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Pannullo AG, Zbylicki BR, Ellermeier CD. Identification of DraRS in Clostridioides difficile, a Two-Component Regulatory System That Responds to Lipid II-Interacting Antibiotics. J Bacteriol 2023; 205:e0016423. [PMID: 37439672 PMCID: PMC10601625 DOI: 10.1128/jb.00164-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 06/27/2023] [Indexed: 07/14/2023] Open
Abstract
Clostridioides difficile is a Gram-positive opportunistic pathogen that results in 220,000 infections, 12,000 deaths, and upwards of $1 billion in medical costs in the United States each year. C. difficile is highly resistant to a variety of antibiotics, but we have a poor understanding of how C. difficile senses and responds to antibiotic stress and how such sensory systems affect clinical outcomes. We have identified a spontaneous C. difficile mutant that displays increased daptomycin resistance. We performed whole-genome sequencing and found a nonsense mutation, S605*, in draS, which encodes a putative sensor histidine kinase of a two-component system (TCS). The draSS605* mutant has an ~4- to 8-fold increase in the daptomycin MIC compared to the wild type (WT). We found that the expression of constitutively active DraRD54E in the WT increases daptomycin resistance 8- to 16-fold and increases bacitracin resistance ~4-fold. We found that a selection of lipid II-inhibiting compounds leads to the increased activity of the luciferase-based reporter PdraR-slucopt, including vancomycin, bacitracin, ramoplanin, and daptomycin. Using RNA sequencing (RNA-seq), we identified the DraRS regulon. Interestingly, we found that DraRS can induce the expression of the previously identified hex locus required for the synthesis of a novel glycolipid produced in C. difficile. Our data suggest that the induction of the hex locus by DraR explains some, but not all, of the DraR-induced daptomycin and bacitracin resistance. 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. C. difficile encodes ~50 annotated two-component systems (TCSs); however, only a few have been studied. The function of these unstudied TCSs is not known. Here, we show that the TCS DraRS plays a role in responding to a subset of lipid II-inhibiting antibiotics and mediates resistance to daptomycin and bacitracin in part by inducing the expression of the recently identified hex locus, which encodes enzymes required for the production of a novel glycolipid in C. difficile.
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Affiliation(s)
- Anthony G. Pannullo
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Brianne R. Zbylicki
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Craig D. Ellermeier
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
- Graduate Program in Genetics, University of Iowa, Iowa City, Iowa, USA
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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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Willdigg JR, Patel Y, Helmann JD. A Decrease in Fatty Acid Synthesis Rescues Cells with Limited Peptidoglycan Synthesis Capacity. mBio 2023; 14:e0047523. [PMID: 37017514 PMCID: PMC10128001 DOI: 10.1128/mbio.00475-23] [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: 02/24/2023] [Accepted: 03/13/2023] [Indexed: 04/06/2023] Open
Abstract
Proper synthesis and maintenance of a multilayered cell envelope are critical for bacterial fitness. However, whether mechanisms exist to coordinate synthesis of the membrane and peptidoglycan layers is unclear. In Bacillus subtilis, synthesis of peptidoglycan (PG) during cell elongation is mediated by an elongasome complex acting in concert with class A penicillin-binding proteins (aPBPs). We previously described mutant strains limited in their capacity for PG synthesis due to a loss of aPBPs and an inability to compensate by upregulation of elongasome function. Growth of these PG-limited cells can be restored by suppressor mutations predicted to decrease membrane synthesis. One suppressor mutation leads to an altered function repressor, FapR*, that functions as a super-repressor and leads to decreased transcription of fatty acid synthesis (FAS) genes. Consistent with fatty acid limitation mitigating cell wall synthesis defects, inhibition of FAS by cerulenin also restored growth of PG-limited cells. Moreover, cerulenin can counteract the inhibitory effect of β-lactams in some strains. These results imply that limiting PG synthesis results in impaired growth, in part, due to an imbalance of PG and cell membrane synthesis and that B. subtilis lacks a robust physiological mechanism to reduce membrane synthesis when PG synthesis is impaired. IMPORTANCE Understanding how a bacterium coordinates cell envelope synthesis is essential to fully appreciate how bacteria grow, divide, and resist cell envelope stresses, such as β-lactam antibiotics. Balanced synthesis of the peptidoglycan cell wall and the cell membrane is critical for cells to maintain shape and turgor pressure and to resist external cell envelope threats. Using Bacillus subtilis, we show that cells deficient in peptidoglycan synthesis can be rescued by compensatory mutations that decrease the synthesis of fatty acids. Further, we show that inhibiting fatty acid synthesis with cerulenin is sufficient to restore growth of cells deficient in peptidoglycan synthesis. Understanding the coordination of cell wall and membrane synthesis may provide insights relevant to antimicrobial treatment.
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Affiliation(s)
| | - Yesha Patel
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - John D. Helmann
- Department of Microbiology, Cornell University, Ithaca, New York, USA
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4
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Disruption of the tagF Orthologue in the epa Locus Variable Region of Enterococcus faecalis Causes Cell Surface Changes and Suppresses an eep-Dependent Lysozyme Resistance Phenotype. J Bacteriol 2022; 204:e0024722. [PMID: 36094307 PMCID: PMC9578411 DOI: 10.1128/jb.00247-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The disease-producing capacity of the opportunistic pathogen Enterococcus faecalis is enhanced by the ability of the bacterium to evade killing by antimicrobial agents. Survival of E. faecalis in the presence of the human antimicrobial enzyme lysozyme is mediated in part by the site 2 metalloprotease Eep; however, a complete model of enterococcal lysozyme resistance has not been elucidated. To better understand the molecular basis for lysozyme resistance in E. faecalis, we analyzed Δeep suppressor mutants that acquire resistance to lysozyme through mutation of the gene OG1RF_11713, a predicted teichoic acid biosynthesis-encoding gene located within the variable region of the enterococcal polysaccharide antigen (epa) locus. Sequence comparisons revealed that OG1RF_11713 is most similar to the cytidine-5'-diphosphate (CDP)-glycerol:poly-(glycerolphosphate)glycerophosphotransferase TagF from Staphylococcus epidermidis. Inactivation of OG1RF_11713 in both the wild-type and Δeep genetic backgrounds was sufficient to increase the resistance of E. faecalis OG1RF to lysozyme. Minimal amounts of N-acetylgalactosamine were detectable in cell wall carbohydrate extracts of OG1RF_11713 deletion mutants, and this was associated with a reduction in negative cell surface charge. Targeted disruption of OG1RF_11713 was also associated with increased susceptibility to the antibiotic polymyxin B and membrane-targeting detergents and decreased susceptibility to the lantibiotic nisin. This work implicates OG1RF_11713 as a major determinant of cell envelope integrity and provides further validation that lysozyme resistance is intrinsically linked to the modification of enterococcal cell wall polysaccharides. IMPORTANCE Enterococcus faecalis is a leading cause of health-care-associated infections for which there are limited treatment options. E. faecalis is resistant to several antibiotics and to high concentrations of the human antimicrobial enzyme lysozyme. The molecular mechanisms that mediate lysozyme resistance in E. faecalis are complex and remain incompletely characterized. This work demonstrates that a gene located within the variable region of the enterococcal polysaccharide antigen locus of E. faecalis strain OG1RF (OG1RF_11713), which is predicted to encode a component of the teichoic acid biosynthesis machinery, is part of the lysozyme resistance circuitry and is important for enterococcal cell wall integrity. These findings suggest that OG1RF_11713 is a potential target for new therapeutic strategies to combat enterococcal infections.
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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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8
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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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Kaus GM, Snyder LF, Müh U, Flores MJ, Popham DL, Ellermeier CD. Lysozyme Resistance in Clostridioides difficile Is Dependent on Two Peptidoglycan Deacetylases. J Bacteriol 2020; 202:e00421-20. [PMID: 32868404 PMCID: PMC7585060 DOI: 10.1128/jb.00421-20] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 08/25/2020] [Indexed: 12/18/2022] Open
Abstract
Clostridioides (Clostridium) difficile is a major cause of hospital-acquired infections leading to antibiotic-associated diarrhea. C. difficile exhibits a very high level of resistance to lysozyme. Bacteria commonly resist lysozyme through modification of the cell wall. In C. difficile, σV is required for lysozyme resistance, and σV is activated in response to lysozyme. Once activated, σV, encoded by csfV, directs transcription of genes necessary for lysozyme resistance. Here, we analyze the contribution of individual genes in the σV regulon to lysozyme resistance. Using CRISPR-Cas9-mediated mutagenesis we constructed in-frame deletions of single genes in the csfV operon. We find that pdaV, which encodes a peptidoglycan deacetylase, is partially responsible for lysozyme resistance. We then performed CRISPR inhibition (CRISPRi) to identify a second peptidoglycan deacetylase, encoded by pgdA, that is important for lysozyme resistance. Deletion of either pgdA or pdaV resulted in modest decreases in lysozyme resistance. However, deletion of both pgdA and pdaV resulted in a 1,000-fold decrease in lysozyme resistance. Further, muropeptide analysis revealed that loss of either PgdA or PdaV had modest effects on peptidoglycan deacetylation but that loss of both PgdA and PdaV resulted in almost complete loss of peptidoglycan deacetylation. This suggests that PgdA and PdaV are redundant peptidoglycan deacetylases. We also used CRISPRi to compare other lysozyme resistance mechanisms and conclude that peptidoglycan deacetylation is the major mechanism of lysozyme resistance in C. difficileIMPORTANCEClostridioides difficile is the leading cause of hospital-acquired diarrhea. C. difficile is highly resistant to lysozyme. We previously showed that the csfV operon is required for lysozyme resistance. Here, we used CRISPR-Cas9 mediated mutagenesis and CRISPRi knockdown to show that peptidoglycan deacetylation is necessary for lysozyme resistance and is the major lysozyme resistance mechanism in C. difficile We show that two peptidoglycan deacetylases in C. difficile are partially redundant and are required for lysozyme resistance. PgdA provides an intrinsic level of deacetylation, and PdaV, encoded by a part of the csfV operon, provides lysozyme-induced peptidoglycan deacetylation.
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Affiliation(s)
- Gabriela M Kaus
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Lindsey F Snyder
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, Iowa, USA
| | - Ute Müh
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Matthew J Flores
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - David L Popham
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Craig D Ellermeier
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, Iowa, USA
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13
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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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14
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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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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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Tran NT, Huang X, Hong HJ, Bush MJ, Chandra G, Pinto D, Bibb MJ, Hutchings MI, Mascher T, Buttner MJ. Defining the regulon of genes controlled by σ E , a key regulator of the cell envelope stress response in Streptomyces coelicolor. Mol Microbiol 2019; 112:461-481. [PMID: 30907454 PMCID: PMC6767563 DOI: 10.1111/mmi.14250] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2019] [Indexed: 01/01/2023]
Abstract
The extracytoplasmic function (ECF) σ factor, σE , is a key regulator of the cell envelope stress response in Streptomyces coelicolor. Although its role in maintaining cell wall integrity has been known for over a decade, a comprehensive analysis of the genes under its control has not been undertaken. Here, using a combination of chromatin immunoprecipitation-sequencing (ChIP-seq), microarray transcriptional profiling and bioinformatic analysis, we attempt to define the σE regulon. Approximately half of the genes identified encode proteins implicated in cell envelope function. Seventeen novel targets were validated by S1 nuclease mapping or in vitro transcription, establishing a σE -binding consensus. Subsequently, we used bioinformatic analysis to look for conservation of the σE target promoters identified in S. coelicolor across 19 Streptomyces species. Key proteins under σE control across the genus include the actin homolog MreB, three penicillin-binding proteins, two L,D-transpeptidases, a LytR-CpsA-Psr-family protein predicted to be involved in cell wall teichoic acid deposition and a predicted MprF protein, which adds lysyl groups to phosphatidylglycerol to neutralize membrane surface charge. Taken together, these analyses provide biological insight into the σE -mediated cell envelope stress response in the genus Streptomyces.
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Affiliation(s)
- Ngat T Tran
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Xiaoluo Huang
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Department Biology I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, Planegg-Martinsried, 82152, Germany
| | - Hee-Jeon Hong
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Matthew J Bush
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Daniela Pinto
- Department Biology I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, Planegg-Martinsried, 82152, Germany
| | - Maureen J Bibb
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Matthew I Hutchings
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Thorsten Mascher
- Department Biology I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, Planegg-Martinsried, 82152, Germany
| | - Mark J Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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17
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Seki T, Furumi T, Hashimoto M, Hara H, Matsuoka S. Activation of extracytoplasmic function sigma factors upon removal of glucolipids and reduction of phosphatidylglycerol content in Bacillus subtilis cells lacking lipoteichoic acid. Genes Genet Syst 2019; 94:71-80. [PMID: 30971625 DOI: 10.1266/ggs.18-00046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In Bacillus subtilis, extracytoplasmic function (ECF) sigma factors are activated by reduction of phosphatidylglycerol (PG) content, absence of glucolipids, or absence of lipoteichoic acid (LTA). LTA is synthesized by polymerization of the glycerophosphate moiety of PG onto diglucosyldiacylglycerol (DGlcDG), a major glucolipid in B. subtilis, in the plasma membrane. Thus, reduction of PG content or absence of glucolipids might cause some changes in LTA, and hence we investigated whether reduction of PG content or absence of glucolipids induces the activation of ECF sigma factors independently from an ensuing change in LTA. Disruption of ugtP, responsible for glucolipid synthesis, in cells lacking LTA caused an additive increase of activation levels of σM, σX, σV and σY (3.1-, 2.2-, 2.1- and 1.4-fold, respectively), relative to their activation levels in cells lacking LTA alone. Reduction of PG content (by repressing Pspac-pgsA) in the cells lacking LTA caused an additive increase of activation levels of σM, σW and σV (2.3-, 1.9- and 2.2-fold, respectively). These results suggested that absence of glucolipids or reduction of PG alone, not the possible secondary alteration in LTA, leads to changes that affect the regulation systems of some ECF sigma factors in the plasma membrane.
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Affiliation(s)
- Takahiro Seki
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Takuya Furumi
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Michihiro Hashimoto
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Hiroshi Hara
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Satoshi Matsuoka
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University
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18
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Gupta AK, Behera D, Gopal B. The crystal structure of Mycobacterium tuberculosis high-temperature requirement A protein reveals an autoregulatory mechanism. Acta Crystallogr F Struct Biol Commun 2018; 74:803-809. [PMID: 30511675 PMCID: PMC6277966 DOI: 10.1107/s2053230x18016217] [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: 09/19/2018] [Accepted: 11/15/2018] [Indexed: 11/11/2022] Open
Abstract
The crystal structure of Mycobacterium tuberculosis high-temperature requirement A (HtrA) protein was determined at 1.83 Å resolution. This membrane-associated protease is essential for the survival of M. tuberculosis. The crystal structure reveals that interactions between the PDZ domain and the catalytic domain in HtrA lead to an inactive conformation. This finding is consistent with its proposed role as a regulatory protease that is conditionally activated upon appropriate environmental triggers. The structure provides a basis for directed studies to evaluate the role of this essential protein and the regulatory pathways that are influenced by this protease.
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Affiliation(s)
- Arvind Kumar Gupta
- Molecular Biophysics Unit, Indian Institute of Science, C. V. Raman Road, Bangalore 560 012, India
| | - Debashree Behera
- Molecular Biophysics Unit, Indian Institute of Science, C. V. Raman Road, Bangalore 560 012, India
| | - Balasubramanian Gopal
- Molecular Biophysics Unit, Indian Institute of Science, C. V. Raman Road, Bangalore 560 012, India
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19
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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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20
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Ragland SA, Humbert MV, Christodoulides M, Criss AK. Neisseria gonorrhoeae employs two protein inhibitors to evade killing by human lysozyme. PLoS Pathog 2018; 14:e1007080. [PMID: 29975775 PMCID: PMC6033460 DOI: 10.1371/journal.ppat.1007080] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 05/08/2018] [Indexed: 12/25/2022] Open
Abstract
The bacterial pathogen Neisseria gonorrhoeae (Gc) infects mucosal sites rich in antimicrobial proteins, including the bacterial cell wall-degrading enzyme lysozyme. Certain Gram-negative bacteria produce protein inhibitors that bind to and inhibit lysozyme. Here, we identify Ng_1063 as a new inhibitor of lysozyme in Gc, and we define its functions in light of a second, recently identified lysozyme inhibitor, Ng_1981. In silico analyses indicated that Ng_1063 bears sequence and structural homology to MliC-type inhibitors of lysozyme. Recombinant Ng_1063 inhibited lysozyme-mediated killing of a susceptible mutant of Gc and the lysozyme-sensitive bacterium Micrococcus luteus. This inhibitory activity was dependent on serine 83 and lysine 103 of Ng_1063, which are predicted to interact with lysozyme’s active site residues. Lysozyme co-immunoprecipitated with Ng_1063 and Ng_1981 from intact Gc. Ng_1063 and Ng_1981 protein levels were also increased in Gc exposed to lysozyme. Gc lacking both ng1063 and ng1981 was significantly more sensitive to killing by lysozyme than wild-type or single mutant bacteria. When exposed to human tears or saliva, in which lysozyme is abundant, survival of Δ1981Δ1063 Gc was significantly reduced compared to wild-type, and survival was restored upon addition of recombinant Ng_1981. Δ1981Δ1063 mutant Gc survival was additionally reduced in the presence of human neutrophils, which produce lysozyme. We found that while Ng_1063 was exposed on the surface of Gc, Ng_1981 was both in an intracellular pool and extracellularly released from the bacteria, suggesting that Gc employs these two proteins at multiple spatial barriers to fully neutralize lysozyme activity. Together, these findings identify Ng_1063 and Ng_1981 as critical components for Gc defense against lysozyme. These proteins may be attractive targets for antimicrobial therapy aimed to render Gc susceptible to host defenses and/or for vaccine development, both of which are urgently needed against drug-resistant gonorrhea. The mucosal pathogen Neisseria gonorrhoeae has acquired resistance to almost all recommended antibiotics, and no gonorrhea vaccine currently exists. Attractive targets for therapeutic discovery include bacterial factors that, when inactivated, enhance bacterial susceptibility to host-derived antimicrobial components. The bacterial cell wall-degrading enzyme lysozyme is abundant in mucosal secretions and innate immune cells. To resist killing by lysozyme, some bacteria produce proteins that bind to and directly inhibit the activity of lysozyme. Here, we demonstrate lysozyme inhibitory activity in the N. gonorrhoeae protein Ng_1063. We found that both Ng_1063 and a second, recently described lysozyme inhibitor, Ng_1981, contribute to full resistance of N. gonorrhoeae to lysozyme, including resistance to lysozyme-rich mucosal secretions and human neutrophils. Although Ng_1063 and Ng_1981 are both inhibitors of lysozyme, they are distinct in their sequences, biological activities, and cellular localizations. Because both Ng_1063 and Ng_1981 are extracellular, we propose they can be targeted for vaccines and drugs that sensitize Gc to human antimicrobial defenses.
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Affiliation(s)
- Stephanie A. Ragland
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Marίa V. Humbert
- Neisseria Research, Molecular Microbiology, Academic Unit of Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, University of Southampton Faculty of Medicine, Southampton, United Kingdom
| | - Myron Christodoulides
- Neisseria Research, Molecular Microbiology, Academic Unit of Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, University of Southampton Faculty of Medicine, Southampton, United Kingdom
| | - Alison K. Criss
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, United States of America
- * E-mail:
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21
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Baktash A, Terveer EM, Zwittink RD, Hornung BVH, Corver J, Kuijper EJ, Smits WK. Mechanistic Insights in the Success of Fecal Microbiota Transplants for the Treatment of Clostridium difficile Infections. Front Microbiol 2018; 9:1242. [PMID: 29946308 PMCID: PMC6005852 DOI: 10.3389/fmicb.2018.01242] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 05/23/2018] [Indexed: 12/12/2022] Open
Abstract
Fecal microbiota transplantation has proven to be an effective treatment for infections with the gram-positive enteropathogen Clostridium difficile. Despite its effectiveness, the exact mechanisms that underlie its success are largely unclear. In this review, we highlight the pleiotropic effectors that are transferred during fecal microbiota transfer and relate this to the C. difficile lifecycle. In doing so, we show that it is likely that multiple factors contribute to the elimination of symptoms of C. difficile infections after fecal microbiota transplantation.
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Affiliation(s)
- Amoe Baktash
- Clinical Microbiology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Elisabeth M Terveer
- Clinical Microbiology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands.,Netherlands Donor Feces Bank, Leiden, Netherlands
| | - Romy D Zwittink
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands.,Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Bastian V H Hornung
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands.,Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Jeroen Corver
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands.,Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Ed J Kuijper
- Clinical Microbiology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands.,Netherlands Donor Feces Bank, Leiden, Netherlands.,Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Wiep Klaas Smits
- Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
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22
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Signal Peptidase Is Necessary and Sufficient for Site 1 Cleavage of RsiV in Bacillus subtilis in Response to Lysozyme. J Bacteriol 2018; 200:JB.00663-17. [PMID: 29358498 DOI: 10.1128/jb.00663-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 01/18/2018] [Indexed: 01/09/2023] Open
Abstract
Extracytoplasmic function (ECF) σ factors are a diverse family of alternative σ factors that allow bacteria to sense and respond to changes in the environment. σV is an ECF σ factor found primarily in low-GC Gram-positive bacteria and is required for lysozyme resistance in several opportunistic pathogens. In the absence of lysozyme, σV is inhibited by the anti-σ factor RsiV. In response to lysozyme, RsiV is degraded via the process of regulated intramembrane proteolysis (RIP). RIP is initiated by cleavage of RsiV at site 1, which allows the intramembrane protease RasP to cleave RsiV within the transmembrane domain at site 2 and leads to activation of σV Previous work suggested that RsiV is cleaved by signal peptidase at site 1. Here we demonstrate in vitro that signal peptidase is sufficient for cleavage of RsiV only in the presence of lysozyme and provide evidence that multiple Bacillus subtilis signal peptidases can cleave RsiV in vitro This cleavage is dependent upon the concentration of lysozyme, consistent with previous work that showed that binding to RsiV was required for σV activation. We also show that signal peptidase activity is required for site 1 cleavage of RsiV in vivo Thus, we demonstrate that signal peptidase is the site 1 protease for RsiV.IMPORTANCE Extracytoplasmic function (ECF) σ factors are a diverse family of alternative σ factors that respond to extracellular signals. The ECF σ factor σV is present in many low-GC Gram-positive bacteria and induces resistance to lysozyme, a component of the innate immune system. The anti-σ factor RsiV inhibits σV activity in the absence of lysozyme. Lysozyme binds RsiV, which initiates a proteolytic cascade leading to destruction of RsiV and activation of σV This proteolytic cascade is initiated by signal peptidase, a component of the general secretory system. We show that signal peptidase is necessary and sufficient for cleavage of RsiV at site 1 in the presence of lysozyme. This report describes a role for signal peptidase in controlling gene expression.
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Toyoda K, Inui M. Extracytoplasmic function sigma factor σDconfers resistance to environmental stress by enhancing mycolate synthesis and modifying peptidoglycan structures inCorynebacterium glutamicum. Mol Microbiol 2017; 107:312-329. [DOI: 10.1111/mmi.13883] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Koichi Toyoda
- Research institute of Innovative Technology for the Earth (RITE), 9-2 Kizugawa; Kyoto 619-0292 Japan
| | - Masayuki Inui
- Research institute of Innovative Technology for the Earth (RITE), 9-2 Kizugawa; Kyoto 619-0292 Japan
- Graduate School of Biological Sciences; Nara Institute of Science and Technology, 8916-5; Takayama, Ikoma, Nara 630-0101 Japan
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Abstract
Lysozyme is a cornerstone of innate immunity. The canonical mechanism for bacterial killing by lysozyme occurs through the hydrolysis of cell wall peptidoglycan (PG). Conventional type (c-type) lysozymes are also highly cationic and can kill certain bacteria independently of PG hydrolytic activity. Reflecting the ongoing arms race between host and invading microorganisms, both gram-positive and gram-negative bacteria have evolved mechanisms to thwart killing by lysozyme. In addition to its direct antimicrobial role, more recent evidence has shown that lysozyme modulates the host immune response to infection. The degradation and lysis of bacteria by lysozyme enhance the release of bacterial products, including PG, that activate pattern recognition receptors in host cells. Yet paradoxically, lysozyme is important for the resolution of inflammation at mucosal sites. This review will highlight recent advances in our understanding of the diverse mechanisms that bacteria use to protect themselves against lysozyme, the intriguing immunomodulatory function of lysozyme, and the relationship between these features in the context of infection.
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Affiliation(s)
- Stephanie A. Ragland
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Alison K. Criss
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, United States of America
- * E-mail:
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Sineva E, Savkina M, Ades SE. Themes and variations in gene regulation by extracytoplasmic function (ECF) sigma factors. Curr Opin Microbiol 2017; 36:128-137. [PMID: 28575802 DOI: 10.1016/j.mib.2017.05.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 04/15/2017] [Accepted: 05/13/2017] [Indexed: 01/08/2023]
Abstract
The ECF sigma family was identified 23 years ago as a distinct group of σ70-like factors. ECF sigma factors have since emerged as a major form of bacterial signal transduction that can be grouped into over 50 phylogenetically distinct subfamilies. Advances in our understanding of these sigma factors and the signaling pathways governing their activity have elucidated conserved features as well as aspects that have evolved over time. All ECF sigma factors are predicted to share a common streamlined domain structure and mode of promoter interaction. The activity of most ECF sigma factors is controlled by an anti-sigma factor. The nature of the anti-sigma factor and the activating signaling pathways appear to be conserved within ECF families, while considerable diversity exists between different families.
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Affiliation(s)
- Elena Sineva
- Department of Biochemistry and Molecular Biology, 408 Althouse Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
| | - Maria Savkina
- Department of Biochemistry and Molecular Biology, 408 Althouse Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
| | - Sarah E Ades
- Department of Biochemistry and Molecular Biology, 408 Althouse Laboratory, The Pennsylvania State University, University Park, PA 16802, USA.
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26
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Woods EC, McBride SM. Regulation of antimicrobial resistance by extracytoplasmic function (ECF) sigma factors. Microbes Infect 2017; 19:238-248. [PMID: 28153747 DOI: 10.1016/j.micinf.2017.01.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 01/20/2017] [Accepted: 01/21/2017] [Indexed: 11/27/2022]
Abstract
Extracytoplasmic function (ECF) sigma factors are a subfamily of σ70 sigma factors that activate genes involved in stress-response functions. In many bacteria, ECF sigma factors regulate resistance to antimicrobial compounds. This review will summarize the ECF sigma factors that regulate antimicrobial resistance in model organisms and clinically relevant pathogens.
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Affiliation(s)
- Emily C Woods
- Department of Microbiology and Immunology, Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Shonna M McBride
- Department of Microbiology and Immunology, Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, USA.
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27
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Hastie JL, Williams KB, Bohr LL, Houtman JC, Gakhar L, Ellermeier CD. The Anti-sigma Factor RsiV Is a Bacterial Receptor for Lysozyme: Co-crystal Structure Determination and Demonstration That Binding of Lysozyme to RsiV Is Required for σV Activation. PLoS Genet 2016; 12:e1006287. [PMID: 27602573 PMCID: PMC5014341 DOI: 10.1371/journal.pgen.1006287] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/09/2016] [Indexed: 01/25/2023] Open
Abstract
σ factors provide RNA polymerase with promoter specificity in bacteria. Some σ factors require activation in order to interact with RNA polymerase and transcribe target genes. The Extra-Cytoplasmic Function (ECF) σ factor, σV, is encoded by several Gram-positive bacteria and is specifically activated by lysozyme. This activation requires the proteolytic destruction of the anti-σ factor RsiV via a process of regulated intramembrane proteolysis (RIP). In many cases proteases that cleave at site-1 are thought to directly sense a signal and initiate the RIP process. We previously suggested binding of lysozyme to RsiV initiated the proteolytic destruction of RsiV and activation of σV. Here we determined the X-ray crystal structure of the RsiV-lysozyme complex at 2.3 Å which revealed that RsiV and lysozyme make extensive contacts. We constructed RsiV mutants with altered abilities to bind lysozyme. We find that mutants that are unable to bind lysozyme block site-1 cleavage of RsiV and σV activation in response to lysozyme. Taken together these data demonstrate that RsiV is a receptor for lysozyme and binding of RsiV to lysozyme is required for σV activation. In addition, the co-structure revealed that RsiV binds to the lysozyme active site pocket. We provide evidence that in addition to acting as a sensor for the presence of lysozyme, RsiV also inhibits lysozyme activity. Thus we have demonstrated that RsiV is a protein with multiple functions. RsiV inhibits σV activity in the absence of lysozyme, RsiV binds lysozyme triggering σV activation and RsiV inhibits the enzymatic activity of lysozyme. The exposed cell wall of Gram-positive bacteria renders them particularly susceptible to the innate immune defense enzyme lysozyme. Several Gram-positive bacteria activate lysozyme resistance via a signal transduction system, σV, which is induced by lysozyme. Here we report the co-structure of lysozyme with its bacterial receptor the anti-σ factor RsiV. In the absence of lysozyme, RsiV inhibits activity of σV. In the presence of lysozyme, RsiV is destroyed via proteolytic cascade. We demonstrate that binding of lysozyme to RsiV triggers the proteolytic destruction of the anti-σ factor RsiV and thus activation of σV. In addition, we demonstrate that RsiV also acts as an inhibitor of lysozyme activity. Thus, the anti-σ factor RsiV allows for the cell to sense lysozyme and inhibit its activity as well as inducing additional lysozyme resistance mechanisms.
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Affiliation(s)
- Jessica L. Hastie
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Kyle B. Williams
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Lindsey L. Bohr
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Jon C. Houtman
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Lokesh Gakhar
- Department of Biochemistry & Protein Crystallography Facility, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Craig D. Ellermeier
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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28
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The Clostridium difficile Dlt Pathway Is Controlled by the Extracytoplasmic Function Sigma Factor σV in Response to Lysozyme. Infect Immun 2016; 84:1902-1916. [PMID: 27068095 DOI: 10.1128/iai.00207-16] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 04/06/2016] [Indexed: 12/18/2022] Open
Abstract
Clostridium difficile (also known as Peptoclostridium difficile) is a major nosocomial pathogen and a leading cause of antibiotic-associated diarrhea throughout the world. Colonization of the intestinal tract is necessary for C. difficile to cause disease. Host-produced antimicrobial proteins (AMPs), such as lysozyme, are present in the intestinal tract and can deter colonization by many bacterial pathogens, and yet C. difficile is able to survive in the colon in the presence of these AMPs. Our prior studies established that the Dlt pathway, which increases the surface charge of the bacterium by addition of d-alanine to teichoic acids, is important for C. difficile resistance to a variety of AMPs. We sought to determine what genetic mechanisms regulate expression of the Dlt pathway. In this study, we show that a dlt null mutant is severely attenuated for growth in lysozyme and that expression of the dltDABC operon is induced in response to lysozyme. Moreover, we found that a mutant lacking the extracytoplasmic function (ECF) sigma factor σ(V) does not induce dlt expression in response to lysozyme, indicating that σ(V) is required for regulation of lysozyme-dependent d-alanylation of the cell wall. Using reporter gene fusions and 5' RACE (rapid amplification of cDNA ends) analysis, we identified promoter elements necessary for lysozyme-dependent and lysozyme-independent dlt expression. In addition, we observed that both a sigV mutant and a dlt mutant are more virulent in a hamster model of infection. These findings demonstrate that cell wall d-alanylation in C. difficile is induced by lysozyme in a σ(V)-dependent manner and that this pathway impacts virulence in vivo.
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29
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Helmann JD. Bacillus subtilis extracytoplasmic function (ECF) sigma factors and defense of the cell envelope. Curr Opin Microbiol 2016; 30:122-132. [PMID: 26901131 DOI: 10.1016/j.mib.2016.02.002] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 01/29/2016] [Accepted: 02/02/2016] [Indexed: 01/20/2023]
Abstract
Bacillus subtilis provides a model for investigation of the bacterial cell envelope, the first line of defense against environmental threats. Extracytoplasmic function (ECF) sigma factors activate genes that confer resistance to agents that threaten the integrity of the envelope. Although their individual regulons overlap, σ(W) is most closely associated with membrane-active agents, σ(X) with cationic antimicrobial peptide resistance, and σ(V) with resistance to lysozyme. Here, I highlight the role of the σ(M) regulon, which is strongly induced by conditions that impair peptidoglycan synthesis and includes the core pathways of envelope synthesis and cell division, as well as stress-inducible alternative enzymes. Studies of these cell envelope stress responses provide insights into how bacteria acclimate to the presence of antibiotics.
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Affiliation(s)
- John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA.
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30
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Davis MC, Smith LK, MacLellan SR. The atypical two-subunit σ factor from Bacillus subtilis is regulated by an integral membrane protein and acid stress. MICROBIOLOGY-SGM 2015; 162:398-407. [PMID: 26651345 DOI: 10.1099/mic.0.000223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Extracytoplasmic function (ECF) σ factors constitute a major component of the physicochemical sensory apparatus in bacteria. Most ECF σ factors are co-expressed with a negative regulator called an anti-σ factor that binds to its cognate σ factor and sequesters it from productive association with core RNA polymerase (RNAP). Anti-σ factors constitute an important element of signal transduction pathways that mediate an appropriate transcriptional response to changing environmental conditions. The Bacillus subtilis genome encodes seven canonical ECF σ factors and six of these are co-expressed with experimentally verified anti-σ factors. B. subtilis also expresses an ECF-like atypical two-subunit σ factor composed of subunits SigO and RsoA that becomes active after exposure to certain cell-wall-acting antibiotics and to growth under acidic conditions. This work describes the identification and preliminary characterization of a protein (RsiO, formerly YvrL) that constitutes the anti-σ factor cognate to SigO-RsoA. Synthesis of RsiO represses SigO-RsoA-dependent transcription initiation by binding the N-terminus of SigO under neutral (pH 7) conditions. Reconstitution of the SigO-RsoA-RsiO regulatory system into a heterologous host reveals that the imposition of acid stress (pH 5.4) abolishes the ability of RsiO to repress SigO-RsoA-dependent transcription and this correlates with loss of RsiO binding affinity for SigO. A current model for RsiO function indicates that RsiO responds, either directly or indirectly, to increased extracytoplasmic hydrogen ion concentration and becomes inactivated. This results in the release of SigO into the cytoplasm, where it productively associates with RsoA and core RNAP to initiate transcription from target promoters in the cell.
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Affiliation(s)
- Maria C Davis
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - Logan K Smith
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - Shawn R MacLellan
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
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31
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Craney A, Romesberg FE. The inhibition of type I bacterial signal peptidase: Biological consequences and therapeutic potential. Bioorg Med Chem Lett 2015; 25:4761-4766. [PMID: 26276537 DOI: 10.1016/j.bmcl.2015.07.072] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 07/16/2015] [Accepted: 07/21/2015] [Indexed: 01/05/2023]
Abstract
The general secretory pathway has long been regarded as a potential antibiotic drug target. In particular, bacterial type I signal peptidase (SPase) is emerging as a strong candidate for therapeutic use. In this review, we focus on the information gained from the use of SPase inhibitors as probes of prokaryote biology. A thorough understanding of the consequences of SPase inhibition and the mechanisms of resistance that arise are essential to the success of SPase as an antibiotic target. In addition to the role of SPase in processing secreted proteins, the use of SPase inhibitors has elucidated a previously unknown function for SPase in regulating cleavage events of membrane proteins.
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Affiliation(s)
- Arryn Craney
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Floyd E Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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32
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Paget MS. Bacterial Sigma Factors and Anti-Sigma Factors: Structure, Function and Distribution. Biomolecules 2015; 5:1245-65. [PMID: 26131973 PMCID: PMC4598750 DOI: 10.3390/biom5031245] [Citation(s) in RCA: 216] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/20/2015] [Accepted: 06/01/2015] [Indexed: 12/18/2022] Open
Abstract
Sigma factors are multi-domain subunits of bacterial RNA polymerase (RNAP) that play critical roles in transcription initiation, including the recognition and opening of promoters as well as the initial steps in RNA synthesis. This review focuses on the structure and function of the major sigma-70 class that includes the housekeeping sigma factor (Group 1) that directs the bulk of transcription during active growth, and structurally-related alternative sigma factors (Groups 2-4) that control a wide variety of adaptive responses such as morphological development and the management of stress. A recurring theme in sigma factor control is their sequestration by anti-sigma factors that occlude their RNAP-binding determinants. Sigma factors are then released through a wide variety of mechanisms, often involving branched signal transduction pathways that allow the integration of distinct signals. Three major strategies for sigma release are discussed: regulated proteolysis, partner-switching, and direct sensing by the anti-sigma factor.
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Affiliation(s)
- Mark S Paget
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK.
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33
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Splice variants and regulatory networks associated with host resistance to the intestinal worm Cooperia oncophora in cattle. Vet Parasitol 2015; 211:241-50. [PMID: 26025321 DOI: 10.1016/j.vetpar.2015.05.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/27/2015] [Accepted: 05/09/2015] [Indexed: 11/21/2022]
Abstract
To elucidate the molecular mechanism of host resistance, we characterized the jejunal transcriptome of Angus cattle selected for parasite resistance for over 20 years in response to infection caused by the intestinal worm Cooperia oncophora. The transcript abundance of 56 genes, such as that of mucin 12 (MUC12) and intestinal alkaline phosphatase (ALPI), was significantly higher in resistant cattle. Novel splicing variants, exon skipping events, and gene fusion events, were also detected. An algorithm for the reconstruction of accurate cellular networks (ARACNE) was used to infer de novo regulatory molecular networks in the interactome between the parasite and host. Under a combined cutoff of an error tolerance (ϵ = 0.10) and a stringent P-value threshold of mutual information (1.0 × 10(-5)), a total of 229,100 direct interactions controlled by 20,288 hub genes were identified. Among these hub genes, 7651 genes had ≥ 100 direct neighbors while the top 9778 hub genes controlled more than 50% of total direct interactions. Three lysozyme genes (LYZ1, LYZ2, and LYZ3), which are co-located in bovine chromosome 5 in tandem and are strongly upregulated in resistant cattle, shared a common regulatory network of 55 genes. These ancient antimicrobials were likely involved in regulating host-parasite interactions by affecting host gut microbiome. Notably, ALPI, known as a gut mucosal defense factor, controlled a molecular network consisting 410 genes, including 14 transcription factors (TF) and 10 genes that were significantly regulated in resistant cattle. Several large regulatory networks were controlled by TF, such as STAT6, SREBF1, and ELF4. Gene ontology (GO) processes significantly enriched in the regulatory network controlled by STAT6 included lipid metabolism. Our findings provide insights into the immune regulation of host-parasite interactions and the molecular mechanisms of host resistance in cattle.
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Seki T, Mineshima R, Hashimoto M, Matsumoto K, Hara H, Matsuoka S. Repression of the activities of two extracytoplasmic function σ factors, σM and σV, of Bacillus subtilis by glucolipids in Escherichia coli cells. Genes Genet Syst 2015; 90:109-14. [DOI: 10.1266/ggs.90.109] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Takahiro Seki
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Ryota Mineshima
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Michihiro Hashimoto
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Kouji Matsumoto
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Hiroshi Hara
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Satoshi Matsuoka
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University
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