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Biofilm ecology associated with dental caries: Understanding of microbial interactions in oral communities leads to development of therapeutic strategies targeting cariogenic biofilms. ADVANCES IN APPLIED MICROBIOLOGY 2023; 122:27-75. [PMID: 37085193 DOI: 10.1016/bs.aambs.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
A biofilm is a sessile community characterized by cells attached to the surface and organized into a complex structural arrangement. Dental caries is a biofilm-dependent oral disease caused by infection with cariogenic pathogens, such as Streptococcus mutans, and associated with frequent exposure to a sugar-rich diet and poor oral hygiene. The virulence of cariogenic biofilms is often associated with the spatial organization of S. mutans enmeshed with exopolysaccharides on tooth surfaces. However, in the oral cavity, S. mutans does not act alone, and several other microbes contribute to cariogenic biofilm formation. Microbial communities in cariogenic biofilms are spatially organized into complex structural arrangements of various microbes and extracellular matrices. The balance of microbiota diversity with reduced diversity and a high proportion of acidogenic-aciduric microbiota within the biofilm is closely related to the disease state. Understanding the characteristics of polymicrobial biofilms and the association of microbial interactions within the biofilm (e.g., symbiosis, cooperation, and competition) in terms of their potential role in the pathogenesis of oral disease would help develop new strategies for interventions in virulent biofilm formation.
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Rom JS, Le Breton Y, Islam E, Belew AT, El-Sayed NM, McIver KS. Loss of rpoE Encoding the δ-Factor of RNA Polymerase Impacts Pathophysiology of the Streptococcus pyogenes M1T1 Strain 5448. Microorganisms 2022; 10:microorganisms10081686. [PMID: 36014103 PMCID: PMC9412562 DOI: 10.3390/microorganisms10081686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/08/2022] [Accepted: 08/19/2022] [Indexed: 12/01/2022] Open
Abstract
Streptococcus pyogenes, also known as the Group A Streptococcus (GAS), is a Gram-positive bacterial pathogen of major clinical significance. Despite remaining relatively susceptible to conventional antimicrobial therapeutics, GAS still causes millions of infections and hundreds of thousands of deaths each year worldwide. Thus, a need for prophylactic and therapeutic interventions for GAS is in great demand. In this study, we investigated the importance of the gene encoding the delta (δ) subunit of the GAS RNA polymerase, rpoE, for its impact on virulence during skin and soft-tissue infection. A defined 5448 mutant with an insertionally-inactivated rpoE gene was defective for survival in whole human blood and was attenuated for both disseminated lethality and lesion size upon mono-culture infection in mouse soft tissue. Furthermore, the mutant had reduced competitive fitness when co-infected with wild type (WT) 5448 in the mouse model. We were unable to attribute this attenuation to any observable growth defect, although colony size and the ability to grow at higher temperatures were both affected when grown with nutrient-rich THY media. RNA-seq of GAS grown in THY to late log phase found that mutation of rpoE significantly impacted (>2-fold) the expression of 429 total genes (205 upregulated, 224 downregulated), including multiple virulence and “housekeeping” genes. The arc operon encoding the arginine deiminase (ADI) pathway was the most upregulated in the rpoE mutant and this could be confirmed phenotypically. Taken together, these findings demonstrate that the delta (δ) subunit of RNA polymerase is vital in GAS gene expression and virulence.
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The Potential Application of Natural Photosensitizers Used in Antimicrobial Photodynamic Therapy against Oral Infections. Pharmaceuticals (Basel) 2022; 15:ph15060767. [PMID: 35745686 PMCID: PMC9227410 DOI: 10.3390/ph15060767] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/14/2022] [Accepted: 06/16/2022] [Indexed: 02/05/2023] Open
Abstract
Oral health problems and the emergence of antimicrobial resistance among pathogenic bacterial strains have become major global challenges and are essential elements that negatively affect general well-being. Antimicrobial photodynamic therapy (APDT) is based on a light source and oxygen that activates a nontoxic photosensitizer, resulting in microbial destruction. Synthetic and natural products can be used to help the APDT against oral microorganisms. The undesirable consequences of conventional photosensitizers, including toxicity, and cost encourage researchers to explore new promising photosensitizers based on natural compounds such as curcumin, chlorella, chlorophyllin, phycocyanin, 5-aminolevulinic acid, and riboflavin. In this review, we summarize in vitro studies describing the potential use of APDT therapy conjugated with some natural products against selected microorganisms that are considered to be responsible for oral infections.
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Hwang G. In it together: Candida-bacterial oral biofilms and therapeutic strategies. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:183-196. [PMID: 35218311 PMCID: PMC8957517 DOI: 10.1111/1758-2229.13053] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 05/16/2023]
Abstract
Under natural environmental settings or in the human body, the majority of microorganisms exist in complex polymicrobial biofilms adhered to abiotic and biotic surfaces. These microorganisms exhibit symbiotic, mutualistic, synergistic, or antagonistic relationships with other species during biofilm colonization and development. These polymicrobial interactions are heterogeneous, complex and hard to control, thereby often yielding worse outcomes than monospecies infections. Concerning fungi, Candida spp., in particular, Candida albicans is often detected with various bacterial species in oral biofilms. These Candida-bacterial interactions may induce the transition of C. albicans from commensal to pathobiont or dysbiotic organism. Consequently, Candida-bacterial interactions are largely associated with various oral diseases, including dental caries, denture stomatitis, periodontitis, peri-implantitis, and oral cancer. Given the severity of oral diseases caused by cross-kingdom consortia that develop hard-to-remove and highly drug-resistant biofilms, fundamental research is warranted to strategically develop cost-effective and safe therapies to prevent and treat cross-kingdom interactions and subsequent biofilm development. While studies have shed some light, targeting fungal-involved polymicrobial biofilms has been limited. This mini-review outlines the key features of Candida-bacterial interactions and their impact on various oral diseases. In addition, current knowledge on therapeutic strategies to target Candida-bacterial polymicrobial biofilms is discussed.
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Affiliation(s)
- Geelsu Hwang
- Department of Preventive and Restorative Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Center for Innovation & Precision Dentistry, School of Dental Medicine, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corresponding Author: Geelsu Hwang,
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Wang Y, Li Q, Tian P, Tan T. Charting the landscape of RNA polymerases to unleash their potential in strain improvement. Biotechnol Adv 2021; 54:107792. [PMID: 34216775 DOI: 10.1016/j.biotechadv.2021.107792] [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: 02/16/2021] [Revised: 05/28/2021] [Accepted: 06/26/2021] [Indexed: 11/19/2022]
Abstract
One major mission of microbial cell factory is overproduction of desired chemicals. To this end, it is necessary to orchestrate enzymes that affect metabolic fluxes. However, only modification of a small number of enzymes in most cases cannot maximize desired metabolites, and global regulation is required. Of myriad enzymes influencing global regulation, RNA polymerase (RNAP) may be the most versatile enzyme in biological realm because it not only serves as the workhorse of central dogma but also participates in a plethora of biochemical events. In fact, recent years have witnessed extensive exploitation of RNAPs for phenotypic engineering. While a few impressive reviews showcase the structures and functionalities of RNAPs, this review not only summarizes the state-of-the-art advance in the structures of RNAPs but also points out their enormous potentials in metabolic engineering and synthetic biology. This review aims to provide valuable insights for strain improvement.
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Affiliation(s)
- Ye Wang
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Qingyang Li
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, PR China
| | - Pingfang Tian
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China.
| | - Tianwei Tan
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
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Contribution of Streptococcus mutans Strains with Collagen-Binding Proteins in the Presence of Serum to the Pathogenesis of Infective Endocarditis. Infect Immun 2017; 85:IAI.00401-17. [PMID: 28947650 DOI: 10.1128/iai.00401-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 09/18/2017] [Indexed: 12/31/2022] Open
Abstract
Streptococcus mutans, a major pathogen of dental caries, is considered one of the causative agents of infective endocarditis (IE). Recently, bacterial DNA encoding 120-kDa cell surface collagen-binding proteins (CBPs) has frequently been detected from S. mutans-positive IE patients. In addition, some of the CBP-positive S. mutans strains lacked a 190-kDa protein antigen (PA), whose absence strengthened the adhesion to and invasion of endothelial cells. The interaction between pathogenic bacteria and serum or plasma is considered an important virulence factor in developing systemic diseases; thus, we decided to analyze the pathogenesis of IE induced by S. mutans strains with different patterns of CBP and PA expression by focusing on the interaction with serum or plasma. CBP-positive (CBP+)/PA-negative (PA-) strains showed prominent aggregation in the presence of human serum or plasma, which was significantly greater than that with CBP+/PA-positive (PA+) and CBP-negative (CBP-)/PA+ strains. Aggregation of CBP+/PA- strains was also observed in the presence of a high concentration of type IV collagen, a major extracellular matrix protein in serum. In addition, aggregation of CBP+/PA- strains was drastically reduced when serum complement was inactivated. Furthermore, an ex vivo adherence model and an in vivo rat model of IE showed that extirpated heart valves infected with CBP+/PA- strains displayed prominent bacterial mass formation, which was not observed following infection with CBP+/PA+ and CBP-/PA+ strains. These results suggest that CBP+/PA-S. mutans strains utilize serum to contribute to their pathogenicity in IE.
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Prajapati RK, Sur R, Mukhopadhyay J. A Novel Function of δ Factor from Bacillus subtilis as a Transcriptional Repressor. J Biol Chem 2016; 291:24029-24035. [PMID: 27679485 DOI: 10.1074/jbc.m116.746065] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 09/23/2016] [Indexed: 01/01/2023] Open
Abstract
δ, a small protein found in most Gram-positive bacteria was, for a long time, thought to be a subunit of RNA polymerase (RNAP) and was shown to be involved in recycling of RNAP at the end of each round of transcription. However, how δ participates in both up-regulation and down-regulation of genes in vivo remains unclear. We have recently shown, in addition to the recycling of RNAP, δ functions as a transcriptional activator by binding to an A-rich sequence located immediately upstream of the -35 element, consequently facilitating the open complex formation. The result had explained the mechanism of up-regulation of the genes by δ. Here, we show that Bacillus subtilis δ could also function as a transcriptional repressor. Our results demonstrate that δ binds to an A-rich sequence located near the -35 element of the spo0B promoter, the gene involved in the regulatory cascade of bacterial sporulation and inhibits the open complex formation due to steric clash with σ region 4.2. We observed a significant increase in the mRNA level of the spo0B gene in a δ-knock-out strain of B. subtilis compared with the wild-type. Thus, the results report a novel function of δ, and suggest the mechanism of down-regulation of genes in vivo by the protein.
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Affiliation(s)
| | - Runa Sur
- the Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata 700009, India
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Churton NWV, Misra RV, Howlin RP, Allan RN, Jefferies J, Faust SN, Gharbia SE, Edwards RJ, Clarke SC, Webb JS. Parallel Evolution in Streptococcus pneumoniae Biofilms. Genome Biol Evol 2016; 8:1316-26. [PMID: 27190203 PMCID: PMC4898793 DOI: 10.1093/gbe/evw072] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Streptococcus pneumoniae is a commensal human pathogen and the causative agent of various invasive and noninvasive diseases. Carriage of the pneumococcus in the nasopharynx is thought to be mediated by biofilm formation, an environment where isogenic populations frequently give rise to morphological colony variants, including small colony variant (SCV) phenotypes. We employed metabolic characterization and whole-genome sequencing of biofilm-derived S. pneumoniae serotype 22F pneumococcal SCVs to investigate diversification during biofilm formation. Phenotypic profiling revealed that SCVs exhibit reduced growth rates, reduced capsule expression, altered metabolic profiles, and increased biofilm formation compared to the ancestral strain. Whole-genome sequencing of 12 SCVs from independent biofilm experiments revealed that all SCVs studied had mutations within the DNA-directed RNA polymerase delta subunit (RpoE). Mutations included four large-scale deletions ranging from 51 to 264 bp, one insertion resulting in a coding frameshift, and seven nonsense single-nucleotide substitutions that result in a truncated gene product. This work links mutations in the rpoE gene to SCV formation and enhanced biofilm development in S. pneumoniae and therefore may have important implications for colonization, carriage, and persistence of the organism. Furthermore, recurrent mutation of the pneumococcal rpoE gene presents an unprecedented level of parallel evolution in pneumococcal biofilm development.
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Affiliation(s)
- Nicholas W V Churton
- Centre for Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, United Kingdom Institute for Life Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom
| | - Raju V Misra
- Genomics Research Unit, Microbiology Services, Public Health England, Colindale, United Kingdom
| | - Robert P Howlin
- Centre for Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom Institute for Life Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom
| | - Raymond N Allan
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, United Kingdom Institute for Life Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom Southampton NIHR Wellcome Trust Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, United Kingdom
| | - Johanna Jefferies
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, United Kingdom Institute for Life Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom
| | - Saul N Faust
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, United Kingdom NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom Southampton NIHR Wellcome Trust Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, United Kingdom
| | - Saheer E Gharbia
- Genomics Research Unit, Microbiology Services, Public Health England, Colindale, United Kingdom
| | - Richard J Edwards
- Centre for Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom Institute for Life Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Stuart C Clarke
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, United Kingdom Institute for Life Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom Public Health England, Southampton, United Kingdom
| | - Jeremy S Webb
- Centre for Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom Institute for Life Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom
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Prajapati RK, Sengupta S, Rudra P, Mukhopadhyay J. Bacillus subtilis δ Factor Functions as a Transcriptional Regulator by Facilitating the Open Complex Formation. J Biol Chem 2015; 291:1064-75. [PMID: 26546673 DOI: 10.1074/jbc.m115.686170] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Indexed: 01/05/2023] Open
Abstract
Most bacterial RNA polymerases (RNAP) contain five conserved subunits, viz. 2α, β, β', and ω. However, in many Gram-positive bacteria, especially in fermicutes, RNAP is associated with an additional factor, called δ. For over three decades since its identification, it had been thought that δ functioned as a subunit of RNAP to enhance the level of transcripts by recycling RNAP. In support of the previous observations, we also find that δ is involved in recycling of RNAP by releasing the RNA from the ternary complex. We further show that δ binds to RNA and is able to recycle RNAP when the length of the nascent RNA reaches a critical length. However, in this work we decipher a new function of δ. Performing biochemical and mutational analysis, we show that Bacillus subtilis δ binds to DNA immediately upstream of the promoter element at A-rich sequences on the abrB and rrnB1 promoters and facilitates open complex formation. As a result, δ facilitates RNAP to initiate transcription in the second scale, compared with minute scale in the absence of δ. Using transcription assay, we show that δ-mediated recycling of RNAP cannot be the sole reason for the enhancement of transcript yield. Our observation that δ does not bind to RNAP holo enzyme but is required to bind to DNA upstream of the -35 promoter element for transcription activation suggests that δ functions as a transcriptional regulator.
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Affiliation(s)
| | - Shreya Sengupta
- From the Department of Chemistry, Bose Institute, Kolkata-700009, India
| | - Paulami Rudra
- From the Department of Chemistry, Bose Institute, Kolkata-700009, India
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10
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He Z, Liang J, Tang Z, Ma R, Peng H, Huang Z. Role of the luxS gene in initial biofilm formation by Streptococcus mutans. J Mol Microbiol Biotechnol 2015; 25:60-8. [PMID: 25766758 DOI: 10.1159/000371816] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Quorum sensing (QS) is a process by which bacteria communicate with each other by secreting chemical signals called autoinducers (AIs). Among Gram-negative and Gram-positive bacteria, AI-2 synthesized by the LuxS enzyme is widespread. The aim of this study was to evaluate the effect of QS luxS gene on initial biofilm formation by Streptococcus mutans. The bacterial cell surface properties, including cell hydrophobicity (bacterial adherence to hydrocarbons) and aggregation, which are important for initial adherence during biofilm development, were investigated. The biofilm adhesion assay was evaluated by the MTT method. The structures of the 5-hour biofilms were observed by using confocal laser scanning microscopy, and QS-related gene expressions were investigated by real-time PCR. The luxS mutant strain exhibited higher biofilm adherence and aggregation, but lower hydrophobicity than the wild-type strain. The confocal laser scanning microscopy images revealed that the wild-type strain tended to form smaller aggregates with uniform distribution, whereas the luxS mutant strain aggregated into distinct clusters easily discernible in the generated biofilm. Most of the genes examined were downregulated in the biofilms formed by the luxS mutant strain, except the gtfB gene. QS luxS gene can affect the initial biofilm formation by S. mutans.
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Weiss A, Shaw LN. Small things considered: the small accessory subunits of RNA polymerase in Gram-positive bacteria. FEMS Microbiol Rev 2015; 39:541-54. [PMID: 25878038 DOI: 10.1093/femsre/fuv005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2015] [Indexed: 01/21/2023] Open
Abstract
The DNA-dependent RNA polymerase core enzyme in Gram-positive bacteria consists of seven subunits. Whilst four of them (α2ββ(')) are essential, three smaller subunits, δ, ε and ω (∼9-21.5 kDa), are considered accessory. Both δ and ω have been viewed as integral components of RNAP for several decades; however, ε has only recently been described. Functionally these three small subunits carry out a variety of tasks, imparting important, supportive effects on the transcriptional process of Gram-positive bacteria. While ω is thought to have a wide range of roles, reaching from maintaining structural integrity of RNAP to σ factor recruitment, the only suggested function for ε thus far is in protecting cells from phage infection. The third subunit, δ, has been shown to have distinct influences in maintaining transcriptional specificity, and thus has a key role in cellular fitness. Collectively, all three accessory subunits, although dispensable under laboratory conditions, are often thought to be crucial for proper RNAP function. Herein we provide an overview of the available literature on each subunit, summarizing landmark findings that have deepened our understanding of these proteins and their function, and outline future challenges in understanding the role of these small subunits in the transcriptional process.
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Affiliation(s)
- Andy Weiss
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA
| | - Lindsey N Shaw
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA
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Karlskås IL, Eijsink VGH, Saleihan Z, Holo H, Mathiesen G. EF0176 and EF0177 from Enterococcus faecalis V583 are substrate-binding lipoproteins involved in ABC transporter mediated ribonucleoside uptake. Microbiology (Reading) 2015; 161:754-64. [DOI: 10.1099/mic.0.000045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/26/2015] [Indexed: 12/12/2022] Open
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The δ subunit of RNA polymerase guides promoter selectivity and virulence in Staphylococcus aureus. Infect Immun 2014; 82:1424-35. [PMID: 24491578 DOI: 10.1128/iai.01508-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In Gram-positive bacteria, and particularly the Firmicutes, the DNA-dependent RNA polymerase (RNAP) complex contains an additional subunit, termed the δ factor, or RpoE. This enigmatic protein has been studied for more than 30 years for various organisms, but its function is still not well understood. In this study, we investigated its role in the major human pathogen Staphylococcus aureus. We showed conservation of important structural regions of RpoE in S. aureus and other species and demonstrated binding to core RNAP that is mediated by the β and/or β' subunits. To identify the impact of the δ subunit on transcription, we performed transcriptome sequencing (RNA-seq) analysis and observed 191 differentially expressed genes in the rpoE mutant. Ontological analysis revealed, quite strikingly, that many of the downregulated genes were known virulence factors, while several mobile genetic elements (SaPI5 and prophage SA3usa) were strongly upregulated. Phenotypically, the rpoE mutant had decreased accumulation and/or activity of a number of key virulence factors, including alpha toxin, secreted proteases, and Panton-Valentine leukocidin (PVL). We further observed significantly decreased survival of the mutant in whole human blood, increased phagocytosis by human leukocytes, and impaired virulence in a murine model of infection. Collectively, our results demonstrate that the δ subunit of RNAP is a critical component of the S. aureus transcription machinery and plays an important role during infection.
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Weber K, Delben J, Bromage TG, Duarte S. Comparison of SEM and VPSEM imaging techniques with respect toStreptococcus mutansbiofilm topography. FEMS Microbiol Lett 2013; 350:175-9. [DOI: 10.1111/1574-6968.12334] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 10/31/2013] [Accepted: 11/13/2013] [Indexed: 12/22/2022] Open
Affiliation(s)
- Kathryn Weber
- Basic Science and Craniofacial Biology; New York University College of Dentistry; New York NY USA
| | - Juliana Delben
- Basic Science and Craniofacial Biology; New York University College of Dentistry; New York NY USA
| | - Timothy G. Bromage
- Department of Biomaterials and Biomimetics; New York University College of Dentistry; New York NY USA
| | - Simone Duarte
- Basic Science and Craniofacial Biology; New York University College of Dentistry; New York NY USA
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Visualization and curve-parameter estimation strategies for efficient exploration of phenotype microarray kinetics. PLoS One 2012; 7:e34846. [PMID: 22536335 PMCID: PMC3334903 DOI: 10.1371/journal.pone.0034846] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 03/08/2012] [Indexed: 11/19/2022] Open
Abstract
Background The Phenotype MicroArray (OmniLog® PM) system is able to simultaneously capture a large number of phenotypes by recording an organism's respiration over time on distinct substrates. This technique targets the object of natural selection itself, the phenotype, whereas previously addressed ‘-omics’ techniques merely study components that finally contribute to it. The recording of respiration over time, however, adds a longitudinal dimension to the data. To optimally exploit this information, it must be extracted from the shapes of the recorded curves and displayed in analogy to conventional growth curves. Methodology The free software environment R was explored for both visualizing and fitting of PM respiration curves. Approaches using either a model fit (and commonly applied growth models) or a smoothing spline were evaluated. Their reliability in inferring curve parameters and confidence intervals was compared to the native OmniLog® PM analysis software. We consider the post-processing of the estimated parameters, the optimal classification of curve shapes and the detection of significant differences between them, as well as practically relevant questions such as detecting the impact of cultivation times and the minimum required number of experimental repeats. Conclusions We provide a comprehensive framework for data visualization and parameter estimation according to user choices. A flexible graphical representation strategy for displaying the results is proposed, including 95% confidence intervals for the estimated parameters. The spline approach is less prone to irregular curve shapes than fitting any of the considered models or using the native PM software for calculating both point estimates and confidence intervals. These can serve as a starting point for the automated post-processing of PM data, providing much more information than the strict dichotomization into positive and negative reactions. Our results form the basis for a freely available R package for the analysis of PM data.
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Xue X, Li J, Wang W, Sztajer H, Wagner-Döbler I. The global impact of the delta subunit RpoE of the RNA polymerase on the proteome of Streptococcus mutans. Microbiology (Reading) 2012; 158:191-206. [DOI: 10.1099/mic.0.047936-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Xiaoli Xue
- Research Group Microbial Communication, Division of Cell Biology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany
| | - Jinshan Li
- Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, 100101 Beijing, PR China
- Institute of Bioprocess and Biosystems Engineering, Technical University Hamburg-Harburg, Denickestr. 15, D-21071 Hamburg, Germany
| | - Wei Wang
- Institute of Bioprocess and Biosystems Engineering, Technical University Hamburg-Harburg, Denickestr. 15, D-21071 Hamburg, Germany
| | - Helena Sztajer
- Research Group Microbial Communication, Division of Cell Biology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany
| | - Irene Wagner-Döbler
- Research Group Microbial Communication, Division of Cell Biology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany
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