lysozyme was associated with reductions in cell viability of >99.9% for both strains. Lysozyme-treated OG1RF and OG1RFΔeep biofilms contained a higher percentage of dead cells by Live/Dead staining and were associated with more extracellular DNA. Heat-inactivated human lysozyme, which was devoid of muramidase activity, as well as the lysozyme-derived CAMP LP9 and the CAMP polymyxin B, decreased biofilm cell viability. These results are consistent with a model in which the CAMP activity, rather than the muramidase activity, of lysozyme causes lysis of E. faecalis biofilm cells despite them having an intact lysozyme resistance-inducing signaling pathway. Finally, lysozyme was also effective in reducing viable biofilm cells of several other E. faecalis strains, including the vancomycin-resistant strain V583 and multidrug-resistant strain MMH594. This study demonstrates the potential for lysozyme to be developed as a novel antibiofilm therapeutic.
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Ho TD, Ellermeier CD. Activation of the extracytoplasmic function σ factor σ V by lysozyme in Clostridioides difficile. Curr Opin Microbiol 2022; 65:162-166. [PMID: 34894542 PMCID: PMC8792214 DOI: 10.1016/j.mib.2021.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/12/2021] [Accepted: 11/18/2021] [Indexed: 02/03/2023]
Abstract
Clostridioides difficile is naturally resistant to high levels of lysozyme an important component of the innate immune defense system. C. difficile encodes both constitutive as well as inducible lysozyme resistance genes. The inducible lysozyme resistance genes are controlled by an alternative σ factor σV that belongs to the Extracytoplasmic function σ factor family. In the absence of lysozyme, the activity of σV is inhibited by the anti-σ factor RsiV. In the presence of lysozyme RsiV is destroyed via a proteolytic cascade that leads to σV activation and increased lysozyme resistance. This review highlights how activity of σV is controlled.
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Affiliation(s)
- Theresa D. Ho
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, 431 Newton Rd, Iowa City, IA 52242
| | - Craig D. Ellermeier
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, 431 Newton Rd, Iowa City, IA 52242,Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA,Corresponding author: , 319-384-4565
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5
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Parthasarathy S, Wang X, Carr KR, Varahan S, Hancock EB, Hancock LE. SigV Mediates Lysozyme Resistance in Enterococcus faecalis via RsiV and PgdA. J Bacteriol 2021; 203:e0025821. [PMID: 34370556 PMCID: PMC8459761 DOI: 10.1128/jb.00258-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Enterococcus faecalis is a gut commensal but transitions to a pathogenic state as a consequence of intestinal dysbiosis and/or the presence of indwelling medical devices, causing a wide range of infections. One of the unique features of E. faecalis is its ability to display high level resistance to lysozyme, an important host defense of the innate immune response. Lysozyme resistance in E. faecalis is known to be mediated by the extracytoplasmic function (ECF) sigma factor SigV. PgdA and RsiV expression is directly regulated by SigV, but pgdA and rsiV mutants display nominal changes in lysozyme resistance, suggesting that additional gene products in the SigV regulon contribute to lysozyme resistance. Using transcriptome sequencing (RNA-seq) analysis, we compared the transcriptional profile of the parental strain to that of an isogenic sigV mutant and show that apart from sigV, only rsiV and pgdA expression was induced upon lysozyme exposure. The combined deletion mutant of both rsiV and pgdA rendered E. faecalis sensitive to lysozyme at a level comparable to that of the sigV mutant, highlighting the limited SigV regulon. Several additional genes were also induced upon lysozyme exposure, but in a SigV-independent fashion. Overexpression of pgdA from a SigV-independent promoter restored lysozyme resistance in a sigV deletion mutant and also induced cell chaining. Overexpression of rsiV from a SigV-independent promoter only partially restored lysozyme resistance in a sigV mutant. Overall, we provide evidence for a simple adaptation to lysozyme stress, in which SigV controls the expression of rsiV and pgdA, and that both gene products contribute to lysozyme resistance. IMPORTANCE Enterococcus faecalis causes health care-associated infections and displays resistance to a variety of antibiotics and molecules of the innate immune system. SigV has been shown to play an important role in enterococcal lysozyme resistance. Even though several proteins have been implicated in enterococcal lysozyme resistance, a complete SigV-dependent regulon has not been functionally characterized as being responsible for the dramatic increase in lysozyme susceptibility displayed by a sigV mutant. Using RNA-seq, we have identified the SigV regulon to be comprised of two gene loci, sigV-rsiV and pgdA. Deletion of both rsiV and pgdA renders E. faecalis susceptible to lysozyme on par with a sigV mutant. We also demonstrate that overproduction of rsiV and pgdA contributes to lysozyme resistance in susceptible strains.
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Affiliation(s)
- Srivatsan Parthasarathy
- Department of Molecular Biosciences, University of Kansasgrid.266515.3, Lawrence, Kansas, USA
| | - Xiaofei Wang
- Department of Molecular Biosciences, University of Kansasgrid.266515.3, Lawrence, Kansas, USA
| | - Kristen R. Carr
- Department of Molecular Biosciences, University of Kansasgrid.266515.3, Lawrence, Kansas, USA
| | - Sriram Varahan
- Department of Molecular Biosciences, University of Kansasgrid.266515.3, Lawrence, Kansas, USA
| | - Elyssa B. Hancock
- Department of Molecular Biosciences, University of Kansasgrid.266515.3, Lawrence, Kansas, USA
| | - Lynn E. Hancock
- Department of Molecular Biosciences, University of Kansasgrid.266515.3, Lawrence, Kansas, USA
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Schwall CP, Loman TE, Martins BMC, Cortijo S, Villava C, Kusmartsev V, Livesey T, Saez T, Locke JCW. Tunable phenotypic variability through an autoregulatory alternative sigma factor circuit. Mol Syst Biol 2021; 17:e9832. [PMID: 34286912 PMCID: PMC8287880 DOI: 10.15252/msb.20209832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 11/17/2022] Open
Abstract
Genetically identical individuals in bacterial populations can display significant phenotypic variability. This variability can be functional, for example by allowing a fraction of stress prepared cells to survive an otherwise lethal stress. The optimal fraction of stress prepared cells depends on environmental conditions. However, how bacterial populations modulate their level of phenotypic variability remains unclear. Here we show that the alternative sigma factor σV circuit in Bacillus subtilis generates functional phenotypic variability that can be tuned by stress level, environmental history and genetic perturbations. Using single-cell time-lapse microscopy and microfluidics, we find the fraction of cells that immediately activate σV under lysozyme stress depends on stress level and on a transcriptional memory of previous stress. Iteration between model and experiment reveals that this tunability can be explained by the autoregulatory feedback structure of the sigV operon. As predicted by the model, genetic perturbations to the operon also modulate the response variability. The conserved sigma-anti-sigma autoregulation motif is thus a simple mechanism for bacterial populations to modulate their heterogeneity based on their environment.
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Affiliation(s)
| | | | - Bruno M C Martins
- Sainsbury LaboratoryUniversity of CambridgeCambridgeUK
- School of Life SciencesUniversity of WarwickCoventryUK
| | | | | | | | - Toby Livesey
- Sainsbury LaboratoryUniversity of CambridgeCambridgeUK
| | - Teresa Saez
- Sainsbury LaboratoryUniversity of CambridgeCambridgeUK
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The Penicillin-Binding Protein PbpP Is a Sensor of β-Lactams and Is Required for Activation of the Extracytoplasmic Function σ Factor σ P in Bacillus thuringiensis. mBio 2021; 12:mBio.00179-21. [PMID: 33758089 PMCID: PMC8092216 DOI: 10.1128/mbio.00179-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
β-Lactams are a class of antibiotics that target the synthesis of peptidoglycan, an essential component of the cell wall. β-Lactams inhibit the function of penicillin-binding proteins (PBPs), which form the cross-links between strands of peptidoglycan. Resistance to β-lactams complicates the treatment of bacterial infections. In recent years, the spread of β-lactam resistance has increased with growing intensity. Resistance is often conferred by β-lactamases, which inactivate β-lactams, or the expression of alternative β-lactam-resistant PBPs. σP is an extracytoplasmic function (ECF) σ factor that controls β-lactam resistance in the species Bacillus thuringiensis, Bacillus cereus, and Bacillus anthracis σP is normally held inactive by the anti-σ factor RsiP. σP is activated by β-lactams that trigger the proteolytic destruction of RsiP. Here, we identify the penicillin-binding protein PbpP and demonstrate its essential role in the activation of σP Our data show that PbpP is required for σP activation and RsiP degradation. Our data suggest that PbpP acts as a β-lactam sensor since the binding of a subset of β-lactams to PbpP is required for σP activation. We find that PbpP likely directly or indirectly controls site 1 cleavage of RsiP, which results in the degradation of RsiP and, thus, σP activation. σP activation results in increased expression of β-lactamases and, thus, increased β-lactam resistance. This work is the first report of a PBP acting as a sensor for β-lactams and controlling the activation of an ECF σ factor.IMPORTANCE The bacterial cell envelope is the target for numerous antibiotics. Many antibiotics target the synthesis of peptidoglycan, which is a central metabolic pathway essential for bacterial survival. One of the most important classes of antibiotics has been β-lactams, which inhibit the transpeptidase activity of penicillin-binding proteins to decrease the cross-linking of peptidoglycan and the strength of the cell wall. While β-lactam antibiotics have historically proven to be effective, resistance to β-lactams is a growing problem. The ECF σ factor σP is required for β-lactam resistance in B. thuringiensis and close relatives, including B. anthracis Here, we provide insight into the mechanism of activation of σP by β-lactams.
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Signal Peptidase-Mediated Cleavage of the Anti-σ Factor RsiP at Site 1 Controls σ P Activation and β-Lactam Resistance in Bacillus thuringiensis. mBio 2021; 13:e0370721. [PMID: 35164554 PMCID: PMC8844934 DOI: 10.1128/mbio.03707-21] [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: 12/04/2022] Open
Abstract
In Bacillus thuringiensis, β-lactam antibiotic resistance is controlled by the extracytoplasmic function (ECF) σ factor σP. σP activity is inhibited by the anti-σ factor RsiP. In the presence of β-lactam antibiotics, RsiP is degraded and σP is activated. Previous work found that RsiP degradation requires cleavage of RsiP at site 1 by an unknown protease, followed by cleavage at site 2 by the site 2 protease RasP. The penicillin-binding protein PbpP acts as a sensor for β-lactams. PbpP initiates σP activation and is required for site 1 cleavage of RsiP but is not the site 1 protease. Here, we describe the identification of a signal peptidase, SipP, which cleaves RsiP at a site 1 signal peptidase cleavage site and is required for σP activation. Finally, many B. anthracis strains are sensitive to β-lactams yet encode the σP-RsiP signal transduction system. We identified a naturally occurring mutation in the signal peptidase cleavage site of B. anthracis RsiP that renders it resistant to SipP cleavage. We find that B. anthracis RsiP is not degraded in the presence of β-lactams. Altering the B. anthracis RsiP site 1 cleavage site by a single residue to resemble B. thuringiensis RsiP results in β-lactam-dependent degradation of RsiP. We show that mutation of the B. thuringiensis RsiP cleavage site to resemble the sequence of B. anthracis RsiP blocks degradation by SipP. The change in the cleavage site likely explains many reasons why B. anthracis strains are sensitive to β-lactams. IMPORTANCE β-Lactam antibiotics are important for the treatment of many bacterial infections. However, resistance mechanisms have become increasingly more prevalent. Understanding how β-lactam resistance is conferred and how bacteria control expression of β-lactam resistance is important for informing the future treatment of bacterial infections. σP is an alternative σ factor that controls the transcription of genes that confer β-lactam resistance in Bacillus thuringiensis, Bacillus cereus, and Bacillus anthracis. Here, we identify a signal peptidase as the protease required for initiating activation of σP by the degradation of the anti-σ factor RsiP. The discovery that the signal peptidase SipP is required for σP activation highlights an increasing role for signal peptidases in signal transduction, as well as in antibiotic resistance.
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Wettstadt S, Llamas MA. Role of Regulated Proteolysis in the Communication of Bacteria With the Environment. Front Mol Biosci 2020; 7:586497. [PMID: 33195433 PMCID: PMC7593790 DOI: 10.3389/fmolb.2020.586497] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/22/2020] [Indexed: 12/29/2022] Open
Abstract
For bacteria to flourish in different niches, they need to sense signals from the environment and translate these into appropriate responses. Most bacterial signal transduction systems involve proteins that trigger the required response through the modification of gene transcription. These proteins are often produced in an inactive state that prevents their interaction with the RNA polymerase and/or the DNA in the absence of the inducing signal. Among other mechanisms, regulated proteolysis is becoming increasingly recognized as a key process in the modulation of the activity of these signal response proteins. Regulated proteolysis can either produce complete degradation or specific cleavage of the target protein, thus modifying its function. Because proteolysis is a fast process, the modulation of signaling proteins activity by this process allows for an immediate response to a given signal, which facilitates adaptation to the surrounding environment and bacterial survival. Moreover, regulated proteolysis is a fundamental process for the transmission of extracellular signals to the cytosol through the bacterial membranes. By a proteolytic mechanism known as regulated intramembrane proteolysis (RIP) transmembrane proteins are cleaved within the plane of the membrane to liberate a cytosolic domain or protein able to modify gene transcription. This allows the transmission of a signal present on one side of a membrane to the other side where the response is elicited. In this work, we review the role of regulated proteolysis in the bacterial communication with the environment through the modulation of the main bacterial signal transduction systems, namely one- and two-component systems, and alternative σ factors.
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Affiliation(s)
- Sarah Wettstadt
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - María A Llamas
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
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Casas-Pastor D, Diehl A, Fritz G. Coevolutionary Analysis Reveals a Conserved Dual Binding Interface between Extracytoplasmic Function σ Factors and Class I Anti-σ Factors. mSystems 2020; 5:e00310-20. [PMID: 32753504 PMCID: PMC7406223 DOI: 10.1128/msystems.00310-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/17/2020] [Indexed: 11/30/2022] Open
Abstract
Extracytoplasmic function σ factors (ECFs) belong to the most abundant signal transduction mechanisms in bacteria. Among the diverse regulators of ECF activity, class I anti-σ factors are the most important signal transducers in response to internal and external stress conditions. Despite the conserved secondary structure of the class I anti-σ factor domain (ASDI) that binds and inhibits the ECF under noninducing conditions, the binding interface between ECFs and ASDIs is surprisingly variable between the published cocrystal structures. In this work, we provide a comprehensive computational analysis of the ASDI protein family and study the different contact themes between ECFs and ASDIs. To this end, we harness the coevolution of these diverse protein families and predict covarying amino acid residues as likely candidates of an interaction interface. As a result, we find two common binding interfaces linking the first alpha-helix of the ASDI to the DNA-binding region in the σ4 domain of the ECF, and the fourth alpha-helix of the ASDI to the RNA polymerase (RNAP)-binding region of the σ2 domain. The conservation of these two binding interfaces contrasts with the apparent quaternary structure diversity of the ECF/ASDI complexes, partially explaining the high specificity between cognate ECF and ASDI pairs. Furthermore, we suggest that the dual inhibition of RNAP- and DNA-binding interfaces is likely a universal feature of other ECF anti-σ factors, preventing the formation of nonfunctional trimeric complexes between σ/anti-σ factors and RNAP or DNA.IMPORTANCE In the bacterial world, extracytoplasmic function σ factors (ECFs) are the most widespread family of alternative σ factors, mediating many cellular responses to environmental cues, such as stress. This work uses a computational approach to investigate how these σ factors interact with class I anti-σ factors-the most abundant regulators of ECF activity. By comprehensively classifying the anti-σs into phylogenetic groups and by comparing this phylogeny to the one of the cognate ECFs, the study shows how these protein families have coevolved to maintain their interaction over evolutionary time. These results shed light on the common contact residues that link ECFs and anti-σs in different phylogenetic families and set the basis for the rational design of anti-σs to specifically target certain ECFs. This will help to prevent the cross talk between heterologous ECF/anti-σ pairs, allowing their use as orthogonal regulators for the construction of genetic circuits in synthetic biology.
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Affiliation(s)
- Delia Casas-Pastor
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Angelika Diehl
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
- School of Molecular Sciences, University of Western Australia, Perth, Australia
| | - Georg Fritz
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
- School of Molecular Sciences, University of Western Australia, Perth, Australia
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Effect of Lipidation on the Localization and Activity of a Lysozyme Inhibitor in Neisseria gonorrhoeae. J Bacteriol 2020; 202:JB.00633-19. [PMID: 32041800 DOI: 10.1128/jb.00633-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 02/01/2020] [Indexed: 01/02/2023] Open
Abstract
The Gram-negative pathogen Neisseria gonorrhoeae (gonococcus [Gc]) colonizes lysozyme-rich mucosal surfaces. Lysozyme hydrolyzes peptidoglycan, leading to bacterial lysis. Gc expresses two proteins, SliC and NgACP, that bind and inhibit the enzymatic activity of lysozyme. SliC is a surface-exposed lipoprotein, while NgACP is found in the periplasm and also released extracellularly. Purified SliC and NgACP similarly inhibit lysozyme. However, whereas mutation of ngACP increases Gc susceptibility to lysozyme, the sliC mutant is only susceptible to lysozyme when ngACP is inactivated. In this work, we examined how lipidation contributes to SliC expression, cellular localization, and resistance of Gc to killing by lysozyme. To do so, we mutated the conserved cysteine residue (C18) in the N-terminal lipobox motif of SliC, the site for lipid anchor attachment, to alanine. SliC(C18A) localized to soluble rather than membrane fractions in Gc and was not displayed on the bacterial surface. Less SliC(C18A) was detected in Gc lysates compared to the wild-type protein. This was due in part to some release of the C18A mutant, but not wild-type, protein into the extracellular space. Surprisingly, Gc expressing SliC(C18A) survived better than SliC (wild type)-expressing Gc after exposure to lysozyme. We conclude that lipidation is not required for the ability of SliC to inhibit lysozyme, even though the lipidated cysteine is 100% conserved in Gc SliC alleles. These findings shed light on how members of the growing family of lysozyme inhibitors with distinct subcellular localizations contribute to bacterial defense against lysozyme.IMPORTANCE Neisseria gonorrhoeae is one of many bacterial species that express multiple lysozyme inhibitors. It is unclear how inhibitors that differ in their subcellular localization contribute to defense from lysozyme. We investigated how lipidation of SliC, an MliC (membrane-bound lysozyme inhibitor of c-type lysozyme)-type inhibitor, contributes to its localization and lysozyme inhibitory activity. We found that lipidation was required for surface exposure of SliC and yet was dispensable for protecting the gonococcus from killing by lysozyme. To our knowledge, this is the first time the role of lipid anchoring of a lysozyme inhibitor has been investigated. These results help us understand how different lysozyme inhibitors are localized in bacteria and how this impacts resistance to lysozyme.
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12
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Wiegand S, Jogler M, Boedeker C, Pinto D, Vollmers J, Rivas-Marín E, Kohn T, Peeters SH, Heuer A, Rast P, Oberbeckmann S, Bunk B, Jeske O, Meyerdierks A, Storesund JE, Kallscheuer N, Lücker S, Lage OM, Pohl T, Merkel BJ, Hornburger P, Müller RW, Brümmer F, Labrenz M, Spormann AM, Op den Camp HJM, Overmann J, Amann R, Jetten MSM, Mascher T, Medema MH, Devos DP, Kaster AK, Øvreås L, Rohde M, Galperin MY, Jogler C. Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology. Nat Microbiol 2019; 5:126-140. [PMID: 31740763 DOI: 10.1038/s41564-019-0588-1] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 09/12/2019] [Indexed: 01/01/2023]
Abstract
When it comes to the discovery and analysis of yet uncharted bacterial traits, pure cultures are essential as only these allow detailed morphological and physiological characterization as well as genetic manipulation. However, microbiologists are struggling to isolate and maintain the majority of bacterial strains, as mimicking their native environmental niches adequately can be a challenging task. Here, we report the diversity-driven cultivation, characterization and genome sequencing of 79 bacterial strains from all major taxonomic clades of the conspicuous bacterial phylum Planctomycetes. The samples were derived from different aquatic environments but close relatives could be isolated from geographically distinct regions and structurally diverse habitats, implying that 'everything is everywhere'. With the discovery of lateral budding in 'Kolteria novifilia' and the capability of the members of the Saltatorellus clade to divide by binary fission as well as budding, we identified previously unknown modes of bacterial cell division. Alongside unobserved aspects of cell signalling and small-molecule production, our findings demonstrate that exploration beyond the well-established model organisms has the potential to increase our knowledge of bacterial diversity. We illustrate how 'microbial dark matter' can be accessed by cultivation techniques, expanding the organismic background for small-molecule research and drug-target detection.
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Affiliation(s)
| | | | | | | | - John Vollmers
- Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Elena Rivas-Marín
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, Pablo de Olavide University, Seville, Spain
| | - Timo Kohn
- Radboud University, Nijmegen, The Netherlands
| | | | - Anja Heuer
- Leibniz Institute DSMZ, Braunschweig, Germany
| | | | - Sonja Oberbeckmann
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ, Braunschweig, Germany
| | - Olga Jeske
- Leibniz Institute DSMZ, Braunschweig, Germany
| | | | | | | | | | | | | | | | | | | | | | - Matthias Labrenz
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock, Germany
| | | | | | | | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | | | | | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, Pablo de Olavide University, Seville, Spain
| | | | | | | | | | - Christian Jogler
- Radboud University, Nijmegen, The Netherlands. .,Friedrich Schiller University Jena, Jena, Germany.
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13
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Activation of the Extracytoplasmic Function σ Factor σ P by β-Lactams in Bacillus thuringiensis Requires the Site-2 Protease RasP. mSphere 2019; 4:4/4/e00511-19. [PMID: 31391284 PMCID: PMC6686233 DOI: 10.1128/msphere.00511-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The discovery of antibiotics to treat bacterial infections has had a dramatic and positive impact on human health. However, shortly after the introduction of a new antibiotic, bacteria often develop resistance. The bacterial cell envelope is essential for cell viability and is the target of many of the most commonly used antibiotics, including β-lactam antibiotics. Resistance to β-lactams is often dependent upon β-lactamases. In B. cereus, B. thuringiensis, and some B. anthracis strains, the expression of some β-lactamases is inducible. This inducible β-lactamase expression is controlled by activation of an alternative σ factor called σP. Here, we show that β-lactam antibiotics induce σP activation by degradation of the anti-σ factor RsiP. Bacteria can utilize alternative σ factors to regulate sets of genes in response to changes in the environment. The largest and most diverse group of alternative σ factors are the extracytoplasmic function (ECF) σ factors. σP is an ECF σ factor found in Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis. Previous work showed that σP is induced by ampicillin, a β-lactam antibiotic, and required for resistance to ampicillin. However, it was not known how activation of σP is controlled or what other antibiotics may activate σP. Here, we report that activation of σP is specific to a subset of β-lactams and that σP is required for resistance to these β-lactams. We demonstrate that activation of σP is controlled by the proteolytic destruction of the anti-σ factor RsiP and that degradation of RsiP requires multiple proteases. Upon exposure to β-lactams, the extracellular domain of RsiP is cleaved by an unknown protease, which we predict cleaves at site-1. Following cleavage by the unknown protease, the N terminus of RsiP is further degraded by the site-2 intramembrane protease RasP. Our data indicate that RasP cleavage of RsiP is not the rate-limiting step in σP activation. This proteolytic cascade leads to activation of σP, which induces resistance to β-lactams likely via increased expression of β-lactamases. IMPORTANCE The discovery of antibiotics to treat bacterial infections has had a dramatic and positive impact on human health. However, shortly after the introduction of a new antibiotic, bacteria often develop resistance. The bacterial cell envelope is essential for cell viability and is the target of many of the most commonly used antibiotics, including β-lactam antibiotics. Resistance to β-lactams is often dependent upon β-lactamases. In B. cereus, B. thuringiensis, and some B. anthracis strains, the expression of some β-lactamases is inducible. This inducible β-lactamase expression is controlled by activation of an alternative σ factor called σP. Here, we show that β-lactam antibiotics induce σP activation by degradation of the anti-σ factor RsiP.
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14
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Zhao H, Roistacher DM, Helmann JD. Deciphering the essentiality and function of the anti-σ M factors in Bacillus subtilis. Mol Microbiol 2019; 112:482-497. [PMID: 30715747 PMCID: PMC6679829 DOI: 10.1111/mmi.14216] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2019] [Indexed: 12/27/2022]
Abstract
Bacteria use alternative sigma factors to adapt to different growth and stress conditions. The Bacillus subtilis extracytoplasmic function sigma factor SigM regulates genes for cell wall synthesis and is crucial for maintaining cell wall homeostasis under stress conditions. The activity of SigM is regulated by its anti-sigma factor, YhdL, and the accessory protein YhdK. Here, we show that dysregulation of SigM caused by the absence of either component of the anti-sigma factor complex leads to toxic levels of SigM and severe growth defects. High SigM activity results from a dysregulated positive feedback loop, and can be suppressed by overexpression of the housekeeping sigma, SigA. Using a sigM merodiploid strain, we selected for suppressor mutations that allow survival of yhdL depletion strain. The recovered suppressor mutations map to the beta and beta-prime subunits of RNA polymerase core enzyme and selectively reduce SigM activity, and in some cases increase the activity of other alternative sigma factors. This work highlights the ability of mutations in RNA polymerase that remodel the sigma-core interface to differentially affect sigma factor activity, and thereby alter the transcriptional landscape of the cell.
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Affiliation(s)
- Heng Zhao
- Cornell University, Department of Microbiology, Ithaca, NY, USA
| | | | - John D. Helmann
- Cornell University, Department of Microbiology, Ithaca, NY, USA
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15
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Ho TD, Ellermeier CD. Activation of the extracytoplasmic function σ factor σ V by lysozyme. Mol Microbiol 2019; 112:410-419. [PMID: 31286585 DOI: 10.1111/mmi.14348] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2019] [Indexed: 01/01/2023]
Abstract
σV is an extracytoplasmic function (ECF) σ factor that is found exclusively in Firmicutes including Bacillus subtilis and the opportunistic pathogens Clostridioides difficile and Enterococcus faecalis. σV is activated by lysozyme and is required for lysozyme resistance. The activity of σV is normally inhibited by the anti-σ factor RsiV, a transmembrane protein. RsiV acts as a receptor for lysozyme. The binding of lysozyme to RsiV triggers a signal transduction cascade which results in degradation of RsiV and activation of σV . Like the anti-σ factors for several other ECF σ factors, RsiV is degraded by a multistep proteolytic cascade that is regulated at the step of site-1 cleavage. Unlike other anti-σ factors, site-1 cleavage of RsiV is not dependent upon a site-1 protease whose activity is regulated. Instead constitutively active signal peptidase cleaves RsiV at site-1 in a lysozyme-dependent manner. The activation of σV leads to the transcription of genes, which encode proteins required for lysozyme resistance.
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Affiliation(s)
- Theresa D Ho
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, 431 Newton Rd, Iowa City, IA, 52242, USA
| | - Craig D Ellermeier
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, 431 Newton Rd, Iowa City, IA, 52242, USA.,Graduate Program in Genetics, University of Iowa, Iowa City, IA, 52242, USA
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16
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Lewerke LT, Kies PJ, Müh U, Ellermeier CD. Bacterial sensing: A putative amphipathic helix in RsiV is the switch for activating σV in response to lysozyme. PLoS Genet 2018; 14:e1007527. [PMID: 30020925 PMCID: PMC6066255 DOI: 10.1371/journal.pgen.1007527] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/30/2018] [Accepted: 07/01/2018] [Indexed: 02/06/2023] Open
Abstract
Extra Cytoplasmic Function (ECF) σ factors are a diverse group of alternate σ factors bacteria use to respond to changes in the environment. The Bacillus subtilis ECF σ factor σV responds to lysozyme. In the absence of lysozyme, σV is held inactive by the anti-σ factor, RsiV. In the presence of lysozyme RsiV is degraded via regulated intramembrane proteolysis, which results in the release of σV and thus activation of lysozyme resistance genes. Signal peptidase is required to initiate degradation of RsiV. Previous work indicated that RsiV only becomes sensitive to signal peptidase upon direct binding to lysozyme. We have identified a unique domain of RsiV that is responsible for protecting RsiV from cleavage by signal peptidase in the absence of lysozyme. We provide evidence that this domain contains putative amphipathic helices. Disruption of the hydrophobic surface of these helices by introducing positively charged residues results in constitutive cleavage of RsiV by signal peptidase and thus constitutive σV activation. We provide further evidence that this domain contains amphipathic helices using a membrane-impermeable reagent. Finally, we show that upon lysozyme binding to RsiV, the hydrophobic face of the amphipathic helix becomes accessible to a membrane-impermeable reagent. Thus, we propose the amphipathic helices protect RsiV from cleavage in the absence of lysozyme. Additionally, we propose the amphipathic helices rearrange to form a suitable signal peptidase substrate upon binding of RsiV to lysozyme leading to the activation of σV. Signal transduction involves (i) sensing a signal, (ii) a molecular switch triggering a response, and (iii) altering gene expression. For Bacillus subtilis’ response to lysozyme, we have a detailed understanding of (i) and (iii). Here we provide insights for a molecular switch that triggers the lysozyme response via σV activation. RsiV, an inhibitor of σV activity, is cleaved by signal peptidase only in the presence of lysozyme. Signal peptidase constitutively cleaves substrates that are translocated across the membrane. A domain-of-unknown-function (DUF4179) in RsiV contains the signal peptidase cleavage site, and protects RsiV from cleavage in the absence of lysozyme via amphipathic helices. In addition to RsiV, DUF4179 is found in an unrelated and uncharacterized anti-σ factor present in Firmicutes including within some clinically-relevant species.
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Affiliation(s)
- Lincoln T Lewerke
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America
| | - Paige J Kies
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America
| | - Ute Müh
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America
| | - Craig D Ellermeier
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America.,Graduate Program in Genetics, University of Iowa, Iowa City, IA, United States of America
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17
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Champion PA, Shrout JD. The 24th Annual Midwest Microbial Pathogenesis Meeting. J Bacteriol 2018; 200:e000950-18. [PMID: 29483166 PMCID: PMC5952387 DOI: 10.1128/jb.00095-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The 24th Annual Midwest Microbial Pathogenesis Conference (MMPC) was held at the University of Notre Dame from August 25-27, 2017. The conference provided an opportunity for scientists from the Midwest to discuss new advances in microbial pathogenesis, including how pathogens promote disease, and how they interact with each other, the microbiome and the host. This commentary highlights the MMPC history, the topics presented at the conference and the reports in this issue.
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Affiliation(s)
- Patricia A. Champion
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Joshua D. Shrout
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana, USA
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