1
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Michaelis C, Grohmann E. Horizontal Gene Transfer of Antibiotic Resistance Genes in Biofilms. Antibiotics (Basel) 2023; 12:antibiotics12020328. [PMID: 36830238 PMCID: PMC9952180 DOI: 10.3390/antibiotics12020328] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Most bacteria attach to biotic or abiotic surfaces and are embedded in a complex matrix which is known as biofilm. Biofilm formation is especially worrisome in clinical settings as it hinders the treatment of infections with antibiotics due to the facilitated acquisition of antibiotic resistance genes (ARGs). Environmental settings are now considered as pivotal for driving biofilm formation, biofilm-mediated antibiotic resistance development and dissemination. Several studies have demonstrated that environmental biofilms can be hotspots for the dissemination of ARGs. These genes can be encoded on mobile genetic elements (MGEs) such as conjugative and mobilizable plasmids or integrative and conjugative elements (ICEs). ARGs can be rapidly transferred through horizontal gene transfer (HGT) which has been shown to occur more frequently in biofilms than in planktonic cultures. Biofilm models are promising tools to mimic natural biofilms to study the dissemination of ARGs via HGT. This review summarizes the state-of-the-art of biofilm studies and the techniques that visualize the three main HGT mechanisms in biofilms: transformation, transduction, and conjugation.
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2
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Bechtel TD, Gibbons JG. Population Genomic Analysis of Listeria monocytogenes From Food Reveals Substrate-Specific Genome Variation. Front Microbiol 2021; 12:620033. [PMID: 33633707 PMCID: PMC7902062 DOI: 10.3389/fmicb.2021.620033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/18/2021] [Indexed: 11/13/2022] Open
Abstract
Listeria monocytogenes is the major causative agent of the foodborne illness listeriosis. Listeriosis presents as flu-like symptoms in healthy individuals, and can be fatal for children, elderly, pregnant women, and immunocompromised individuals. Estimates suggest that L. monocytogenes results in ∼1,600 illnesses and ∼260 deaths annually in the United States. L. monocytogenes can survive and persist in a variety of harsh environments, including conditions encountered in production of fermented dairy products such as cheese. For instance, microbial growth is often limited in soft cheese fermentation because of harsh pH, water content, and salt concentrations. However, L. monocytogenes has caused a number of deadly listeriosis outbreaks through the contamination of cheese. The purpose of this study was to understand if genetically distinct populations of L. monocytogenes are associated with particular foods, including cheese and dairy. To address this goal, we analyzed the population genetic structure of 504 L. monocytogenes strains isolated from food with publicly available genome assemblies. We identified 10 genetically distinct populations spanning L. monocytogenes lineages 1, II, and III and serotypes 1/2a, 1/2b, 1/2c, 4b, and 4c. We observed an overrepresentation of isolates from specific populations with cheese (population 2), fruit/vegetable (population 2), seafood (populations 5, 8 and 9) and meat (population 10). We used the Large Scale Blast Score Ratio pipeline and Roary to identify genes unique to population 1 and population 2 in comparison with all other populations, and screened for the presence of antimicrobial resistance genes and virulence genes across all isolates. We identified > 40 genes that were present at high frequency in population 1 and population 2 and absent in most other isolates. Many of these genes encoded for transcription factors, and cell surface anchored proteins. Additionally, we found that the virulence genes aut and ami were entirely or partially deleted in population 2. These results indicate that some L. monocytogenes populations may exhibit associations with particular foods, including cheese, and that gene content may contribute to this pattern.
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Affiliation(s)
- Tyler D Bechtel
- Department of Food Science, University of Massachusetts, Amherst, MA, United States
| | - John G Gibbons
- Department of Food Science, University of Massachusetts, Amherst, MA, United States.,Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, United States.,Organismic and Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, MA, United States
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3
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Louha S, Meinersmann RJ, Glenn TC. Whole genome genetic variation and linkage disequilibrium in a diverse collection of Listeria monocytogenes isolates. PLoS One 2021; 16:e0242297. [PMID: 33630832 PMCID: PMC7906370 DOI: 10.1371/journal.pone.0242297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/11/2021] [Indexed: 12/04/2022] Open
Abstract
We performed whole-genome multi-locus sequence typing for 2554 genes in a large and heterogenous panel of 180 Listeria monocytogenes strains having diverse geographical and temporal origins. The subtyping data was used for characterizing genetic variation and evaluating patterns of linkage disequilibrium in the pan-genome of L. monocytogenes. Our analysis revealed the presence of strong linkage disequilibrium in L. monocytogenes, with ~99% of genes showing significant non-random associations with a large majority of other genes in the genome. Twenty-seven loci having lower levels of association with other genes were considered to be potential “hot spots” for horizontal gene transfer (i.e., recombination via conjugation, transduction, and/or transformation). The patterns of linkage disequilibrium in L. monocytogenes suggest limited exchange of foreign genetic material in the genome and can be used as a tool for identifying new recombinant strains. This can help understand processes contributing to the diversification and evolution of this pathogenic bacteria, thereby facilitating development of effective control measures.
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Affiliation(s)
- Swarnali Louha
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
- * E-mail:
| | - Richard J. Meinersmann
- USDA Agricultural Research Service, U.S. National Poultry Research Center, Athens, GA, United States of America
| | - Travis C. Glenn
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
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4
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Zamudio R, Haigh RD, Ralph JD, De Ste Croix M, Tasara T, Zurfluh K, Kwun MJ, Millard AD, Bentley SD, Croucher NJ, Stephan R, Oggioni MR. Lineage-specific evolution and gene flow in Listeria monocytogenes are independent of bacteriophages. Environ Microbiol 2020; 22:5058-5072. [PMID: 32483914 PMCID: PMC7614921 DOI: 10.1111/1462-2920.15111] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/26/2020] [Accepted: 05/30/2020] [Indexed: 11/29/2022]
Abstract
Listeria monocytogenes is a foodborne pathogen causing systemic infection with high mortality. To allow efficient tracking of outbreaks a clear definition of the genomic signature of a cluster of related isolates is required, but lineage-specific characteristics call for a more detailed understanding of evolution. In our work, we used core genome MLST (cgMLST) to identify new outbreaks combined to core genome SNP analysis to characterize the population structure and gene flow between lineages. Whilst analysing differences between the four lineages of L. monocytogenes we have detected differences in the recombination rate, and interestingly also divergence in the SNP differences between sub-lineages. In addition, the exchange of core genome variation between the lineages exhibited a distinct pattern, with lineage III being the best donor for horizontal gene transfer. Whilst attempting to link bacteriophage-mediated transduction to observed gene transfer, we found an inverse correlation between phage presence in a lineage and the extent of recombination. Irrespective of the profound differences in recombination rates observed between sub-lineages and lineages, we found that the previously proposed cut-off of 10 allelic differences in cgMLST can be still considered valid for the definition of a foodborne outbreak cluster of L. monocytogenes.
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Affiliation(s)
- Roxana Zamudio
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Richard D Haigh
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Joseph D Ralph
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Megan De Ste Croix
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Taurai Tasara
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Katrin Zurfluh
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Min Jung Kwun
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Andrew D Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Stephen D Bentley
- Parasites and Microbes, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Marco R Oggioni
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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5
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Baquero F, F Lanza V, Duval M, Coque TM. Ecogenetics of antibiotic resistance in Listeria monocytogenes. Mol Microbiol 2020; 113:570-579. [PMID: 32185838 DOI: 10.1111/mmi.14454] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 12/25/2019] [Accepted: 01/09/2020] [Indexed: 12/17/2022]
Abstract
The acquisition process of antibiotic resistance in an otherwise susceptible organism is shaped by the ecology of the species. Unlike other relevant human pathogens, Listeria monocytogenes has maintained a high rate of susceptibility to the antibiotics used for decades to treat human and animal infections. However, L. monocytogenes can acquire antibiotic resistance genes from other organisms' plasmids and conjugative transposons. Ecological factors could account for its susceptibility. L. monocytogenes is ubiquitous in nature, most frequently including reservoirs unexposed to antibiotics, including intracellular sanctuaries. L. monocytogenes has a remarkably closed genome, reflecting limited community interactions, small population sizes and high niche specialization. The L. monocytogenes species is divided into variants that are specialized in small specific niches, which reduces the possibility of coexistence with potential donors of antibiotic resistance. Interactions with potential donors are also hampered by interspecies antagonism. However, occasional increases in population sizes (and thus the possibility of acquiring antibiotic resistance) can derive from selection of the species based on intrinsic or acquired resistance to antibiotics, biocides, heavy metals or by a natural tolerance to extreme conditions. High-quality surveillance of the emergence of resistance to the key drugs used in primary therapy is mandatory.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal Institute for Health Research, Ramón y Cajal University Hospital, Madrid, Spain
| | - Val F Lanza
- Department of Microbiology, Ramón y Cajal Institute for Health Research, Ramón y Cajal University Hospital, Madrid, Spain.,Bioinformatics Unit, Ramón y Cajal Institute for Health Research, Ramón y Cajal University Hospital, Madrid, Spain
| | - Mélodie Duval
- Département de Biologie Cellulaire et Infection, Unité des interactions Bactéries-Cellules, Institut Pasteur, and Inserm, Paris, France
| | - Teresa M Coque
- Department of Microbiology, Ramón y Cajal Institute for Health Research, Ramón y Cajal University Hospital, Madrid, Spain
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6
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Abstract
The ancestral strain of Bacillus subtilis NCIB3610 (3610) bears a large, low-copy-number plasmid, called pBS32, that was lost during the domestication of laboratory strain derivatives. Selection against pBS32 may have been because it encodes a potent inhibitor of natural genetic competence (ComI), as laboratory strains were selected for high-frequency transformation. Previous studies have shown that pBS32 and its sibling, pLS32 in Bacillus subtilis subsp. natto, encode a replication initiation protein (RepN), a plasmid partitioning system (AlfAB), a biofilm inhibitor (RapP), and an alternative sigma factor (SigN) that can induce plasmid-mediated cell death in response to DNA damage. Here, we review the literature on pBS32/pLS32, the genes found on it, and their associated phenotypes.
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7
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Yang M, Cousineau A, Liu X, Luo Y, Sun D, Li S, Gu T, Sun L, Dillow H, Lepine J, Xu M, Zhang B. Direct Metatranscriptome RNA-seq and Multiplex RT-PCR Amplicon Sequencing on Nanopore MinION - Promising Strategies for Multiplex Identification of Viable Pathogens in Food. Front Microbiol 2020; 11:514. [PMID: 32328039 PMCID: PMC7160302 DOI: 10.3389/fmicb.2020.00514] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/10/2020] [Indexed: 12/20/2022] Open
Abstract
Viable pathogenic bacteria are major biohazards that pose a significant threat to food safety. Despite the recent developments in detection platforms, multiplex identification of viable pathogens in food remains a major challenge. A novel strategy is developed through direct metatranscriptome RNA-seq and multiplex RT-PCR amplicon sequencing on Nanopore MinION to achieve real-time multiplex identification of viable pathogens in food. Specifically, this study reports an optimized universal Nanopore sample extraction and library preparation protocol applicable to both Gram-positive and Gram-negative pathogenic bacteria, demonstrated using a cocktail culture of E. coli O157:H7, Salmonella enteritidis, and Listeria monocytogenes, which were selected based on their impact on economic loss or prevalence in recent outbreaks. Further evaluation and validation confirmed the accuracy of direct metatranscriptome RNA-seq and multiplex RT-PCR amplicon sequencing using Sanger sequencing and selective media. The study also included a comparison of different bioinformatic pipelines for metatranscriptomic and amplicon genomic analysis. MEGAN without rRNA mapping showed the highest accuracy of multiplex identification using the metatranscriptomic data. EPI2ME also demonstrated high accuracy using multiplex RT-PCR amplicon sequencing. In addition, a systemic comparison was drawn between Nanopore sequencing of the direct metatranscriptome RNA-seq and RT-PCR amplicons. Both methods are comparable in accuracy and time. Nanopore sequencing of RT-PCR amplicons has higher sensitivity, but Nanopore metatranscriptome sequencing excels in read length and dealing with complex microbiome and non-bacterial transcriptome backgrounds.
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Affiliation(s)
- Manyun Yang
- Department of Biomedical and Nutritional Sciences, University of Massachusetts, Lowell, MA, United States
| | | | - Xiaobo Liu
- Department of Biomedical and Nutritional Sciences, University of Massachusetts, Lowell, MA, United States
| | - Yaguang Luo
- Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD, United States
| | - Daniel Sun
- New England Biolabs, Inc., Ipswich, MA, United States
- Department of Chemistry, Brandeis University, Waltham, MA, United States
| | - Shaohua Li
- New England Biolabs, Inc., Ipswich, MA, United States
- U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Tingting Gu
- Department of Biomedical and Nutritional Sciences, University of Massachusetts, Lowell, MA, United States
| | - Luo Sun
- New England Biolabs, Inc., Ipswich, MA, United States
| | - Hayden Dillow
- Department of Biomedical and Nutritional Sciences, University of Massachusetts, Lowell, MA, United States
| | - Jack Lepine
- Biomolecular Characterization Lab, University of Massachusetts Lowell, Lowell, MA, United States
| | - Mingqun Xu
- New England Biolabs, Inc., Ipswich, MA, United States
| | - Boce Zhang
- Department of Biomedical and Nutritional Sciences, University of Massachusetts, Lowell, MA, United States
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8
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Brooks MR, Padilla-Vélez L, Khan TA, Qureshi AA, Pieper JB, Maddox CW, Alam MT. Prophage-Mediated Disruption of Genetic Competence in Staphylococcus pseudintermedius. mSystems 2020; 5:e00684-19. [PMID: 32071159 PMCID: PMC7029219 DOI: 10.1128/msystems.00684-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 01/27/2020] [Indexed: 11/20/2022] Open
Abstract
Methicillin-resistant Staphylococcus pseudintermedius (MRSP) is a major cause of soft tissue infections in dogs and occasionally infects humans. Hypervirulent multidrug-resistant (MDR) MRSP clones have emerged globally. The sequence types ST71 and ST68, the major epidemic clones of Europe and North America, respectively, have spread to other regions. The genetic factors underlying the success of these clones have not been investigated thoroughly. Here, we performed a comprehensive genomic analysis of 371 S. pseudintermedius isolates to dissect the differences between major clonal lineages. We show that the prevalence of genes associated with antibiotic resistance, virulence, prophages, restriction-modification (RM), and CRISPR/Cas systems differs significantly among MRSP clones. The isolates with GyrA+GrlA mutations, conferring fluoroquinolone resistance, carry more of these genes than those without GyrA+GrlA mutations. ST71 and ST68 clones carry lineage-specific prophages with genes that are likely associated with their increased fitness and virulence. We have discovered that a prophage, SpST71A, is inserted within the comGA gene of the late competence operon comG in the ST71 lineage. A functional comG is essential for natural genetic competence, which is one of the major modes of horizontal gene transfer (HGT) in bacteria. The RM and CRISPR/Cas systems, both major genetic barriers to HGT, are also lineage specific. Clones harboring CRISPR/Cas or a prophage-disrupted comG exhibited less genetic diversity and lower rates of recombination than clones lacking these systems. After Listeria monocytogenes, this is the second example of prophage-mediated competence disruption reported in any bacteria. These findings are important for understanding the evolution and clonal expansion of MDR MRSP clones.IMPORTANCE Staphylococcus pseudintermedius is a bacterium responsible for clinically important infections in dogs and can infect humans. In this study, we performed genomic analysis of 371 S. pseudintermedius isolates to understand the evolution of antibiotic resistance and virulence in this organism. The analysis covered significant reported clones, including ST71 and ST68, the major epidemic clones of Europe and North America, respectively. We show that the prevalence of genes associated with antibiotic resistance, virulence, prophages, and horizontal gene transfer differs among clones. ST71 and ST68 carry prophages with novel virulence and antibiotic resistance genes. Importantly, site-specific integration of a prophage, SpST71A, has led to the disruption of the genetic competence operon comG in ST71 clone. A functional comG is essential for the natural uptake of foreign DNA and thus plays an important role in the evolution of bacteria. This study provides insight into the emergence and evolution of antibiotic resistance and virulence in S. pseudintermedius, which may help in efforts to combat this pathogen.
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Affiliation(s)
- Michael R Brooks
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Lyan Padilla-Vélez
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Tarannum A Khan
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Azaan A Qureshi
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jason B Pieper
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Carol W Maddox
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Md Tauqeer Alam
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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9
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Rojas-Tapias DF, Helmann JD. Roles and regulation of Spx family transcription factors in Bacillus subtilis and related species. Adv Microb Physiol 2019; 75:279-323. [PMID: 31655740 DOI: 10.1016/bs.ampbs.2019.05.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Bacillus subtilis Spx is the prototype for a large family of redox-responsive transcription factors found in many bacteria, most notably those from the phylum Firmicutes. Unusually for a transcription factor, B. subtilis Spx protein modulates gene expression by binding as a monomer to the αCTD domain of RNA polymerase (RNAP), and only interacts with DNA during subsequent promoter engagement. B. subtilis Spx drives the expression of a large regulon in response to proteotoxic conditions, such as heat and disulfide stress, as well as cell wall stress. Here, we review the detailed mechanisms that control the expression, stability, and activity of Spx in response to a variety of stress conditions. We also summarize current knowledge regarding Spx homologs in other Firmicutes, the environmental conditions in which those homologs are activated, and their biological role.
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Affiliation(s)
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY, United States
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10
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Vivant AL, Desneux J, Pourcher AM, Piveteau P. Transcriptomic Analysis of the Adaptation of Listeria monocytogenes to Lagoon and Soil Matrices Associated with a Piggery Environment: Comparison of Expression Profiles. Front Microbiol 2017; 8:1811. [PMID: 29018416 PMCID: PMC5623016 DOI: 10.3389/fmicb.2017.01811] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 09/05/2017] [Indexed: 12/20/2022] Open
Abstract
Understanding how Listeria monocytogenes, the causative agent of listeriosis, adapts to the environment is crucial. Adaptation to new matrices requires regulation of gene expression. To determine how the pathogen adapts to lagoon effluent and soil, two matrices where L. monocytogenes has been isolated, we compared the transcriptomes of L. monocytogenes CIP 110868 20 min and 24 h after its transfer to effluent and soil extract. Results showed major variations in the transcriptome of L. monocytogenes in the lagoon effluent but only minor modifications in the soil. In both the lagoon effluent and in the soil, genes involved in mobility and chemotaxis and in the transport of carbohydrates were the most frequently represented in the set of genes with higher transcript levels, and genes with phage-related functions were the most represented in the set of genes with lower transcript levels. A modification of the cell envelop was only found in the lagoon environment. Finally, the differential analysis included a large proportion of regulators, regulons, and ncRNAs.
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Affiliation(s)
- Anne-Laure Vivant
- UR OPAALE, IRSTEA, Rennes, France
- Université Bretagne Loire, Rennes, France
| | - Jeremy Desneux
- UR OPAALE, IRSTEA, Rennes, France
- Université Bretagne Loire, Rennes, France
| | | | - Pascal Piveteau
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté, Dijon, France
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11
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Blokesch M. In and out-contribution of natural transformation to the shuffling of large genomic regions. Curr Opin Microbiol 2017; 38:22-29. [PMID: 28458094 DOI: 10.1016/j.mib.2017.04.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/01/2017] [Accepted: 04/06/2017] [Indexed: 01/28/2023]
Abstract
Naturally competent bacteria can pull free DNA from their surroundings. This incoming DNA can serve various purposes, ranging from acting as a source of nutrients or DNA stretches for repair to the acquisition of novel genetic information. The latter process defines the natural competence for transformation as a mode of horizontal gene transfer (HGT) and led to its discovery almost a century ago. However, although it is widely accepted that natural competence can contribute to the spread of genetic material among prokaryotes, the question remains whether this mode of HGT can foster the transfer of larger DNA regions or only transfers shorter fragments, given that extracellular DNA is often heavily fragmented. Here, I outline examples of competence-mediated movement of large genomic segments. Moreover, I discuss a recent proposition that transformation is used to cure bacteria of selfish mobile genetic elements. Such a transformation-mediated genome maintenance mechanism could indeed be an important and underappreciated function of natural competence.
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Affiliation(s)
- Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
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12
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A Redox-Responsive Transcription Factor Is Critical for Pathogenesis and Aerobic Growth of Listeria monocytogenes. Infect Immun 2017; 85:IAI.00978-16. [PMID: 28193635 PMCID: PMC5400837 DOI: 10.1128/iai.00978-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/07/2017] [Indexed: 11/25/2022] Open
Abstract
Bacterial pathogens have evolved sophisticated mechanisms to sense and adapt to redox stress in nature and within the host. However, deciphering the redox environment encountered by intracellular pathogens in the mammalian cytosol is challenging, and that environment remains poorly understood. In this study, we assessed the contributions of the two redox-responsive, Spx-family transcriptional regulators to the virulence of Listeria monocytogenes, a Gram-positive facultative intracellular pathogen. Spx-family proteins are highly conserved in Firmicutes, and the L. monocytogenes genome contains two paralogues, spxA1 and spxA2. Here, we demonstrate that spxA1, but not spxA2, is required for the oxidative stress response and pathogenesis. SpxA1 function appeared to be conserved with the Bacillus subtilis homologue, and resistance to oxidative stress required the canonical CXXC redox-sensing motif. Remarkably, spxA1 was essential for aerobic growth, demonstrating that L. monocytogenes SpxA1 likely regulates a distinct set of genes. Although the ΔspxA1 mutant did not grow in the presence of oxygen in the laboratory, it was able to replicate in macrophages and colonize the spleens, but not the livers, of infected mice. These data suggest that the redox state of bacteria during infection differs significantly from that of bacteria growing in vitro. Further, the host cell cytosol may resemble an anaerobic environment, with tissue-specific variations in redox stress and oxygen concentration.
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13
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Xayarath B, Freitag NE. When being alone is enough: noncanonical functions of canonical bacterial quorum-sensing systems. Future Microbiol 2016; 11:1447-1459. [PMID: 27750441 DOI: 10.2217/fmb-2016-0066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A number of bacterial pathogens are capable of detecting the presence of other bacteria located within their surrounding niche through a process of bacterial signaling and cell-to-cell communication commonly referred to as quorum sensing (QS). QS systems are commonly now described in the context of collective behaviors exhibited by groups of bacteria coordinating diverse arrays of physiological functions to enhance survival of the community. However, QS systems have also been implicated in a variety of processes distinct from the measure of bacterial cell density. This review will highlight noncanonical adaptations of canonical QS systems that have evolved to enable bacteria to detect nonself individuals within a population or to detect occupation of confined spaces.
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Affiliation(s)
- Bobbi Xayarath
- Department of Microbiology & Immunology, University of Illinois at Chicago, Chicago, IL 60612-7344, USA
| | - Nancy E Freitag
- Department of Microbiology & Immunology, University of Illinois at Chicago, Chicago, IL 60612-7344, USA
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14
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An In Vivo Selection Identifies Listeria monocytogenes Genes Required to Sense the Intracellular Environment and Activate Virulence Factor Expression. PLoS Pathog 2016; 12:e1005741. [PMID: 27414028 PMCID: PMC4945081 DOI: 10.1371/journal.ppat.1005741] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 06/14/2016] [Indexed: 11/19/2022] Open
Abstract
Listeria monocytogenes is an environmental saprophyte and facultative intracellular bacterial pathogen with a well-defined life-cycle that involves escape from a phagosome, rapid cytosolic growth, and ActA-dependent cell-to-cell spread, all of which are dependent on the master transcriptional regulator PrfA. The environmental cues that lead to temporal and spatial control of L. monocytogenes virulence gene expression are poorly understood. In this study, we took advantage of the robust up-regulation of ActA that occurs intracellularly and expressed Cre recombinase from the actA promoter and 5' untranslated region in a strain in which loxP sites flanked essential genes, so that activation of actA led to bacterial death. Upon screening for transposon mutants that survived intracellularly, six genes were identified as necessary for ActA expression. Strikingly, most of the genes, including gshF, spxA1, yjbH, and ohrA, are predicted to play important roles in bacterial redox regulation. The mutants identified in the genetic selection fell into three broad categories: (1) those that failed to reach the cytosolic compartment; (2) mutants that entered the cytosol, but failed to activate the master virulence regulator PrfA; and (3) mutants that entered the cytosol and activated transcription of actA, but failed to synthesize it. The identification of mutants defective in vacuolar escape suggests that up-regulation of ActA occurs in the host cytosol and not the vacuole. Moreover, these results provide evidence for two non-redundant cytosolic cues; the first results in allosteric activation of PrfA via increased glutathione levels and transcriptional activation of actA while the second results in translational activation of actA and requires yjbH. Although the precise host cues have not yet been identified, we suggest that intracellular redox stress occurs as a consequence of both host and pathogen remodeling their metabolism upon infection.
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Listeria monocytogenes σH Contributes to Expression of Competence Genes and Intracellular Growth. J Bacteriol 2016; 198:1207-17. [PMID: 26833412 DOI: 10.1128/jb.00718-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 01/26/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The alternative sigma factor σ(H)has two functions in Gram-positive bacteria: it regulates sporulation and the development of genetic competence. Listeria monocytogenes is a nonsporulating species in which competence has not yet been detected. Nevertheless, the main competence regulators and a series of orthologous genes that form the competence machinery are present in its genome; some of the competence genes play a role in optimal phagosomal escape. In this study, strains overexpressing σ(H) and strains with a σ(H) deletion were used to elucidate the contribution of σ(H) to the expression of the competence machinery genes inL. monocytogenes Gene expression analysis showed that σ(H) is, indeed, involved in comG and come regulation. Unexpectedly, we observed a unique regulation scheme in which σ(H) and the transcription factor ComK were involved. Population-level analysis showed that even with the overexpression of both factors, only a fraction of the cells expressed the competence machinery genes. Although we could not detect competence, σ(H) was crucial for phagosomal escape, which implies that this alternative sigma factor has specifically evolved to regulate the L. monocytogenes intracellular life cycle. IMPORTANCE Listeria monocytogenes can be an intracellular pathogen capable of causing serious infections in humans and animal species. Recently, the competence machinery genes were described as being necessary for optimal phagosomal escape, in which the transcription factor ComK plays an important role. On the other hand, our previous phylogenetic analysis suggested that the alternative sigma factor σ(H) might play a role in the regulation of competence genes. The present study shows that some of the competence genes belong to the σ(H) regulon and, importantly, that σ(H) is essential for intracellular growth, implying a unique physiological role of σ(H) among Firmicutes.
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Croucher NJ, Mostowy R, Wymant C, Turner P, Bentley SD, Fraser C. Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict. PLoS Biol 2016; 14:e1002394. [PMID: 26934590 PMCID: PMC4774983 DOI: 10.1371/journal.pbio.1002394] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 01/29/2016] [Indexed: 01/21/2023] Open
Abstract
Horizontal DNA transfer (HDT) is a pervasive mechanism of diversification in many microbial species, but its primary evolutionary role remains controversial. Much recent research has emphasised the adaptive benefit of acquiring novel DNA, but here we argue instead that intragenomic conflict provides a coherent framework for understanding the evolutionary origins of HDT. To test this hypothesis, we developed a mathematical model of a clonally descended bacterial population undergoing HDT through transmission of mobile genetic elements (MGEs) and genetic transformation. Including the known bias of transformation toward the acquisition of shorter alleles into the model suggested it could be an effective means of counteracting the spread of MGEs. Both constitutive and transient competence for transformation were found to provide an effective defence against parasitic MGEs; transient competence could also be effective at permitting the selective spread of MGEs conferring a benefit on their host bacterium. The coordination of transient competence with cell-cell killing, observed in multiple species, was found to result in synergistic blocking of MGE transmission through releasing genomic DNA for homologous recombination while simultaneously reducing horizontal MGE spread by lowering the local cell density. To evaluate the feasibility of the functions suggested by the modelling analysis, we analysed genomic data from longitudinal sampling of individuals carrying Streptococcus pneumoniae. This revealed the frequent within-host coexistence of clonally descended cells that differed in their MGE infection status, a necessary condition for the proposed mechanism to operate. Additionally, we found multiple examples of MGEs inhibiting transformation through integrative disruption of genes encoding the competence machinery across many species, providing evidence of an ongoing "arms race." Reduced rates of transformation have also been observed in cells infected by MGEs that reduce the concentration of extracellular DNA through secretion of DNases. Simulations predicted that either mechanism of limiting transformation would benefit individual MGEs, but also that this tactic's effectiveness was limited by competition with other MGEs coinfecting the same cell. A further observed behaviour we hypothesised to reduce elimination by transformation was MGE activation when cells become competent. Our model predicted that this response was effective at counteracting transformation independently of competing MGEs. Therefore, this framework is able to explain both common properties of MGEs, and the seemingly paradoxical bacterial behaviours of transformation and cell-cell killing within clonally related populations, as the consequences of intragenomic conflict between self-replicating chromosomes and parasitic MGEs. The antagonistic nature of the different mechanisms of HDT over short timescales means their contribution to bacterial evolution is likely to be substantially greater than previously appreciated.
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Affiliation(s)
- Nicholas J. Croucher
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Rafal Mostowy
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Christopher Wymant
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Stephen D. Bentley
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Christophe Fraser
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
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Liu Y, Orsi RH, Boor KJ, Wiedmann M, Guariglia-Oropeza V. An advanced bioinformatics approach for analyzing RNA-seq data reveals sigma H-dependent regulation of competence genes in Listeria monocytogenes. BMC Genomics 2016; 17:115. [PMID: 26880300 PMCID: PMC4754846 DOI: 10.1186/s12864-016-2432-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 02/03/2016] [Indexed: 11/14/2022] Open
Abstract
Background Alternative σ factors are important transcriptional regulators in bacteria. While σB has been shown to control a large regulon and play important roles in stress response and virulence in the pathogen Listeria monocytogenes, the function of σH has not yet been well defined in Listeria, even though σH controls a large regulon in the closely related non-pathogenic Bacillus subtilis. Results Using RNA-seq characterization of a L. monocytogenes strain with deletions of all 4 genes encoding alternative σ factors (ΔBCHL), which was further modified to overexpress sigH (ΔBCHL::Prha-sigH), we identified 6 transcription units (TUs) that are transcribed from σH-dependent promoters. Five of these TUs had not been previously identified. Identification of these promoters was facilitated by use of a bio-informatics approach that compared normalized RNA-seq coverage (NRC), between ΔBCHL::Prha-sigH and a ΔBCHL control, using sliding windows of 51 nt along the whole genome rather than comparing NRC calculated only for whole genes. Interestingly, we found that three operons that encode competence genes (comGABCDEFG, comEABC, coiA) are transcribed from σH-dependent promoters. While these promoters were highly conserved in L. monocytogenes, none of them were found in all Listeria spp. and coiA and its σH-dependent promoter were only found in L. monocytogenes. Conclusions Our data indicate that a number of L. monocytogenes competence genes are regulated by σH. This σH-dependent regulation of competence related genes is conserved in the pathogen L. monocytogenes, but not in other non-pathogenic Listeria strains. Combined with prior data that indicated a role of σH in virulence in a mouse model, this suggests a possible novel role of σH-dependent competence genes in L. monocytogenes virulence. Development and implementation of a sliding window approach to identify differential transcription using RNA-seq data, not only allowed for identification of σH-dependent promoters, but also provides a general approach for sensitive identification of differentially transcribed promoters and genes, particularly for genes that are transcribed from multiple promoter elements only some of which show differential transcription. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2432-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yichang Liu
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA.
| | - Renato Hohl Orsi
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA.
| | - Kathryn Jean Boor
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA.
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA.
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Yan S, Wu G. Evolutionary evidence on suitability of SecD as a target for development of antibacterial agents against Staphylococcus aureus. Ecol Evol 2016; 6:1393-410. [PMID: 27087922 PMCID: PMC4775529 DOI: 10.1002/ece3.1951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 12/15/2015] [Accepted: 12/16/2015] [Indexed: 11/22/2022] Open
Abstract
Staphylococcus aureus causes many infections and its drug resistance is a worrying challenge for medical care. The SecD subunit of Sec secretion system in methicillin‐resistant S. aureus is an attractive target because SecD dysfunction leads to the death of bacteria and SecD as a target is more efficient than SecA and SecF. Evolution could have made SecD to become insensitive to antibacterial agents although the drugs directly against SecD have yet to develop. So far, no detailed information on SecD evolution has been available, thus 2686 SecD sequences with full taxonomic information from kingdom to species were analyzed. First, the variance of pairwise p‐distance was evaluated for each taxonomic group. Second, the variance was further partitioned into intergroup and intragroup variances for quantification of horizontal and vertical gene transfer. Third, phylogenetic tree was built to trace the evolutionary pathway. The results showed that overall evolution of SecDs appears to have undergone horizontal and vertical gene transfer. Only 0.5% horizontal transfers were found between any two SecDs in S. aureus, 6.8% and 8.8% horizontal transfers were found between any two Staphylococcus SecDs from different and the same species, and only one SecD from S. aureus was located far away from its sister cluster. Thus, statistic and evolutionary analyses demonstrate that the SecDs from staphylococcus species have a small chance of mutating, and provide taxonomic evidence to use the SecD as a potential target for new generation of antibacterial agents against S. aureus.
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Affiliation(s)
- Shaomin Yan
- Guangxi Bioscience and Biotechnology Research Center Guangxi Academy of Sciences 98 Daling Road Nanning Guangxi 530007 China
| | - Guang Wu
- Guangxi Bioscience and Biotechnology Research Center Guangxi Academy of Sciences 98 Daling Road Nanning Guangxi 530007 China
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Feiner R, Argov T, Rabinovich L, Sigal N, Borovok I, Herskovits AA. A new perspective on lysogeny: prophages as active regulatory switches of bacteria. Nat Rev Microbiol 2016; 13:641-50. [PMID: 26373372 DOI: 10.1038/nrmicro3527] [Citation(s) in RCA: 269] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Unlike lytic phages, temperate phages that enter lysogeny maintain a long-term association with their bacterial host. In this context, mutually beneficial interactions can evolve that support efficient reproduction of both phages and bacteria. Temperate phages are integrated into the bacterial chromosome as large DNA insertions that can disrupt gene expression, and they may pose a fitness burden on the cell. However, they have also been shown to benefit their bacterial hosts by providing new functions in a bacterium-phage symbiotic interaction termed lysogenic conversion. In this Opinion article, we discuss another type of bacterium-phage interaction, active lysogeny, in which phages or phage-like elements are integrated into the bacterial chromosome within critical genes or operons and serve as switches that regulate bacterial genes via genome excision.
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Affiliation(s)
- Ron Feiner
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tal Argov
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel
| | - Lev Rabinovich
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel
| | - Nadejda Sigal
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel
| | - Anat A Herskovits
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel
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The evolution and epidemiology of Listeria monocytogenes in Europe and the United States. INFECTION GENETICS AND EVOLUTION 2015; 35:172-83. [DOI: 10.1016/j.meegid.2015.08.008] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 08/03/2015] [Accepted: 08/04/2015] [Indexed: 11/20/2022]
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Giaouris E, Heir E, Desvaux M, Hébraud M, Møretrø T, Langsrud S, Doulgeraki A, Nychas GJ, Kačániová M, Czaczyk K, Ölmez H, Simões M. Intra- and inter-species interactions within biofilms of important foodborne bacterial pathogens. Front Microbiol 2015; 6:841. [PMID: 26347727 PMCID: PMC4542319 DOI: 10.3389/fmicb.2015.00841] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 07/31/2015] [Indexed: 12/15/2022] Open
Abstract
A community-based sessile life style is the normal mode of growth and survival for many bacterial species. Under such conditions, cell-to-cell interactions are inevitable and ultimately lead to the establishment of dense, complex and highly structured biofilm populations encapsulated in a self-produced extracellular matrix and capable of coordinated and collective behavior. Remarkably, in food processing environments, a variety of different bacteria may attach to surfaces, survive, grow, and form biofilms. Salmonella enterica, Listeria monocytogenes, Escherichia coli, and Staphylococcus aureus are important bacterial pathogens commonly implicated in outbreaks of foodborne diseases, while all are known to be able to create biofilms on both abiotic and biotic surfaces. Particularly challenging is the attempt to understand the complexity of inter-bacterial interactions that can be encountered in such unwanted consortia, such as competitive and cooperative ones, together with their impact on the final outcome of these communities (e.g., maturation, physiology, antimicrobial resistance, virulence, dispersal). In this review, up-to-date data on both the intra- and inter-species interactions encountered in biofilms of these pathogens are presented. A better understanding of these interactions, both at molecular and biophysical levels, could lead to novel intervention strategies for controlling pathogenic biofilm formation in food processing environments and thus improve food safety.
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Affiliation(s)
- Efstathios Giaouris
- Department of Food Science and Nutrition, Faculty of the Environment, University of the Aegean, Myrina, Lemnos Island, Greece
| | - Even Heir
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Mickaël Desvaux
- INRA, UR454 Microbiologie, Centre Auvergne-Rhône-Alpes, Saint-Genès-Champanelle, France
| | - Michel Hébraud
- INRA, UR454 Microbiologie, Centre Auvergne-Rhône-Alpes, Saint-Genès-Champanelle, France
| | - Trond Møretrø
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Solveig Langsrud
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Agapi Doulgeraki
- Laboratory of Microbiology and Biotechnology of Foods, Department of Food Science and Human Nutrition, Faculty of Foods, Biotechnology and Development, Agricultural University of Athens, Athens, Greece
| | - George-John Nychas
- Laboratory of Microbiology and Biotechnology of Foods, Department of Food Science and Human Nutrition, Faculty of Foods, Biotechnology and Development, Agricultural University of Athens, Athens, Greece
| | - Miroslava Kačániová
- Department of Microbiology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Nitra, Slovakia
| | - Katarzyna Czaczyk
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Poznań, Poland
| | - Hülya Ölmez
- TÜBİTAK Marmara Research Center, Food Institute, Gebze, Kocaeli, Turkey
| | - Manuel Simões
- Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
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22
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Plasmid-encoded ComI inhibits competence in the ancestral 3610 strain of Bacillus subtilis. J Bacteriol 2013; 195:4085-93. [PMID: 23836866 DOI: 10.1128/jb.00696-13] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Natural competence is a process by which bacteria construct a membrane-associated machine for the uptake and integration of exogenous DNA. Many bacteria harbor genes for the DNA uptake machinery and yet are recalcitrant to DNA uptake for unknown reasons. For example, domesticated laboratory strains of Bacillus subtilis are renowned for high-frequency natural transformation, but the ancestral B. subtilis strain NCIB3610 is poorly competent. Here we find that endogenous plasmid pBS32 encodes a small protein, ComI, that inhibits transformation in the 3610 strain. ComI is a single-pass trans-membrane protein that appears to functionally inhibit the competence DNA uptake machinery. Functional inhibition of transformation may be common, and abolishing such inhibitors could be the key to permitting convenient genetic manipulation of a variety of industrially and medically relevant bacteria.
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Garmyn D, Gal L, Lemaitre JP, Hartmann A, Piveteau P. Communication and autoinduction in the species Listeria monocytogenes: A central role for the agr system. Commun Integr Biol 2013; 2:371-4. [PMID: 19721895 DOI: 10.4161/cib.2.4.8610] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Accepted: 04/03/2009] [Indexed: 11/19/2022] Open
Abstract
In order to withstand changes in their environment, bacteria have evolved mechanisms to sense the surrounding environment, integrate these signals and adapt their physiology to thrive under fluctuating conditions. Among these mechanisms, the ability of bacteria to exchange information between cells has become a dynamic field of interest for microbiologists over the past four decades. First described by Nelson et al.,1 this phenomenon often referred as either cell-cell communication, Quorum Sensing and/or AutoInduction involves the synthesis of small signal molecules called autoinducers. These signal molecules may be sensed by the bacterial population in the vicinity and induce regulation of gene expression. To date, three major communication systems have been described in bacteria. In this mini-review, we discuss the involvement of known communication systems in the transmission of information in the species Listeria monocytogenes. We will also discuss the latest findings on the role of communication in the regulation by Listeria monocytogenes of major adaptive strategies.
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Expression of a cryptic secondary sigma factor gene unveils natural competence for DNA transformation in Staphylococcus aureus. PLoS Pathog 2012; 8:e1003003. [PMID: 23133387 PMCID: PMC3486894 DOI: 10.1371/journal.ppat.1003003] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 09/17/2012] [Indexed: 12/19/2022] Open
Abstract
It has long been a question whether Staphylococcus aureus, a major human pathogen, is able to develop natural competence for transformation by DNA. We previously showed that a novel staphylococcal secondary sigma factor, SigH, was a likely key component for competence development, but the corresponding gene appeared to be cryptic as its expression could not be detected during growth under standard laboratory conditions. Here, we have uncovered two distinct mechanisms allowing activation of SigH production in a minor fraction of the bacterial cell population. The first is a chromosomal gene duplication rearrangement occurring spontaneously at a low frequency [≤10−5], generating expression of a new chimeric sigH gene. The second involves post-transcriptional regulation through an upstream inverted repeat sequence, effectively suppressing expression of the sigH gene. Importantly, we have demonstrated for the first time that S. aureus cells producing active SigH become competent for transformation by plasmid or chromosomal DNA, which requires the expression of SigH-controlled competence genes. Additionally, using DNA from the N315 MRSA strain, we successfully transferred the full length SCCmecII element through natural transformation to a methicillin-sensitive strain, conferring methicillin resistance to the resulting S. aureus transformants. Taken together, we propose a unique model for staphylococcal competence regulation by SigH that could help explain the acquisition of antibiotic resistance genes through horizontal gene transfer in this important pathogen. Staphylococcus aureus is a major human pathogen responsible for a broad spectrum of infections, emphasized by the emergence of multiple antibiotic-resistant strains with up to 60% of strains worldwide resistant to methicillin (Methicillin Resistant Staphylococcus aureus or MRSA). Indeed, MRSA-related infections are now one of the leading causes of death in the USA, highlighting the growing threat this bacterium poses to human health. Many bacteria have the ability to acquire novel genetic characteristics, including antibiotic resistance, through the uptake of extracellular DNA, a phenomenon known as natural genetic transformation or competence. We have shown that the SigH staphylococcal sigma factor is a likely key component for competence development, but that its gene is not expressed under standard laboratory conditions. Here, we have uncovered two distinct mechanisms allowing activation of SigH production in S. aureus: a chromosomal gene duplication rearrangement and post-transcriptional regulation through an upstream inverted repeat sequence. Importantly, we have demonstrated for the first time that S. aureus cells producing active SigH become competent for natural transformation by plasmid or chromosomal DNA, and we were able to confer methicillin resistance to a methicillin-sensitive strain by transformation with chromosomal DNA. SigH-dependent competence development in S. aureus could help explain the acquisition of antibiotic resistance genes and the rise of the so-called “superbug."
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Prophage Excision Activates Listeria Competence Genes that Promote Phagosomal Escape and Virulence. Cell 2012; 150:792-802. [DOI: 10.1016/j.cell.2012.06.036] [Citation(s) in RCA: 159] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2011] [Revised: 03/03/2012] [Accepted: 06/25/2012] [Indexed: 11/23/2022]
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Wang C, Fan J, Niu C, Wang C, Villaruz AE, Otto M, Gao Q. Role of spx in biofilm formation of Staphylococcus epidermidis. FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY 2010; 59:152-60. [PMID: 20402773 PMCID: PMC3413199 DOI: 10.1111/j.1574-695x.2010.00673.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Infections caused by the leading nosocomial pathogen Staphylococcus epidermidis are characterized by biofilm formation on implanted medical devices. In a previous study, we found that ClpP protease plays an essential role in biofilm formation of S. epidermidis. However, the mechanism by which ClpP impacts S. epidermidis biofilms has remained unknown. Here, we show that the Spx protein accumulates in the clpP mutant strain of S. epidermidis and controls biofilm formation of S. epidermidis via a pronounced effect on the transcription of the icaADBC operon coding for the production of the biofilm exopolysaccharide polysaccharide intercellular adhesion (PIA). Notably, in contrast to Staphylococcus aureus, Spx controls PIA expression via an icaR-independent mechanism. Furthermore, Spx affected primary surface attachment, although not by regulating the production of the autolysin AtlE. Our results indicate that ClpP enhances the formation of S. epidermidis biofilms by degrading Spx, a negative regulator of biofilm formation.
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Affiliation(s)
- Chongzhen Wang
- Key Laboratory of Medical Molecular Virology, Institutes of Biomedical Sciences and Institute of Medical Microbiology, Fudan University, Shanghai 200032, P. R. China
| | - Jiajia Fan
- Key Laboratory of Medical Molecular Virology, Institutes of Biomedical Sciences and Institute of Medical Microbiology, Fudan University, Shanghai 200032, P. R. China
| | - Chen Niu
- Key Laboratory of Medical Molecular Virology, Institutes of Biomedical Sciences and Institute of Medical Microbiology, Fudan University, Shanghai 200032, P. R. China
| | - Chuan Wang
- Key Laboratory of Medical Molecular Virology, Institutes of Biomedical Sciences and Institute of Medical Microbiology, Fudan University, Shanghai 200032, P. R. China
| | - Amer E. Villaruz
- Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, The National Institutes of Health, Hamilton, MT 59840, USA
| | - Michael Otto
- Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, The National Institutes of Health, Hamilton, MT 59840, USA
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology, Institutes of Biomedical Sciences and Institute of Medical Microbiology, Fudan University, Shanghai 200032, P. R. China
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Ells TC, Speers RA, Hansen LT. Insertional mutagenesis of Listeria monocytogenes 568 reveals genes that contribute to enhanced thermotolerance. Int J Food Microbiol 2009; 136:1-9. [PMID: 19836093 DOI: 10.1016/j.ijfoodmicro.2009.09.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2008] [Revised: 08/13/2009] [Accepted: 09/18/2009] [Indexed: 11/19/2022]
Abstract
The objectives of this study were to identify molecular mechanisms of thermotolerance using transposon mutants of Listeria monocytogenes 568, serotype 1/2a, and to compare their thermal death kinetics at 52, 56 and 60 degrees C. Sixteen Tn917 transposon mutants with enhanced heat resistance were acquired from a library of 4300 mutants following a multi-step screening process. Genetic regions with Tn917 insertions encompassed a broad range of functionalities including; transport, metabolism, replication and repair, general stress, and structural properties. Modeling of the heat inactivation data using the Geeraerd et al. and Whiting (Fermi) models showed that the mutants' enhanced thermal resistance was manifested mostly through a significant (p<or=0.05) extension of the lag period on the thermal death curve. This new knowledge impacts our understanding of molecular mechanisms affecting the kinetics of thermally induced cell death and enables the development of safer thermal processes.
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Affiliation(s)
- Timothy C Ells
- Agriculture and Agri-Food Canada, Atlantic Food and Horticulture Research Centre, Kentville, NS, Canada
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Turlan C, Prudhomme M, Fichant G, Martin B, Gutierrez C. SpxA1, a novel transcriptional regulator involved in X-state (competence) development in Streptococcus pneumoniae. Mol Microbiol 2009; 73:492-506. [PMID: 19627499 DOI: 10.1111/j.1365-2958.2009.06789.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Streptococcus pneumoniae is a naturally transformable human pathogen. Genome and phylogenetic analyses uncovered two Spx-like global transcriptional regulators, SpxA1 and SpxA2, encoded by S. pneumoniae. spxA1 and spxA2 are not essential, but their simultaneous inactivation is lethal. SpxA1 represses transcription of the early competence operon comCDE and thereby negatively regulates the initiation of the X-state (competence). The molecular basis of this repression could be similar to that of SpxA of Bacillus subtilis, involving a specific interaction with the alpha subunit of RNA polymerase. S. pneumoniae lacks an SOS-like stress response and the X-state is proposed to be a general stress response mechanism in this species. In light of this, SpxA1-dependent repression could act to sense environmental or metabolic stresses and prevent launching of the X-state in the absence of stress.
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Affiliation(s)
- Catherine Turlan
- Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaire, F31000 Toulouse, France
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Kovács AT, Smits WK, Mirończuk AM, Kuipers OP. Ubiquitous late competence genes in Bacillus species indicate the presence of functional DNA uptake machineries. Environ Microbiol 2009; 11:1911-22. [PMID: 19453701 DOI: 10.1111/j.1462-2920.2009.01937.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Natural competence for genetic transformation, i.e. the ability to take up DNA and stably integrate it in the genome, has so far only been observed in the bacterial kingdom (both in gram-negative and gram-positive species) and may contribute to survival under adverse growth conditions. Bacillus subtilis, the model organism for the Bacillus genus, possesses a well-characterized competence machinery. Phylogenetic analysis of several genome sequences of different Bacillus species reveals the presence of many, but not all genes potentially involved in competence and its regulation. The recent demonstration of functional DNA uptake by B. cereus supports the significance of our genome analyses and shows that the ability for functional DNA uptake might be widespread among Bacilli.
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Affiliation(s)
- Akos T Kovács
- Department of Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9751 NN Haren, The Netherlands
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den Bakker HC, Didelot X, Fortes ED, Nightingale KK, Wiedmann M. Lineage specific recombination rates and microevolution in Listeria monocytogenes. BMC Evol Biol 2008; 8:277. [PMID: 18842152 PMCID: PMC2576243 DOI: 10.1186/1471-2148-8-277] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2008] [Accepted: 10/08/2008] [Indexed: 01/02/2023] Open
Abstract
Background The bacterium Listeria monocytogenes is a saprotroph as well as an opportunistic human foodborne pathogen, which has previously been shown to consist of at least two widespread lineages (termed lineages I and II) and an uncommon lineage (lineage III). While some L. monocytogenes strains show evidence for considerable diversification by homologous recombination, our understanding of the contribution of recombination to L. monocytogenes evolution is still limited. We therefore used STRUCTURE and ClonalFrame, two programs that model the effect of recombination, to make inferences about the population structure and different aspects of the recombination process in L. monocytogenes. Analyses were performed using sequences for seven loci (including the house-keeping genes gap, prs, purM and ribC, the stress response gene sigB, and the virulence genes actA and inlA) for 195 L. monocytogenes isolates. Results Sequence analyses with ClonalFrame and the Sawyer's test showed that recombination is more prevalent in lineage II than lineage I and is most frequent in two house-keeping genes (ribC and purM) and the two virulence genes (actA and inlA). The relative occurrence of recombination versus point mutation is about six times higher in lineage II than in lineage I, which causes a higher genetic variability in lineage II. Unlike lineage I, lineage II represents a genetically heterogeneous population with a relatively high proportion (30% average) of genetic material imported from external sources. Phylograms, constructed with correcting for recombination, as well as Tajima's D data suggest that both lineages I and II have suffered a population bottleneck. Conclusion Our study shows that evolutionary lineages within a single bacterial species can differ considerably in the relative contributions of recombination to genetic diversification. Accounting for recombination in phylogenetic studies is critical, and new evolutionary models that account for the possibility of changes in the rate of recombination would be required. While previous studies suggested that only L. monocytogenes lineage I has experienced a recent bottleneck, our analyses clearly show that lineage II experienced a bottleneck at about the same time, which was subsequently obscured by abundant homologous recombination after the lineage II bottleneck. While lineage I and lineage II should be considered separate species from an evolutionary viewpoint, maintaining single species name may be warranted since both lineages cause the same type of human disease.
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Gueriri I, Cyncynatus C, Dubrac S, Arana AT, Dussurget O, Msadek T. The DegU orphan response regulator of Listeria monocytogenes autorepresses its own synthesis and is required for bacterial motility, virulence and biofilm formation. Microbiology (Reading) 2008; 154:2251-2264. [DOI: 10.1099/mic.0.2008/017590-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ibtissem Gueriri
- Unité de Biologie des Bactéries Pathogènes à Gram Positif, CNRS URA 2172, Institut Pasteur, 25 Rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Camille Cyncynatus
- Unité de Biologie des Bactéries Pathogènes à Gram Positif, CNRS URA 2172, Institut Pasteur, 25 Rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Sarah Dubrac
- Unité de Biologie des Bactéries Pathogènes à Gram Positif, CNRS URA 2172, Institut Pasteur, 25 Rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Alejandro Toledo Arana
- Laboratory of Bacterial Biofilms, Instituto De Agrobiotecnologia Y Recursos Naturales, Universidad Pública de Navarra, 31006 Pamplona, Spain
| | - Olivier Dussurget
- Unité des Interactions Bactéries Cellules, INSERM U604, INRA USC2020, Institut Pasteur, 25 Rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Tarek Msadek
- Unité de Biologie des Bactéries Pathogènes à Gram Positif, CNRS URA 2172, Institut Pasteur, 25 Rue du Dr. Roux, 75724 Paris Cedex 15, France
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Johnsborg O, Eldholm V, Håvarstein LS. Natural genetic transformation: prevalence, mechanisms and function. Res Microbiol 2007; 158:767-78. [PMID: 17997281 DOI: 10.1016/j.resmic.2007.09.004] [Citation(s) in RCA: 229] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Revised: 09/04/2007] [Accepted: 09/21/2007] [Indexed: 02/02/2023]
Abstract
Studies show that gene acquisition through natural transformation has contributed significantly to the adaptation and ecological diversification of several bacterial species. Relatively little is still known, however, about the prevalence and phylogenetic distribution of organisms possessing this property. Thus, whether natural transformation only benefits a limited number of species or has a large impact on lateral gene flow in nature remains a matter of speculation. Here we will review the most recent advances in our understanding of the phenomenon and discuss its possible biological functions.
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Affiliation(s)
- Ola Johnsborg
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, As, Norway
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Mandin P, Repoila F, Vergassola M, Geissmann T, Cossart P. Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets. Nucleic Acids Res 2007; 35:962-74. [PMID: 17259222 PMCID: PMC1807966 DOI: 10.1093/nar/gkl1096] [Citation(s) in RCA: 190] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
To identify noncoding RNAs (ncRNAs) in the pathogenic bacterium Listeria monocytogenes, we analyzed the intergenic regions (IGRs) of strain EGD-e by in silico-based approaches. Among the twelve ncRNAs found, nine are novel and specific to the Listeria genus, and two of these ncRNAs are expressed in a growth-dependent manner. Three of the ncRNAs are transcribed in opposite direction to overlapping open reading frames (ORFs), suggesting that they act as antisense on the corresponding mRNAs. The other ncRNA genes appear as single transcription units. One of them displays five repeats of 29 nucleotides. Five of these new ncRNAs are absent from the non-pathogenic species L. innocua, raising the possibility that they might be involved in virulence. To predict mRNA targets of the ncRNAs, we developed a computational method based on thermodynamic pairing energies and known ncRNA–mRNA hybrids. Three ncRNAs, including one of the putative antisense ncRNAs, were predicted to have more than one mRNA targets. Several of them were shown to bind efficiently to the ncRNAs suggesting that our in silico approach could be used as a general tool to search for mRNA targets of ncRNAs.
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Affiliation(s)
- Pierre Mandin
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Paris, F-75015 France; INSERM, U604, Paris, F-75015 France; INRA, USC2020, Paris, F-75015 France, CNRS URA 2171, Institut Pasteur, UP Génétique in silico, Paris, F-75015 France and UPR 9002 du CNRS, Institut de Biologie Moléculaire et Cellulaire, Université Louis Pasteur, Srasbourg, F-67084 France
| | - Francis Repoila
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Paris, F-75015 France; INSERM, U604, Paris, F-75015 France; INRA, USC2020, Paris, F-75015 France, CNRS URA 2171, Institut Pasteur, UP Génétique in silico, Paris, F-75015 France and UPR 9002 du CNRS, Institut de Biologie Moléculaire et Cellulaire, Université Louis Pasteur, Srasbourg, F-67084 France
| | - Massimo Vergassola
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Paris, F-75015 France; INSERM, U604, Paris, F-75015 France; INRA, USC2020, Paris, F-75015 France, CNRS URA 2171, Institut Pasteur, UP Génétique in silico, Paris, F-75015 France and UPR 9002 du CNRS, Institut de Biologie Moléculaire et Cellulaire, Université Louis Pasteur, Srasbourg, F-67084 France
| | - Thomas Geissmann
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Paris, F-75015 France; INSERM, U604, Paris, F-75015 France; INRA, USC2020, Paris, F-75015 France, CNRS URA 2171, Institut Pasteur, UP Génétique in silico, Paris, F-75015 France and UPR 9002 du CNRS, Institut de Biologie Moléculaire et Cellulaire, Université Louis Pasteur, Srasbourg, F-67084 France
| | - Pascale Cossart
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Paris, F-75015 France; INSERM, U604, Paris, F-75015 France; INRA, USC2020, Paris, F-75015 France, CNRS URA 2171, Institut Pasteur, UP Génétique in silico, Paris, F-75015 France and UPR 9002 du CNRS, Institut de Biologie Moléculaire et Cellulaire, Université Louis Pasteur, Srasbourg, F-67084 France
- *To whom correspondence should be addressed. Tel: (33) 145688841; Fax: (33) 145688706; E-mail:
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Pamp SJ, Frees D, Engelmann S, Hecker M, Ingmer H. Spx is a global effector impacting stress tolerance and biofilm formation in Staphylococcus aureus. J Bacteriol 2006; 188:4861-70. [PMID: 16788195 PMCID: PMC1483011 DOI: 10.1128/jb.00194-06] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Bacillus subtilis, Spx was recently characterized as a novel type of global regulator whose activity is regulated by the redox status of the cells. In the present study, we demonstrate that inactivation of Spx in the important pathogen Staphylococcus aureus renders the cells hypersensitive to a wide range of stress conditions including high and low temperature, high osmolarity, and hydrogen peroxide. Moreover, growth was restricted under nonstress conditions. Two-dimensional gel electrophoresis revealed that the proteome of the spx mutant differs substantially from the proteome of wild-type cells, supporting the finding that Spx is also a global regulator in S. aureus. More specifically, we demonstrated that Spx is required for transcription of trxB, encoding thioredoxin reductase, under all growth conditions examined. As trxB is essential in S. aureus, we speculate that the severely reduced trxB transcription could account for some of the growth defects of the spx mutant. Inactivation of spx also enhanced biofilm formation. S. aureus biofilm formation is associated with the production of the polysaccharide intercellular adhesin encoded by the ica operon. Interestingly, our data indicate that the augmented capacity of the spx mutant to form biofilms is due to Spx modulating the expression of icaR, encoding a repressor of the structural ica genes (icaABCD). In summary, we conclude that Spx fulfills an important role for growth, general stress protection, and biofilm formation in S. aureus.
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Affiliation(s)
- Sünje Johanna Pamp
- Department of Veterinary Pathobiology, Royal Veterinary and Agricultural University (KVL), Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
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Raynaud C, Charbit A. Regulation of expression of type I signal peptidases in Listeria monocytogenes. Microbiology (Reading) 2005; 151:3769-3776. [PMID: 16272398 DOI: 10.1099/mic.0.28066-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The role of type I signal peptidases (SPases I) is to remove the signal peptides of preproteins exported by the general secretory pathway. The genome of Listeria monocytogenes contains a locus encoding three contiguous SPases I (denoted SipX, SipY and SipZ). The authors recently showed that SipX and SipZ perform distinct functions in protein secretion and bacterial pathogenicity. Here, the regulation of sip gene expression in broth and in infected eukaryotic cells was studied. The results show that expression of the three sip genes is (i) controlled by two distinct promoter regions that respond differently to growth phase and temperature variations, and (ii) influenced by PrfA (the transcriptional activator regulating most of the virulence genes of L. monocytogenes) and the stress proteins ClpC and ClpP. It was found that sip gene expression was strongly upregulated upon infection of eukaryotic cells when bacteria were still entrapped in the phagosomal compartment. This upregulation is compatible with the need of L. monocytogenes to optimize its production of virulence factors in the early stage of the intracellular cycle.
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Affiliation(s)
- Catherine Raynaud
- INSERM-U570, Faculté de Médecine Necker-Enfants Malades, 156 rue de Vaugirard, 75730 Paris Cedex-15, France
| | - Alain Charbit
- INSERM-U570, Faculté de Médecine Necker-Enfants Malades, 156 rue de Vaugirard, 75730 Paris Cedex-15, France
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36
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Bierne H, Garandeau C, Pucciarelli MG, Sabet C, Newton S, Garcia-del Portillo F, Cossart P, Charbit A. Sortase B, a new class of sortase in Listeria monocytogenes. J Bacteriol 2004; 186:1972-82. [PMID: 15028680 PMCID: PMC374393 DOI: 10.1128/jb.186.7.1972-1982.2004] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2003] [Accepted: 12/02/2003] [Indexed: 01/30/2023] Open
Abstract
Sortases are transamidases that covalently link proteins to the peptidoglycan of gram-positive bacteria. The genome of the pathogenic bacterium Listeria monocytogenes encodes two sortases genes, srtA and srtB. The srtA gene product anchors internalin and some other LPXTG-containing proteins to the listerial surface. Here, we focus on the role of the second sortase, SrtB. Whereas SrtA acts on most of the proteins in the peptidoglycan fraction, SrtB appears to target minor amounts of surface polypeptides. We identified one of the SrtB-anchored proteins as the virulence factor SvpA, a surface-exposed protein which does not contain the LPXTG motif. Therefore, as in Staphylococcus aureus, the listerial SrtB represents a second class of sortase in L. monocytogenes, involved in the attachment of a subset of proteins to the cell wall, most likely by recognizing an NXZTN sorting motif. The DeltasrtB mutant strain does not have defects in bacterial entry, growth, or motility in tissue-cultured cells and does not show attenuated virulence in mice. SrtB-mediated anchoring could therefore be required to anchor surface proteins involved in the adaptation of this microorganism to different environmental conditions.
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Affiliation(s)
- Hélène Bierne
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, 75724 Paris Cedex 15, France
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37
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Dryla A, Gelbmann D, von Gabain A, Nagy E. Identification of a novel iron regulated staphylococcal surface protein with haptoglobin-haemoglobin binding activity. Mol Microbiol 2003; 49:37-53. [PMID: 12823809 DOI: 10.1046/j.1365-2958.2003.03542.x] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Staphylococcus aureus is an extremely adaptable pathogen causing a wide variety of infections. Staphylococcal surface proteins that directly interact with host extracellular proteins greatly contribute to virulence and are involved in adhesion, immune escape and nutrient acquisition. In our extensive search for highly immunogenic, in vivo-expressed, staphylococcal proteins, previously, we identified a novel member of the family of Gram-positive anchor motif proteins with a predicted 895 amino acid long sequence. In order to determine the ligand for this novel LPXTG cell wall protein, we employed affinity purification of human plasma using the recombinant form of the protein. Two-dimensional electrophoresis of eluted plasma proteins identified haptoglobin as a specific binding partner. Importantly, we also observed this specific ligand binding when living S. aureus cells were exposed to biotin-labelled haptoglobin (Hp) in a FACS-based assay. Targeted deletion of the gene eliminated Hp-binding, a function that has not been attributed to S. aureus before. Based on these data we specified the protein as the staphylococcal haptoglobin receptor A (HarA). Similarly to other haptoglobin receptors identified in Gram-negative pathogens, HarA binds not only Hp, but also haptoglobin-haemoglobin complexes with an even higher affinity, as demonstrated in in vitro binding assays. Employing specific deletion mutants, ligand binding was localized to two homologous regions with about 145 amino acid residues located within the N-terminal part of the protein. In addition, we demonstrated that expression of HarA was strictly controlled by iron through the iron-dependent transcriptional regulator Fur. Based on these data we propose that HarA can be added to the list of staphylococcal virulence factors with a most likely function related to iron acquisition.
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Affiliation(s)
- Agnieszka Dryla
- Intercell AG, Campus Vienna Biocenter 6, A-1030, Vienna, Austria
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38
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Claverys JP, Martin B. Bacterial "competence" genes: signatures of active transformation, or only remnants? Trends Microbiol 2003; 11:161-5. [PMID: 12706993 DOI: 10.1016/s0966-842x(03)00064-7] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
An exhaustive review published ten years ago reported natural genetic transformation, a potential mechanism for intra- and interspecies gene transfer, in approximately 40 species belonging to different taxonomic and trophic groups. Since then, considerable progress has been made in characterizing DNA-uptake machineries and regulatory circuits controlling their expression in cells competent for genetic transformation. In this article, in light of the recent description of a Group A streptococcal isolate capable of DNA transfer in mixed cultures, we discuss whether the detection in completely sequenced microbial genomes of intact homologues of key competence-regulatory and/or DNA-uptake proteins enables the prediction of new transformable species.
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Affiliation(s)
- Jean-Pierre Claverys
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR 5100 CNRS-Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse Cedex, France.
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Réglier-Poupet H, Pellegrini E, Charbit A, Berche P. Identification of LpeA, a PsaA-like membrane protein that promotes cell entry by Listeria monocytogenes. Infect Immun 2003; 71:474-82. [PMID: 12496198 PMCID: PMC143402 DOI: 10.1128/iai.71.1.474-482.2003] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The intracellular life of Listeria monocytogenes starts by a complex process of entry involving several bacterial ligands and eukaryotic receptors. In this work, we identified in silico from the sequence of the genome of L. monocytogenes a previously unknown gene designated lpeA (for lipoprotein promoting entry) encoding a 35-kDa protein homologous to PsaA, a lipoprotein belonging to the LraI family and implicated in the cell adherence of Streptococcus pneumoniae and related species. By constructing a mutant of L. monocytogenes in which lpeA is deleted (lpeA mutant), we show that the PsaA-like protein LpeA is not involved in bacterial adherence but is required for entry of L. monocytogenes in eukaryotic cells. In contrast to wild-type bacteria, mutant bacteria failed to invade the epithelial Caco-2 and hepatocyte TIB73 cell lines, as confirmed by confocal microscopy. The mutant bacteria rapidly penetrated in mouse bone marrow-derived macrophages. Surprisingly, lpeA mutant bacteria survive better in macrophages than do wild-type bacteria. This was correlated with a weak exacerbation of virulence of the lpeA mutant in the mouse. LpeA is therefore a novel invasin favoring the entry of L. monocytogenes into nonprofessional phagocytes but not its invasion of macrophages. This is the first report of a lipoprotein promoting cell invasion of an intracellular pathogen.
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Affiliation(s)
- Hélène Réglier-Poupet
- INSERM U570, Faculté de Médecine Necker-Enfants Malades, 75730 Paris cedex 15, France
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Morrissey JA, Cockayne A, Hammacott J, Bishop K, Denman-Johnson A, Hill PJ, Williams P. Conservation, surface exposure, and in vivo expression of the Frp family of iron-regulated cell wall proteins in Staphylococcus aureus. Infect Immun 2002; 70:2399-407. [PMID: 11953376 PMCID: PMC127940 DOI: 10.1128/iai.70.5.2399-2407.2002] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis identified two conserved, immunogenic Staphylococcus aureus cell wall proteins, of 40 and 87 kDa, expressed under iron-restricted growth conditions in vitro and in vivo. N-terminal sequencing and subsequent genome analysis showed that these proteins are encoded by adjacent monocistronic open reading frames designated frpA and frpB, respectively. Studies with an S. aureus fur mutant confirmed that expression of FrpA and FrpB is regulated by Fur but that there also appears to be differential expression of these proteins in different iron-restricted media in vitro. FrpA and FrpB share some amino acid sequence homology with each other and with a putative S. aureus membrane protein, FrpC. frpC is the first gene of a Fur-regulated operon encoding four proteins of unknown function (FrpC, -D, -G, and -H) and the binding protein (FrpE) and permease (FrpF) of a putative iron transporter. Antisense mutagenesis and bioassays showed that FrpA and FrpB are not required for growth of S. aureus under iron-restricted conditions in vitro and do not appear to be involved in the transport of iron from siderophores or in binding of hemin. Further phenotypic analysis suggested that FrpA may be involved in adhesion of S. aureus to plastic in vitro. Binding of S. aureus to microtiter wells was found to be iron regulated, and iron-restricted S. aureus containing antisense frpA or frpAB but not frpB constructs showed reduced binding compared to vector construct controls.
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Affiliation(s)
- Julie A Morrissey
- Institute of Infections and Immunity, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, United Kingdom
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Lapidus A, Galleron N, Andersen JT, Jørgensen PL, Ehrlich SD, Sorokin A. Co-linear scaffold of the Bacillus licheniformis and Bacillus subtilis genomes and its use to compare their competence genes. FEMS Microbiol Lett 2002; 209:23-30. [PMID: 12007649 DOI: 10.1111/j.1574-6968.2002.tb11104.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
We have established the co-linear regions of Bacillus licheniformis, an industrially important bacterium, and Bacillus subtilis, a model bacterium. In the co-linear regions, revealed by PCR, gene content and order are presumed to be conserved. These regions constitute approximately 60% of the compared chromosomes. Sequencing of the competence genes of B. licheniformis allowed us to validate the approach, and to demonstrate how it can be used for the comparative analysis of complex genetic systems. A new insertion sequence, designated IS3Bli1, was discovered in the competence region of the analyzed B. licheniformis strain.
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Affiliation(s)
- Alla Lapidus
- Génétique Microbienne, INRA, Domaine de Vilvert, 78352 Jouy en Josas Cedex, France
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Borezée E, Pellegrini E, Beretti JL, Berche P. SvpA, a novel surface virulence-associated protein required for intracellular survival of Listeria monocytogenes. MICROBIOLOGY (READING, ENGLAND) 2001; 147:2913-23. [PMID: 11700342 DOI: 10.1099/00221287-147-11-2913] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A previously unknown protein, designated SvpA (surface virulence-associated protein) and implicated in the virulence of the intracellular pathogen Listeria monocytogenes, was identified. This 64 kDa protein, encoded by svpA, is both secreted in culture supernatants and surface-exposed, as shown by immunogold labelling of whole bacteria with an anti-SvpA antibody. Analysis of the peptide sequence revealed that SvpA contains a leader peptide, a predicted C-terminal transmembrane region and a positively charged tail resembling that of the surface protein ActA, suggesting that SvpA might partially reassociate with the bacterial surface by its C-terminal membrane anchor. An allelic mutant was constructed by disrupting svpA in the wild-type strain LO28. The virulence of this mutant was strongly attenuated in the mouse, with a 2 log decrease in the LD50 and restricted bacterial growth in organs as compared to the wild-type strain. This reduced virulence was not related either to a loss of adherence or to a lower expression of known virulence factors, which remained unaffected in the svpA mutant. It was caused by a restriction of intracellular growth of mutant bacteria. By following the intracellular behaviour of bacteria within bone-marrow-derived macrophages by confocal and electron microscopy studies, it was found that most svpA mutant bacteria remained confined within phagosomes, in contrast to wild-type bacteria which rapidly escaped to the cytoplasm. The regulation of svpA was independent of PrfA, the transcriptional activator of virulence genes in L. monocytogenes. In fact, SvpA was down-regulated by MecA, ClpC and ClpP, which are highly homologous to proteins of Bacillus subtilis forming a regulatory complex controlling the competence state of this saprophyte. The results indicate that: (i) SvpA is a novel factor involved in the virulence of L. monocytogenes, promoting bacterial escape from phagosomes of macrophages; (ii) SvpA is, at least partially, associated with the surface of bacteria; and (iii) SvpA is PrfA-independent and controlled by a MecA-dependent regulatory network.
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Affiliation(s)
- E Borezée
- Laboratoire de Microbiologie, Institut National de la Santé et de la Recherche Médicale U411, Faculté de Médecine Necker-Enfants Malades, 156 rue de Vaugirard, 75730 Paris Cedex 15, France
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43
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Nakano MM, Hajarizadeh F, Zhu Y, Zuber P. Loss-of-function mutations in yjbD result in ClpX- and ClpP-independent competence development of Bacillus subtilis. Mol Microbiol 2001; 42:383-94. [PMID: 11703662 DOI: 10.1046/j.1365-2958.2001.02639.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Mutations in clpP and clpX have pleiotropic effects on growth and developmentally regulated gene expression in Bacillus subtilis. ClpP and ClpX are needed for expression of comK, encoding the competence transcription factor required for the expression of genes within the competence regulon. ClpP, in combination with the ATPase ClpC, degrades the inhibitor of ComK, MecA. Proteolysis of MecA is stimulated by a small protein, ComS, which interacts with MecA. Suppressor mutations (cxs) were isolated that bypass the requirement for clpX for comK expression. These were found also to overcome the defect in comK expression conferred by a clpP mutation. These mutations were identified as missense mutations (cxs-5, -7 and -12) and a nonsense (UAG) codon substitution (cxs-10) in the yjbD coding sequence in a locus linked to mecA. That a yjbD disruption confers the cxs phenotype, together with its complementation by an ectopically expressed copy of yjbD, indicated that the suppressor alleles bear recessive, loss-of-function mutations of yjbD. ClpP- and ClpX-independent comK expression rendered by inactivation of yjbD was still medium-dependent and required ComS. MecA levels in a clpP-yjbD mutant were lower that those of clpP mutant cells and ComK protein concentration in the clpP mutant was restored to wild-type levels by the yjbD mutation. Consequently, the yjbD mutation bypasses the defect in competence development conferred by clpP and clpX. YjbD protein is barely detectable in wild-type cells, but is present in large amounts in the clpP mutant cells. The results suggest that the role of ClpP in competence development is to degrade YjbD protein so that ComS can productively interact with the MecA-ClpC-ComK complex. Alternatively, the result could suggest that YjbD has a negative effect on regulated proteolysis and that MecA is degraded independently of ClpP when YjbD is absent.
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Affiliation(s)
- M M Nakano
- Department of Biochemistry and Molecular Biology, OGI School of Science and Engineering, Oregon Health and Science University, Beaverton, OR 97006-8921, USA
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Frees D, Varmanen P, Ingmer H. Inactivation of a gene that is highly conserved in Gram-positive bacteria stimulates degradation of non-native proteins and concomitantly increases stress tolerance in Lactococcus lactis. Mol Microbiol 2001; 41:93-103. [PMID: 11454203 DOI: 10.1046/j.1365-2958.2001.02503.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Exposure of cells to elevated temperatures triggers the synthesis of chaperones and proteases including components of the conserved Clp protease complex. We demonstrated previously that the proteolytic subunit, ClpP, plays a major role in stress tolerance and in the degradation of non-native proteins in the Gram-positive bacterium Lactococcus lactis. Here, we used transposon mutagenesis to generate mutants in which the temperature- and puromycin-sensitive phenotype of a lactococcal clpP null mutant was partly alleviated. In all mutants obtained, the transposon was inserted in the L. lactis trmA gene. When analysing a clpP, trmA double mutant, we found that the expression normally induced from the clpP and dnaK promoters in the clpP mutant was reduced to wild-type level upon introduction of the trmA disruption. Additionally, the degradation of puromycyl-containing polypeptides was increased, suggesting that inactivation of trmA compensates for the absence of ClpP by stimulating an as yet unidentified protease that degrades misfolded proteins. When trmA was disrupted in wild-type cells, both stress tolerance and proteolysis of puromycyl peptides was enhanced above wild-type level. Based on our results, we propose that TrmA, which is well conserved in several Gram-positive bacteria, affects the degradation of non-native proteins and thereby controls stress tolerance.
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Affiliation(s)
- D Frees
- Department of Veterinary Microbiology, Stigbøjlen 4, Denmark
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Borezee E, Pellegrini E, Berche P. OppA of Listeria monocytogenes, an oligopeptide-binding protein required for bacterial growth at low temperature and involved in intracellular survival. Infect Immun 2000; 68:7069-77. [PMID: 11083832 PMCID: PMC97817 DOI: 10.1128/iai.68.12.7069-7077.2000] [Citation(s) in RCA: 156] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We identified a new oligopeptide permease operon in the pathogen Listeria monocytogenes. This opp operon consists of five genes (oppA, oppB, oppC, oppD, and oppF) and displays the same genetic organization as those of several bacterial species. The first gene of this operon, oppA, encodes a 62-kDa protein sharing 33% identity with OppA of Bacillus subtilis and is expressed predominantly during exponential growth. The function of oppA was studied by constructing an oppA deletion mutant. The phenotype analysis of this mutant revealed that OppA mediates the transport of oligopeptides and is required for bacterial growth at low temperature. The wild-type phenotype was restored by complementing the mutant with oppA. We also found that OppA is involved in intracellular survival in macrophages and in bacterial growth in organs of mice infected with L. monocytogenes, although the level of virulence was not altered in the mutant. These results show the major role of OppA in the uptake of oligopeptides and the pleiotropic effects of this oligopeptide-binding protein on the behavior of this pathogen in the environment and in its host.
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Affiliation(s)
- E Borezee
- Inserm U411, Faculté de Médecine Necker, 75730 Paris Cedex 15, France
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