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Zeng Z, Wijnands LM, Boeren S, Smid EJ, Notebaart RA, Abee T. Impact of vitamin B 12 on rhamnose metabolism, stress defense and in-vitro virulence of Listeria monocytogenes. Int J Food Microbiol 2024; 410:110486. [PMID: 37992553 DOI: 10.1016/j.ijfoodmicro.2023.110486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 07/05/2023] [Accepted: 11/11/2023] [Indexed: 11/24/2023]
Abstract
Listeria monocytogenes is a facultative anaerobe which can cause a severe food-borne infection known as listeriosis. L. monocytogenes is capable of utilizing various nutrient sources including rhamnose, a naturally occurring deoxy sugar abundant in foods. L. monocytogenes can degrade rhamnose into lactate, acetate and 1,2-propanediol. Our previous study showed that addition of vitamin B12 stimulated anaerobic growth of L. monocytogenes on rhamnose due to the activation of bacterial microcompartments for 1,2-propanediol utilization (pdu BMC) with concomitant production of propionate and propanol. Notably, anaerobic 1,2-propanediol metabolism has been linked to virulence of enteric pathogens including Salmonella spp. and L. monocytogenes. In this study we investigated the impact of B12 and BMC activation on i) aerobic and anerobic growth of L. monocytogenes on rhamnose and ii) the level of virulence. We observed B12-induced pdu BMC activation and growth stimulation only in anaerobically grown cells. Comparative Caco-2 virulence assays showed that these pdu BMC-induced cells have significantly higher translocation efficiency compared to non-induced cells (anaerobic growth without B12; aerobic growth with or without B12), while adhesion and invasion capacity is similar for all cells. Comparative proteome analysis showed specific and overlapping responses linked to metabolic shifts, activation of stress defense proteins and virulence factors, with RNA polymerase sigma factor SigL, teichoic acid export ATP-binding protein TagH, DNA repair and protection proteins, RadA and DPS, and glutathione synthase GshAB, previously linked to activation of virulence response in L. monocytogenes, uniquely upregulated in anaerobically rhamnose grown pdu-induced cells. Our results shed light on possible effects of B12 on L. monocytogenes competitive fitness and virulence activation when utilizing rhamnose in anaerobic conditions encountered during transmission and the human intestine.
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Affiliation(s)
- Zhe Zeng
- Food Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Lucas M Wijnands
- National Institute of Public Health and the Environment, Bilthoven, the Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University and Research, Wageningen, the Netherlands
| | - Eddy J Smid
- Food Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Richard A Notebaart
- Food Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Tjakko Abee
- Food Microbiology, Wageningen University and Research, Wageningen, the Netherlands.
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2
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Meireles D, Pombinho R, Cabanes D. Signals behind Listeria monocytogenes virulence mechanisms. Gut Microbes 2024; 16:2369564. [PMID: 38979800 PMCID: PMC11236296 DOI: 10.1080/19490976.2024.2369564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/13/2024] [Indexed: 07/10/2024] Open
Abstract
The tight and coordinated regulation of virulence gene expression is crucial to ensure the survival and persistence of bacterial pathogens in different contexts within their hosts. Considering this, bacteria do not express virulence factors homogenously in time and space, either due to their associated fitness cost or to their detrimental effect at specific infection stages. To efficiently infect and persist into their hosts, bacteria have thus to monitor environmental cues or chemical cell-to-cell signaling mechanisms that allow their transition from the external environment to the host, and therefore adjust gene expression levels, intrinsic biological activities, and appropriate behaviors. Listeria monocytogenes (Lm), a major Gram-positive facultative intracellular pathogen, stands out for its adaptability and capacity to thrive in a wide range of environments. Because of that, Lm presents itself as a significant concern in food safety and public health, that can lead to potentially life-threatening infections in humans. A deeper understanding of the intricate bacterial virulence mechanisms and the signals that control them provide valuable insights into the dynamic interplay between Lm and the host. Therefore, this review addresses the role of some crucial signals behind Lm pathogenic virulence mechanisms and explores how the ability to assimilate and interpret these signals is fundamental for pathogenesis, identifying potential targets for innovative antimicrobial strategies.
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Affiliation(s)
- Diana Meireles
- Instituto de Investigação e Inovação em Saúde, Porto, Portugal
- Group of Molecular Microbiology, IBMC, Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar – ICBAS, Porto, Portugal
| | - Rita Pombinho
- Instituto de Investigação e Inovação em Saúde, Porto, Portugal
- Group of Molecular Microbiology, IBMC, Porto, Portugal
| | - Didier Cabanes
- Instituto de Investigação e Inovação em Saúde, Porto, Portugal
- Group of Molecular Microbiology, IBMC, Porto, Portugal
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3
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Monteith W, Pascoe B, Mourkas E, Clark J, Hakim M, Hitchings MD, McCarthy N, Yahara K, Asakura H, Sheppard SK. Contrasting genes conferring short- and long-term biofilm adaptation in Listeria. Microb Genom 2023; 9:001114. [PMID: 37850975 PMCID: PMC10634452 DOI: 10.1099/mgen.0.001114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/28/2023] [Indexed: 10/19/2023] Open
Abstract
Listeria monocytogenes is an opportunistic food-borne bacterium that is capable of infecting humans with high rates of hospitalization and mortality. Natural populations are genotypically and phenotypically variable, with some lineages being responsible for most human infections. The success of L. monocytogenes is linked to its capacity to persist on food and in the environment. Biofilms are an important feature that allow these bacteria to persist and infect humans, so understanding the genetic basis of biofilm formation is key to understanding transmission. We sought to investigate the biofilm-forming ability of L. monocytogenes by identifying genetic variation that underlies biofilm formation in natural populations using genome-wide association studies (GWAS). Changes in gene expression of specific strains during biofilm formation were then investigated using RNA sequencing (RNA-seq). Genetic variation associated with enhanced biofilm formation was identified in 273 genes by GWAS and differential expression in 220 genes by RNA-seq. Statistical analyses show that the number of overlapping genes flagged by either type of experiment is less than expected by random sampling. This novel finding is consistent with an evolutionary scenario where rapid adaptation is driven by variation in gene expression of pioneer genes, and this is followed by slower adaptation driven by nucleotide changes within the core genome.
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Affiliation(s)
- William Monteith
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biology, University of Bath, Claverton Down, Bath, UK
| | - Ben Pascoe
- Department of Biology, University of Oxford, Oxford, UK
- Big Data Institute, University of Oxford, Oxford, UK
| | | | - Jack Clark
- Department of Genetics, University of Leicester, University Road, Leicester, UK
| | - Maliha Hakim
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - Matthew D. Hitchings
- Swasnsea University Medical School, Swansea University, Singleton Campus, Swansea, UK
| | - Noel McCarthy
- School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Koji Yahara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hiroshi Asakura
- Division of Biomedical Food Research, National Institute of Health Sciences, Tonomachi 3-25-26, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, Japan
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Oliveira AH, Tiensuu T, Guerreiro D, Tükenmez H, Dessaux C, García-Del Portillo F, O'Byrne C, Johansson J. The Virulence and Infectivity of Listeria monocytogenes Are Not Substantially Altered by Elevated SigB Activity. Infect Immun 2023:e0057122. [PMID: 37125941 DOI: 10.1128/iai.00571-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Listeria monocytogenes is a bacterial pathogen capable of causing severe infections but also thriving outside the host. To respond to different stress conditions, L. monocytogenes mainly utilizes the general stress response regulon, which largely is controlled by the alternative sigma factor Sigma B (SigB). In addition, SigB is important for virulence gene expression and infectivity. Upon encountering stress, a large multicomponent protein complex known as the stressosome becomes activated, ultimately leading to SigB activation. RsbX is a protein needed to reset a "stressed" stressosome and prevent unnecessary SigB activation in nonstressed conditions. Consequently, absence of RsbX leads to constitutive activation of SigB even without prevailing stress stimulus. To further examine the involvement of SigB in the virulence of this pathogen, we investigated whether a strain with constitutively active SigB would be affected in virulence factor expression and/or infectivity in cultured cells and in a chicken embryo infection model. Our results suggest that increased SigB activity does not substantially alter virulence gene expression compared with the wild-type (WT) strain at transcript and protein levels. Bacteria lacking RsbX were taken up by phagocytic and nonphagocytic cells at a similar frequency to WT bacteria, both in stressed and nonstressed conditions. Finally, the absence of RsbX only marginally affected the ability of bacteria to infect chicken embryos. Our results suggest only a minor role of RsbX in controlling virulence factor expression and infectivity under these conditions.
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Affiliation(s)
- Ana H Oliveira
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Umeå Centre of Microbial Research, Umeå University, Umeå, Sweden
| | - Teresa Tiensuu
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Umeå Centre of Microbial Research, Umeå University, Umeå, Sweden
| | - Duarte Guerreiro
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Umeå Centre of Microbial Research, Umeå University, Umeå, Sweden
- Bacterial Stress Response Group, Microbiology, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | - Hasan Tükenmez
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Umeå Centre of Microbial Research, Umeå University, Umeå, Sweden
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Charlotte Dessaux
- Laboratory of Intracellular Bacterial Pathogens, National Center of Biotechnology, (CNB)-CSIC, Madrid, Spain
| | | | - Conor O'Byrne
- Bacterial Stress Response Group, Microbiology, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | - Jörgen Johansson
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Umeå Centre of Microbial Research, Umeå University, Umeå, Sweden
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The small non-coding RNA rli106 contributes to the environmental adaptation and pathogenicity of Listeria monocytogenes. J Vet Res 2023; 67:67-77. [PMID: 37008770 PMCID: PMC10062041 DOI: 10.2478/jvetres-2023-0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 03/03/2023] [Indexed: 03/18/2023] Open
Abstract
Abstract
Introduction
Listeria monocytogenes (LM) is an important food-borne pathogen, and the risk of its ingestion is a serious public health issue. The better its environmental adaptation mechanisms and pathogenicity are understood, the better the risk it poses can be countered. The regulatory role of the small non-coding RNA (sRNA) rli106 in the environmental adaptation and pathogenicity of LM is still unclear and this study investigated that role through its biological function.
Material and Methods
An LM-Δrli106 gene deletion strain and an LM-Δrli106/rli106 gene complementation strain were constructed using the homologous recombination technique. Then, the adaptation of these strains to temperature, alkalinity, acidity, salinity, ethanol and oxidative stressors, their biofilm-forming ability and their pathogenicity in mice were investigated to show the regulatory roles of sRNA rli106 in LM. The target gene of rli106 was also predicted, and the interaction between it and rli106 was verified by a two-plasmid co-expressing system based on
E.coli
and Western blot analysis.
Results
The adaptation of LM-Δrli106 to environmental stressors of pH 9, 5% NaCl and 8% NaCl, 3.8% ethanol and 5 mM H2O2 was significantly reduced when compared to the parental (LM EGD-e) and complementation strains. Also, the biofilm formation, cell adhesion, invasion, intracellular proliferation and pathogenicity of LM-Δrli106 in mice were significantly reduced. The results of two-plasmid co-expression and Western blot showed that rli106 can interact with the mRNA of the predicted DegU target gene.
Conclusion
The sRNA rli106 may positively regulate the expression of the DegU gene in LM. This study sheds light on its regulatory roles in environmental adaptation and pathogenicity, providing new insights into the molecular mechanism of sRNA mediation in LM .
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6
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Muchaamba F, von Ah U, Stephan R, Stevens MJA, Tasara T. Deciphering the global roles of Cold shock proteins in Listeria monocytogenes nutrient metabolism and stress tolerance. Front Microbiol 2022; 13:1057754. [PMID: 36605504 PMCID: PMC9808409 DOI: 10.3389/fmicb.2022.1057754] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022] Open
Abstract
Listeria monocytogenes (Lm) accounts for serious public health and food safety problems owing to its stress resilience and pathogenicity. Based on their regulatory involvement in global gene expression events, cold-shock domain family proteins (Csps) are crucial in expression of various stress fitness and virulence phenotypes in bacteria. Lm possesses three Csps (CspA, CspB, and CspD) whose regulatory roles in the context of the genetic diversity of this bacterium are not yet fully understood. We examined the impacts of Csps deficiency on Lm nutrient metabolism and stress tolerance using a set of csp deletion mutants generated in different genetic backgrounds. Phenotype microarrays (PM) analysis showed that the absence of Csps in ∆cspABD reduces carbon (C-) source utilization capacity and increases Lm sensitivity to osmotic, pH, various chemical, and antimicrobial stress conditions. Single and double csp deletion mutants in different Lm genetic backgrounds were used to further dissect the roles of individual Csps in these phenotypes. Selected PM-based observations were further corroborated through targeted phenotypic assays, confirming that Csps are crucial in Lm for optimal utilization of various C-sources including rhamnose and glucose as well as tolerance against NaCl, β-phenyethylamine (PEA), and food relevant detergent stress conditions. Strain and genetic lineage background-based differences, division of labour, epistasis, and functional redundancies among the Csps were uncovered with respect to their roles in various processes including C-source utilization, cold, and PEA stress resistance. Finally, targeted transcriptome analysis was performed, revealing the activation of csp gene expression under defined stress conditions and the impact of Csps on expression regulation of selected rhamnose utilization genes. Overall, our study shows that Csps play important roles in nutrient utilization and stress responses in Lm strains, contributing to traits that are central to the public health and food safety impacts of this pathogen.
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Affiliation(s)
- Francis Muchaamba
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland,*Correspondence: Francis Muchaamba,
| | | | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Marc J. A. Stevens
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Taurai Tasara
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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7
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Lu Q, Zhu X, Long Q, Yi X, Yang A, Long X, Cao D. Comparative Genomics Reveal the Utilization Ability of Variable Carbohydrates as Key Genetic Features of Listeria Pathogens in Their Pathogenic Lifestyles. Pathogens 2022; 11:pathogens11121430. [PMID: 36558765 PMCID: PMC9784484 DOI: 10.3390/pathogens11121430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/20/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND L. monocytogenes and L. ivanovii, the only two pathogens of Listeria, can survive in various environments, having different pathogenic characteristics. However, the genetic basis of their excellent adaptability and differences in pathogenicity has still not been completely elucidated. METHODS We performed a comparative genomic analysis based on 275 L. monocytogenes, 10 L. ivanovii, and 22 non-pathogenic Listeria strains. RESULTS Core/pan-genome analysis revealed that 975 gene families were conserved in all the studied strains. Additionally, 204, 242, and 756 gene families existed uniquely in L. monocytogenes, L. ivanovii, and both, respectively. Functional annotation partially verified that these unique gene families were closely related to their adaptability and pathogenicity. Moreover, the protein-protein interaction (PPI) network analysis of these unique gene sets showed that plenty of carbohydrate transport systems and energy metabolism enzymes were clustered in the networks. Interestingly, ethanolamine-metabolic-process-related proteins were significantly enriched in the PPI network of the unique genes of the Listeria pathogens, which can be understood as a determining factor of their pathogenicity. CONCLUSIONS The utilization capacity of multiple carbon sources of Listeria pathogens, especially ethanolamine, is the key genetic basis for their ability to adapt to various environments and pathogenic lifestyles.
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Affiliation(s)
- Qunfeng Lu
- Modern Industrial College of Biomedicine and Great Health, Youjiang Medical University for Nationalities, Baise 533000, China
- School of Medical Laboratory Sciences, Youjiang Medical University for Nationalities, Baise 533000, China
| | - Xiaoying Zhu
- Medical College, Guangxi University, Nanning 530004, China
- Clinical Pathological Diagnosis & Research Center, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, China
- Department of Tumor Pathology, The Key Laboratory of Molecular Pathology (Hepatobiliary Diseases) of Guangxi, Baise 533000, China
| | - Qinqin Long
- Clinical Pathological Diagnosis & Research Center, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, China
- Department of Tumor Pathology, The Key Laboratory of Molecular Pathology (Hepatobiliary Diseases) of Guangxi, Baise 533000, China
| | - Xueli Yi
- Center for Clinical Laboratory Diagnosis and Research, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, China
| | - Anni Yang
- Modern Industrial College of Biomedicine and Great Health, Youjiang Medical University for Nationalities, Baise 533000, China
- School of Medical Laboratory Sciences, Youjiang Medical University for Nationalities, Baise 533000, China
| | - Xidai Long
- Clinical Pathological Diagnosis & Research Center, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, China
- Department of Tumor Pathology, The Key Laboratory of Molecular Pathology (Hepatobiliary Diseases) of Guangxi, Baise 533000, China
- Correspondence: (X.L.); (D.C.)
| | - Demin Cao
- Clinical Pathological Diagnosis & Research Center, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, China
- Department of Tumor Pathology, The Key Laboratory of Molecular Pathology (Hepatobiliary Diseases) of Guangxi, Baise 533000, China
- Correspondence: (X.L.); (D.C.)
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8
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Muchaamba F, Eshwar AK, Stevens MJA, Stephan R, Tasara T. Different Shades of Listeria monocytogenes: Strain, Serotype, and Lineage-Based Variability in Virulence and Stress Tolerance Profiles. Front Microbiol 2022; 12:792162. [PMID: 35058906 PMCID: PMC8764371 DOI: 10.3389/fmicb.2021.792162] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 11/11/2021] [Indexed: 12/30/2022] Open
Abstract
Listeria monocytogenes is a public health and food safety challenge due to its virulence and natural stress resistance phenotypes. The variable distribution of L. monocytogenes molecular subtypes with respect to food products and processing environments and among human and animal clinical listeriosis cases is observed. Sixty-two clinical and food-associated L. monocytogenes isolates were examined through phenome and genome analysis. Virulence assessed using a zebrafish infection model revealed serotype and genotype-specific differences in pathogenicity. Strains of genetic lineage I serotype 4b and multilocus sequence type clonal complexes CC1, CC2, CC4, and CC6 grew and survived better and were more virulent than serotype 1/2a and 1/2c lineage II, CC8, and CC9 strains. Hemolysis, phospholipase activity, and lysozyme tolerance profiles were associated with the differences observed in virulence. Osmotic stress resistance evaluation revealed serotype 4b lineage I CC2 and CC4 strains as more osmotolerant, whereas serotype 1/2c lineage II CC9 strains were more osmo-sensitive than others. Variable tolerance to the widely used quaternary ammonium compound benzalkonium chloride (BC) was observed. Some outbreak and sporadic clinical case associated strains demonstrated BC tolerance, which might have contributed to their survival and transition in the food-processing environment facilitating food product contamination and ultimately outbreaks or sporadic listeriosis cases. Genome comparison uncovered various moderate differences in virulence and stress associated genes between the strains indicating that these differences in addition to gene expression regulation variations might largely be responsible for the observed virulence and stress sensitivity phenotypic differences. Overall, our study uncovered strain and genotype-dependent variation in virulence and stress resilience among clinical and food-associated L. monocytogenes isolates with potential public health risk implications. The extensive genome and phenotypic data generated provide a basis for developing improved Listeria control strategies and policies.
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Affiliation(s)
- Francis Muchaamba
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, Zurich, Switzerland
| | - Athmanya K Eshwar
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, Zurich, Switzerland
| | - Marc J A Stevens
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, Zurich, Switzerland
| | - Taurai Tasara
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, Zurich, Switzerland
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9
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Sharma A, Alajangi HK, Pisignano G, Sood V, Singh G, Barnwal RP. RNA thermometers and other regulatory elements: Diversity and importance in bacterial pathogenesis. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1711. [PMID: 35037405 DOI: 10.1002/wrna.1711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 11/09/2021] [Accepted: 12/16/2021] [Indexed: 01/11/2023]
Abstract
Survival of microorganisms depends to a large extent on environmental conditions and the occupied host. By adopting specific strategies, microorganisms can thrive in the surrounding environment and, at the same time, preserve their viability. Evading the host defenses requires several mechanisms compatible with the host survival which include the production of RNA thermometers to regulate the expression of genes responsible for heat or cold shock as well as of those involved in virulence. Microorganisms have developed a variety of molecules in response to the environmental changes in temperature and even more specifically to the host they invade. Among all, RNA-based regulatory mechanisms are the most common ones, highlighting the importance of such molecules in gene expression control and novel drug development by suitable structure-based alterations. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA in Disease and Development > RNA in Disease RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Akanksha Sharma
- Department of Biophysics, Panjab University, Chandigarh, India.,University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | - Hema Kumari Alajangi
- Department of Biophysics, Panjab University, Chandigarh, India.,University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | | | - Vikas Sood
- Department of Biochemistry, Jamia Hamdard, New Delhi, India
| | - Gurpal Singh
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
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10
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Martín I, Rodríguez A, Alía A, Martínez-Blanco M, Lozano-Ojalvo D, Córdoba JJ. Control of Listeria monocytogenes growth and virulence in a traditional soft cheese model system based on lactic acid bacteria and a whey protein hydrolysate with antimicrobial activity. Int J Food Microbiol 2022; 361:109444. [PMID: 34749186 DOI: 10.1016/j.ijfoodmicro.2021.109444] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 10/08/2021] [Accepted: 10/17/2021] [Indexed: 12/26/2022]
Abstract
"Torta del Casar" is a Spanish soft-ripened cheese made with sheep's raw milk and subjected to a short ripening process, which favors the growth of pathogenic microorganisms including Listeria monocytogenes. The development of strategies to control pathogens and minimize health risks associated with the presence of L. monocytogenes in these products is of great interest. In this regard, the anti-Listeria activity of a whey protein hydrolysate (ProH) alone or combined with six lactic acid bacteria strains isolated from cheese was evaluated in this study as a biocontrol strategy using a "Torta del Casar" cheese-based medium. The most active combinations of lactic acid bacteria assayed induced a reduction higher than two logarithmic units in the growth of L. monocytogenes (serotype 4b) compared to their respective control when they were co-inoculated in "Torta del Casar" cheese-based medium at 7 °C for 7 days. In addition, the observed downregulation of some key virulence genes of L. monocytogenes suggests that the strain Lactiplantibacillus plantarum B2 alone and combined with the strain Lactiplantibacillus spp. B4 are good candidates to be used as biocontrol agents against L. monocytogenes growth in traditional soft cheeses based on raw milk during their storage at refrigeration temperatures.
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Affiliation(s)
- Irene Martín
- Food Hygiene and Safety, Meat and Meat Products Research Institute, Faculty of Veterinary Science, University of Extremadura, Avda. de las Ciencias, s/n, 10003 Cáceres, Spain
| | - Alicia Rodríguez
- Food Hygiene and Safety, Meat and Meat Products Research Institute, Faculty of Veterinary Science, University of Extremadura, Avda. de las Ciencias, s/n, 10003 Cáceres, Spain.
| | - Alberto Alía
- Food Hygiene and Safety, Meat and Meat Products Research Institute, Faculty of Veterinary Science, University of Extremadura, Avda. de las Ciencias, s/n, 10003 Cáceres, Spain
| | - Mónica Martínez-Blanco
- Instituto de Investigación en Ciencias de la Alimentación (CIAL) (CSIC-UAM), Madrid, Spain
| | - Daniel Lozano-Ojalvo
- Instituto de Investigación en Ciencias de la Alimentación (CIAL) (CSIC-UAM), Madrid, Spain
| | - Juan J Córdoba
- Food Hygiene and Safety, Meat and Meat Products Research Institute, Faculty of Veterinary Science, University of Extremadura, Avda. de las Ciencias, s/n, 10003 Cáceres, Spain
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11
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Listeria monocytogenes requires the RsbX protein to prevent SigB-activation under non-stressed conditions. J Bacteriol 2021; 204:e0048621. [PMID: 34694900 PMCID: PMC8765406 DOI: 10.1128/jb.00486-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The survival of microbial cells under changing environmental conditions requires an efficient reprogramming of transcription, often mediated by alternative sigma factors. The Gram-positive human pathogen Listeria monocytogenes senses and responds to environmental stress mainly through the alternative sigma factor σB (SigB), which controls expression of the general stress response regulon. SigB activation is achieved through a complex series of phosphorylation/dephosphorylation events culminating in the release of SigB from its anti-sigma factor RsbW. At the top of the signal transduction pathway lies a large multiprotein complex known as the stressosome that is believed to act as a sensory hub for stresses. Following signal detection, stressosome proteins become phosphorylated. Resetting of the stressosome is hypothesized to be exerted by a putative phosphatase, RsbX, which presumably removes phosphate groups from stressosome proteins poststress. We addressed the role of the RsbX protein in modulating the activity of the stressosome and consequently regulating SigB activity in L. monocytogenes. We show that RsbX is required to reduce SigB activation levels under nonstress conditions and that it is required for appropriate SigB-mediated stress adaptation. A strain lacking RsbX displayed impaired motility and biofilm formation and also an increased survival at low pH. Our results could suggest that absence of RsbX alters the multiprotein composition of the stressosome without dramatically affecting its phosphorylation status. Overall, the data show that RsbX plays a critical role in modulating the signal transduction pathway by blocking SigB activation under nonstressed conditions. IMPORTANCE Pathogenic bacteria need to sense and respond to stresses to survive harsh environments and also to turn off the response when no longer facing stress. Activity of the stress sigma factor SigB in the human pathogen Listeria monocytogenes is controlled by a hierarchic system having a large stress-sensing multiprotein complex known as the stressosome at the top. Following stress exposure, proteins in the stressosome become phosphorylated, leading to SigB activation. We have studied the role of a putative phosphatase, RsbX, which is hypothesized to dephosphorylate stressosome proteins. RsbX is critical not only to switch off the stress response poststress but also to keep the activity of SigB low at nonstressed conditions to prevent unnecessary gene expression and save energy.
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Elements in the LftR Repressor Operator Interface Contributing to Regulation of Aurantimycin Resistance in Listeria monocytogenes. J Bacteriol 2021; 203:JB.00503-20. [PMID: 33649145 DOI: 10.1128/jb.00503-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/18/2021] [Indexed: 12/12/2022] Open
Abstract
The bacterium Listeria monocytogenes ubiquitously occurs in the environment but can cause severe invasive disease in susceptible individuals when ingested. We recently identified the L. monocytogenes genes lieAB and lftRS, encoding a multidrug resistance ABC transporter and a regulatory module, respectively. These genes jointly mediate resistance against aurantimycin, an antibiotic produced by the soil-dwelling species Streptomyces aurantiacus, and thus contribute to the survival of L. monocytogenes in its natural habitat, the soil. Repression of lieAB and lftRS is exceptionally tight but strongly induced in the presence of aurantimycin. Repression depends on LftR, which belongs to subfamily 2 of the PadR-like transcriptional repressors. To better understand this interesting class of transcriptional repressors, we here deduce the LftR operator sequence from a systematic truncation and mutation analysis of the P lieAB promoter. The sequence identified is also present in the P lftRS promoter but not found elsewhere in the chromosome. Mutational analysis of the putative operator in the P lftRS promoter confirmed its relevance for LftR-dependent repression. The proposed operator sequence was sufficient for DNA binding by LftR in vitro, and a mutation in this sequence affected aurantimycin resistance. Our results provide further insights into the transcriptional adaptation of an important human pathogen to survive the conditions in its natural reservoir.IMPORTANCE Listeria monocytogenes is an environmental bacterium that lives in the soil but can infect humans upon ingestion, and this can lead to severe invasive disease. Adaptation to these entirely different habitats involves massive reprogramming of transcription. Among the differentially expressed genes is the lieAB operon, which encodes a transporter for the detoxification of aurantimycin, an antimicrobial compound produced by soil-dwelling competitors. While lieAB is important for survival in the environment, its expression is detrimental during infection. We here identify critical elements in the lieAB promoter and its transcriptional regulator LftR that contribute to habitat-specific expression of the lieAB genes. These results further clarify the molecular mechanisms underlying the aurantimycin resistance of L. monocytogenes.
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Krawczyk-Balska A, Ładziak M, Burmistrz M, Ścibek K, Kallipolitis BH. RNA-Mediated Control in Listeria monocytogenes: Insights Into Regulatory Mechanisms and Roles in Metabolism and Virulence. Front Microbiol 2021; 12:622829. [PMID: 33935989 PMCID: PMC8079631 DOI: 10.3389/fmicb.2021.622829] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/16/2021] [Indexed: 02/01/2023] Open
Abstract
Listeria monocytogenes is an intracellular pathogen that is well known for its adaptability to life in a broad spectrum of different niches. RNA-mediated regulatory mechanisms in L. monocytogenes play important roles in successful adaptation providing fast and versatile responses to a changing environment. Recent findings indicate that non-coding RNAs (ncRNAs) regulate a variety of processes in this bacterium, such as environmental sensing, metabolism and virulence, as well as immune responses in eukaryotic cells. In this review, the current knowledge on RNA-mediated regulation in L. monocytogenes is presented, with special focus on the roles and mechanisms underlying modulation of metabolism and virulence. Collectively, these findings point to ncRNAs as important gene regulatory elements in L. monocytogenes, both outside and inside an infected host. However, the involvement of regulatory ncRNAs in bacterial physiology and virulence is still underestimated and probably will be better assessed in the coming years, especially in relation to discovering the regulatory functions of 5′ and 3′ untranslated regions and excludons, and by exploring the role of ncRNAs in interaction with both bacterial and host proteins.
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Affiliation(s)
- Agata Krawczyk-Balska
- Department of Molecular Microbiology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Magdalena Ładziak
- Department of Molecular Microbiology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Michał Burmistrz
- Department of Molecular Microbiology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Katarzyna Ścibek
- Department of Molecular Microbiology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Birgitte H Kallipolitis
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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14
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Bacterial Microcompartments Coupled with Extracellular Electron Transfer Drive the Anaerobic Utilization of Ethanolamine in Listeria monocytogenes. mSystems 2021; 6:6/2/e01349-20. [PMID: 33850044 PMCID: PMC8547011 DOI: 10.1128/msystems.01349-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Ethanolamine (EA) is a valuable microbial carbon and nitrogen source derived from cell membranes. EA catabolism is suggested to occur in a cellular metabolic subsystem called a bacterial microcompartment (BMC), and the activation of EA utilization (eut) genes is linked to bacterial pathogenesis. Despite reports showing that the activation of eut is regulated by a vitamin B12-binding riboswitch and that upregulation of eut genes occurs in mice, it remains unknown whether EA catabolism is BMC dependent in Listeria monocytogenes Here, we provide evidence for BMC-dependent anaerobic EA utilization via metabolic analysis, proteomics, and electron microscopy. First, we show vitamin B12-induced activation of the eut operon in L. monocytogenes coupled to the utilization of EA, thereby enabling growth. Next, we demonstrate BMC formation connected with EA catabolism with the production of acetate and ethanol in a molar ratio of 2:1. Flux via the ATP-generating acetate branch causes an apparent redox imbalance due to the reduced regeneration of NAD+ in the ethanol branch resulting in a surplus of NADH. We hypothesize that the redox imbalance is compensated by linking eut BMCs to anaerobic flavin-based extracellular electron transfer (EET). Using L. monocytogenes wild-type, BMC mutant, and EET mutant strains, we demonstrate an interaction between BMCs and EET and provide evidence for a role of Fe3+ as an electron acceptor. Taken together, our results suggest an important role of BMC-dependent EA catabolism in L. monocytogenes growth in anaerobic environments like the human gastrointestinal tract, with a crucial role for the flavin-based EET system in redox balancing.IMPORTANCE Listeria monocytogenes is a foodborne pathogen causing severe illness, and as such, it is crucial to understand the molecular mechanisms contributing to pathogenicity. One carbon source that allows L. monocytogenes to grow in humans is ethanolamine (EA), which is derived from phospholipids present in eukaryotic cell membranes. It is hypothesized that EA utilization occurs in bacterial microcompartments (BMCs), self-assembling subcellular proteinaceous structures and analogs of eukaryotic organelles. Here, we demonstrate that BMC-driven utilization of EA in L. monocytogenes results in increased energy production essential for anaerobic growth. However, exploiting BMCs and the encapsulated metabolic pathways also requires the balancing of oxidative and reductive pathways. We now provide evidence that L. monocytogenes copes with this by linking BMC activity to flavin-based extracellular electron transfer (EET) using iron as an electron acceptor. Our results shed new light on an important molecular mechanism that enables L. monocytogenes to grow using host-derived phospholipid degradation products.
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15
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An mRNA-mRNA Interaction Couples Expression of a Virulence Factor and Its Chaperone in Listeria monocytogenes. Cell Rep 2021; 30:4027-4040.e7. [PMID: 32209466 PMCID: PMC8722363 DOI: 10.1016/j.celrep.2020.03.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 01/27/2020] [Accepted: 02/28/2020] [Indexed: 01/21/2023] Open
Abstract
Bacterial pathogens often employ RNA regulatory elements located in the 5' untranslated regions (UTRs) to control gene expression. Using a comparative structural analysis, we examine the structure of 5' UTRs at a global scale in the pathogenic bacterium Listeria monocytogenes under different conditions. In addition to discovering an RNA thermoswitch and detecting simultaneous interaction of ribosomes and small RNAs with mRNA, we identify structural changes in the 5' UTR of an mRNA encoding the post-translocation chaperone PrsA2 during infection conditions. We demonstrate that the 5' UTR of the prsA2 mRNA base pairs with the 3' UTR of the full-length hly mRNA encoding listeriolysin O, thus preventing RNase J1-mediated degradation of the prsA2 transcript. Mutants lacking the hly-prsA2 interaction exhibit reduced virulence properties. This work highlights an additional level of RNA regulation, where the mRNA encoding a chaperone is stabilized by the mRNA encoding its substrate.
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16
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Vieira KCDO, Silva HRAD, Rocha IPM, Barboza E, Eller LKW. Foodborne pathogens in the omics era. Crit Rev Food Sci Nutr 2021; 62:6726-6741. [PMID: 33783282 DOI: 10.1080/10408398.2021.1905603] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Outbreaks and deaths related to Foodborne Diseases (FBD) occur constantly in the world, as a result of the consumption of contaminated foodstuffs with pathogens such as Listeria monocytogenes, Escherichia coli, Staphylococcus aureus, Salmonella spp, Clostridium spp. and Campylobacter spp. The purpose of this review is to discuss the main omic techniques applied in foodborne pathogen and to demonstrate their functionalities through the food chain and to guarantee the food safety. The main techniques presented are genomic, transcriptomic, secretomic, proteomic, and metabolomic, which together, in the field of food and nutrition, are known as "Foodomics." This review had highlighted the potential of omics to integrate variables that contribute to food safety and to enable us to understand their application on foodborne diseases. The appropriate use of these techniques had driven the definition of critical parameters to achieve successful results in the improvement of consumers health, costs and to obtain safe and high-quality products.
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Affiliation(s)
| | | | | | - Emmanuel Barboza
- Health Sciences Faculty, University of Western Sao Paulo, Presidente Prudente, Sao Paulo, Brazil
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17
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Millar JA, Raghavan R. Modulation of Bacterial Fitness and Virulence Through Antisense RNAs. Front Cell Infect Microbiol 2021; 10:596277. [PMID: 33747974 PMCID: PMC7968456 DOI: 10.3389/fcimb.2020.596277] [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: 08/18/2020] [Accepted: 12/30/2020] [Indexed: 01/22/2023] Open
Abstract
Regulatory RNAs contribute to gene expression control in bacteria. Antisense RNAs (asRNA) are a class of regulatory RNAs that are transcribed from opposite strands of their target genes. Typically, these untranslated transcripts bind to cognate mRNAs and rapidly regulate gene expression at the post-transcriptional level. In this article, we review asRNAs that modulate bacterial fitness and increase virulence. We chose examples that underscore the variety observed in nature including, plasmid- and chromosome-encoded asRNAs, a riboswitch-regulated asRNA, and asRNAs that require other RNAs or RNA-binding proteins for stability and activity. We explore how asRNAs improve bacterial fitness and virulence by modulating plasmid acquisition and maintenance, regulating transposon mobility, increasing resistance against bacteriophages, controlling flagellar production, and regulating nutrient acquisition. We conclude with a brief discussion on how this knowledge is helping to inform current efforts to develop new therapeutics.
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Affiliation(s)
- Jess A Millar
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, United States.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
| | - Rahul Raghavan
- Department of Biology and Center for Life in Extreme Environments, Portland State University, Portland, OR, United States.,Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States
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18
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Henderson LO, Gaballa A, Orsi RH, Boor KJ, Wiedmann M, Guariglia-Oropeza V. Transcriptional profiling of the L. monocytogenes PrfA regulon identifies six novel putative PrfA-regulated genes. FEMS Microbiol Lett 2020; 367:5998225. [PMID: 33220686 DOI: 10.1093/femsle/fnaa193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/19/2020] [Indexed: 12/28/2022] Open
Abstract
The transcriptional activator Positive Regulatory Factor A (PrfA) regulates expression of genes essential for virulence in Listeria monocytogenes. To define the PrfA regulon, the 10403S wildtype (WT) strain, a constitutively active prfA* mutant, and an isogenic ∆prfA mutant were grown under PrfA-inducing conditions in a medium containing glucose-1-phosphate and pre-treated with 0.2% activated charcoal. RNA-seq-generated transcript levels were compared as follows: (i) prfA* and WT; (ii) WT and ∆prfA and (iii) prfA* and ∆prfA. Significantly higher transcript levels in the induced WT or constitutively active PrfA* were identified for 18 genes and 2 ncRNAs in at least one of the three comparisons. These genes included: (i) 10/12 of the genes previously identified as directly PrfA-regulated; (ii) 2 genes previously identified as PrfA-regulated, albeit likely indirectly; and (iii) 6 genes newly identified as PrfA-regulated, including one (LMRG_0 2046) with a σA-dependent promoter and PrfA box located within an upstream open reading frame. LMRG_0 2046, which encodes a putative cyanate permease, is reported to be downregulated by a σB-dependent anti-sense RNA. This newly identified overlap between the σB and PrfA regulons highlights the complexity of regulatory networks important for fine-tuning bacterial gene expression in response to the rapidly changing environmental conditions associated with infection.
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Affiliation(s)
- L O Henderson
- Department of Food Science, Cornell University, 352 Stocking Hall Ithaca, NY 14853, USA
| | - A Gaballa
- Department of Food Science, Cornell University, 352 Stocking Hall Ithaca, NY 14853, USA
| | - R H Orsi
- Department of Food Science, Cornell University, 352 Stocking Hall Ithaca, NY 14853, USA
| | - K J Boor
- Department of Food Science, Cornell University, 352 Stocking Hall Ithaca, NY 14853, USA
| | - M Wiedmann
- Department of Food Science, Cornell University, 352 Stocking Hall Ithaca, NY 14853, USA
| | - V Guariglia-Oropeza
- Department of Food Science, Cornell University, 352 Stocking Hall Ithaca, NY 14853, USA
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19
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Villoria Recio M, Lee BH, Lillebæk EMS, Kallipolitis BH, Gahan CGM, Ingmer H, Larsen MH. Chitin Attenuates Expression of Listeria monocytogenes Virulence Genes in vitro. Front Microbiol 2020; 11:588906. [PMID: 33343529 PMCID: PMC7744463 DOI: 10.3389/fmicb.2020.588906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 11/12/2020] [Indexed: 11/13/2022] Open
Abstract
External signals are crucial for bacteria to sense their immediate environment and fine-tune gene expression accordingly. The foodborne pathogen Listeria monocytogenes senses a range of environmental cues in order to activate or deactivate the virulence-inducing transcriptional factor PrfA during transition between infectious and saprophytic lifecycles. Chitin is an abundant biopolymer formed from linked β-(1-4)-N-acetyl-D-glucosamine residues associated with fungi, the exoskeleton of insects and often incorporated into foods as a thickener or stabilizer. L. monocytogenes evolved to hydrolyse chitin, presumably, to facilitate nutrient acquisition from competitive environments such as soil where the polymer is abundant. Since mammals do not produce chitin, we reasoned that the polymer could serve as an environmental signal contributing to repression of L. monocytogenes PrfA-dependent expression. This study shows a significant downregulation of the core PrfA-regulon during virulence-inducing conditions in vitro in the presence of chitin. Our data suggest this phenomenon occurs through a mechanism that differs from PTS-transport of oligosaccharides generated from either degradation or chitinase-mediated hydrolysis of the polymer. Importantly, an indication that chitin can repress virulence expression of a constitutively active PrfA∗ mutant is shown, possibly mediated via a post-translational modification inhibiting PrfA∗ activity. To our knowledge, this is the first time that chitin is reported as a molecule with anti-virulence properties against a pathogenic bacterium. Thus, our findings identify chitin as a signal which may downregulate the virulence potential of the pathogen and may provide an alternative approach toward reducing disease risk.
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Affiliation(s)
- Miguel Villoria Recio
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, Food Safety and Zoonoses-University of Copenhagen, Frederiksberg, Denmark.,Alimentary Pharmabotic Centre Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Bo-Hyung Lee
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | | | - Birgitte H Kallipolitis
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Cormac G M Gahan
- Alimentary Pharmabotic Centre Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, Food Safety and Zoonoses-University of Copenhagen, Frederiksberg, Denmark
| | - Marianne Halberg Larsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, Food Safety and Zoonoses-University of Copenhagen, Frederiksberg, Denmark
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20
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Muchaamba F, Eshwar AK, von Ah U, Stevens MJA, Tasara T. Evolution of Listeria monocytogenes During a Persistent Human Prosthetic Hip Joint Infection. Front Microbiol 2020; 11:1726. [PMID: 32849369 PMCID: PMC7399150 DOI: 10.3389/fmicb.2020.01726] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/01/2020] [Indexed: 11/23/2022] Open
Abstract
Listeria monocytogenes associated prosthetic joint infections (PJI) are a rare but increasing clinical problem of listeriosis. We characterized two isolates of the same L. monocytogenes strain isolated within five years of each other from a recurrent human prosthetic joint infection. The two isolates although clonally identical were phenotypically distinct confirming that the original infection strain had evolved within the human host PJI environment giving rise to a phenotypically distinct variant. The recurrent PJI isolate displayed various phenotypic differences compared to the parental original PJI isolate including diminished growth and carbon source metabolism, as well as altered morphology and increased stress sensitivity. The PJI isolates were both diminished in virulence due to an identical truncation mutation in the major virulence regulator PrfA. Genome wide sequence comparison provided conclusive evidence that the two isolates were identical clonal descendants of the same L. monocytogenes strain that had evolved through acquisition of various single nucleotide polymorphisms (SNPs) as well as insertion and deletion events (InDels) during a persistent human PJI. Acquired genetic changes included a specific mutation causing premature stop codon (PMSC) and truncation of RNAse J1 protein. Based on analysis of this naturally truncated as well as other complete RNAse J1 deletion mutants we show that the long-term survival of this specific L. monocytogenes strain within the prosthetic joint might in part be explained by the rnjA PMSC mutation that diminishes virulence and activation of the host immune system in a zebrafish embryo localized infection model. Overall our analysis of this special natural case provides insights into random mutation events and molecular mechanisms that might be associated with the adaptation and short-term evolution of this specific L. monocytogenes strain within a persistent human PJI environment.
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Affiliation(s)
- Francis Muchaamba
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Athmanya K. Eshwar
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | | | - Marc J. A. Stevens
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Taurai Tasara
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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The transcriptome of Listeria monocytogenes during co-cultivation with cheese rind bacteria suggests adaptation by induction of ethanolamine and 1,2-propanediol catabolism pathway genes. PLoS One 2020; 15:e0233945. [PMID: 32701964 PMCID: PMC7377500 DOI: 10.1371/journal.pone.0233945] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/01/2020] [Indexed: 02/07/2023] Open
Abstract
The survival of Listeria (L.) monocytogenes in foods and food production environments (FPE) is dependent on several genes that increase tolerance to stressors; this includes competing with intrinsic bacteria. We aimed to uncover genes that are differentially expressed (DE) in L. monocytogenes sequence type (ST) 121 strain 6179 when co-cultured with cheese rind bacteria. L. monocytogenes was cultivated in broth or on plates with either a Psychrobacter or Brevibacterium isolate from cheese rinds. RNA was extracted from co-cultures in broth after two or 12 hours and from plates after 24 and 72 hours. Broth co-cultivations with Brevibacterium or Psychrobacter yielded up to 392 and 601 DE genes, while plate co-cultivations significantly affected the expression of up to 190 and 485 L. monocytogenes genes, respectively. Notably, the transcription of virulence genes encoding the Listeria adhesion protein and Listeriolysin O were induced during plate and broth co-cultivations. The expression of several systems under the control of the global stress gene regulator, σB, increased during co-cultivation. A cobalamin-dependent gene cluster, responsible for the catabolism of ethanolamine and 1,2-propanediol, was upregulated in both broth and plate co-cultures conditions. Finally, a small non-coding (nc)RNA, Rli47, was induced after 72 hours of co-cultivation on plates and accounted for 50-90% of the total reads mapped to L. monocytogenes. A recent study has shown that Rli47 may contribute to L. monocytogenes stress survival by slowing growth during stress conditions through the suppression of branch-chained amino acid biosynthesis. We hypothesize that Rli47 may have an impactful role in the response of L. monocytogenes to co-cultivation by regulating a complex network of metabolic and virulence mechanisms.
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22
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Goebel W. From the beginning to the present state of molecular microbial pathogenesis-A tribute to Pascale Cossart. Mol Microbiol 2020; 113:538-540. [PMID: 32185837 DOI: 10.1111/mmi.14450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 01/09/2020] [Indexed: 11/26/2022]
Abstract
The universe of Molecular Microbial Pathogenesis is filled with many female and male stars. But there are two particularly bright shining supernovae-like stars: the late Stanley Falkow and the very lively and creative Pascale Cossart. These two outstanding luminaries, surrounded by numerous planets, do not only belong to different scientific generations but their splendor also comes from very different scientific concepts. Stanley Falkow, often referred to as the 'Father of Molecular Microbial Pathogenesis', made many groundbreaking contributions to this field by addressing almost all important bacterial pathogens. Pascale Cossart, who could be called in analogy the 'Queen of Modern Molecular Microbial Pathogenesis' by combining the Microbiology and Cell Biology, concentrates in her similarly impressive scientific work essentially on a single bacterial species which she studied and still studies in great depth: the facultative intracellular bacterial pathogen Listeria monocytogenes-and the vast majority of her most prominent publications deals with this pathogen in almost all facets. It is certainly not an exaggeration to say that she together with her co-workers and collaborators developed this model bacterium into a paradigm among the intracellular bacterial pathogens.
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Affiliation(s)
- Werner Goebel
- Max von Pettenkofer-Institut, Ludwig-Maximilians-Universität, München, Germany
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23
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Hadjilouka A, Gkolfakis P, Patlaka A, Grounta A, Vourli G, Paramithiotis S, Touloumi G, Triantafyllou K, Drosinos EH. In Vitro Gene Transcription of Listeria monocytogenes after Exposure to Human Gastric and Duodenal Aspirates. J Food Prot 2020; 83:89-100. [PMID: 31855615 DOI: 10.4315/0362-028x.jfp-19-210] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The aim of the present study was to assess, for the first time to our knowledge, Listeria monocytogenes CFU changes, as well as to determine the transcription of key virulence genes, namely, sigB, prfA, hly, plcA, plcB, inlA, inlB, inlC, inlJ, inlP, and lmo2672 after in vitro exposure to human gastric and duodenal aspirates. Furthermore, investigations of the potential correlation between CFU changes and gene regulation with factors influencing gastric (proton pump inhibitor intake and presence of gastric atrophy) and duodenal pH were the secondary study aims. Gastric and duodenal fluids that were collected from 25 individuals undergoing upper gastrointestinal endoscopy were inoculated with L. monocytogenes serotype 4b strain LQC 15257 at 9 log CFU·mL-1 and incubated at 37°C for 100 min and 2 h, respectively, with the time corresponding to the actual exposure time to gastric and duodenal fluids in the human gastrointestinal tract. Sampling was performed upon gastric fluid inoculation, after incubation of the inoculated gastric fluids, upon pathogen resuspension in duodenal fluids and after incubation of the inoculated duodenal fluids. L. monocytogenes CFU changes were assessed by colony counting, as well as reverse transcription quantitative PCR by using inlB as a target. Gene transcription was assessed by reverse transcription quantitative PCR. In 56% of the cases, reduction of the pathogen CFU occurred immediately after exposure to gastric aspirate. Upregulation of hly and inlC was observed in 52 and 58% of the cases, respectively. On the contrary, no upregulation or downregulation was noticed regarding sigB, prfA, plcA, plcB, inlA, inlB, inlJ, inlP, and lmo2672. In addition, sigB and plcA transcription was positively and negatively associated, respectively, with an increase of the pH value, and inlA transcription was negatively associated with the presence of gastric atrophy. Finally, a positive correlation between the transcriptomic responses of plcB, inlA, inlB, inlC, inlJ, inlP, and lmo2672 was detected. This study revealed that the CFU of the pathogen was negatively affected after exposure to human gastroduodenal aspirates, as well as significant correlations between the characteristics of the aspirates with the virulence potential of the pathogen.
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Affiliation(s)
- Agni Hadjilouka
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens 118 55, Greece (ORCID: https://orcid.org/0000-0002-6062-1701 [E.H.D.])
| | - Paraskevas Gkolfakis
- Hepatogastroenterology Unit, Second Department of Internal Medicine-Propaedeutic, Research Institute and Diabetes Center "Attikon" University General Hospital, Haidari 124 62, Greece
| | - Apostolia Patlaka
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens 118 55, Greece (ORCID: https://orcid.org/0000-0002-6062-1701 [E.H.D.])
| | - Athena Grounta
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens 118 55, Greece (ORCID: https://orcid.org/0000-0002-6062-1701 [E.H.D.])
| | - Georgia Vourli
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens 115 27, Greece
| | - Spiros Paramithiotis
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens 118 55, Greece (ORCID: https://orcid.org/0000-0002-6062-1701 [E.H.D.])
| | - Giota Touloumi
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens 115 27, Greece
| | - Konstantinos Triantafyllou
- Hepatogastroenterology Unit, Second Department of Internal Medicine-Propaedeutic, Research Institute and Diabetes Center "Attikon" University General Hospital, Haidari 124 62, Greece
| | - Eleftherios H Drosinos
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens 118 55, Greece (ORCID: https://orcid.org/0000-0002-6062-1701 [E.H.D.])
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Sæbø Pettersen K, Sundaram AYM, Skjerdal T, Wasteson Y, Kijewski A, Lindbäck T, Aspholm M. Exposure to Broad-Spectrum Visible Light Causes Major Transcriptomic Changes in Listeria monocytogenes EGDe. Appl Environ Microbiol 2019; 85:e01462-19. [PMID: 31492665 PMCID: PMC6821972 DOI: 10.1128/aem.01462-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 08/09/2019] [Indexed: 01/22/2023] Open
Abstract
Listeria monocytogenes, the causative agent of the serious foodborne disease listeriosis, can rapidly adapt to a wide range of environmental stresses, including visible light. This study shows that exposure of the L. monocytogenes EGDe strain to low-intensity, broad-spectrum visible light inhibited bacterial growth and caused altered multicellular behavior during growth on semisolid agar compared to when the bacteria were grown in complete darkness. These light-dependent changes were observed regardless of the presence of the blue light receptor (Lmo0799) and the stressosome regulator sigma B (SigB), which have been suggested to be important for the ability of L. monocytogenes to respond to blue light. A genome-wide transcriptional analysis revealed that exposure of L. monocytogenes EGDe to broad-spectrum visible light caused altered expression of 2,409 genes belonging to 18 metabolic pathways compared to bacteria grown in darkness. The light-dependent differentially expressed genes are involved in functions such as glycan metabolism, cell wall synthesis, chemotaxis, flagellar synthesis, and resistance to oxidative stress. Exposure to light conferred reduced bacterial motility in semisolid agar, which correlates well with the light-dependent reduction in transcript levels of flagellar and chemotaxis genes. Similar light-induced reduction in growth and motility was also observed in two different L. monocytogenes food isolates, suggesting that these responses are typical for L. monocytogenes Together, the results show that even relatively small doses of broad-spectrum visible light cause genome-wide transcriptional changes, reduced growth, and motility in L. monocytogenesIMPORTANCE Despite major efforts to control L. monocytogenes, this pathogen remains a major problem for the food industry, where it poses a continuous risk of food contamination. The ability of L. monocytogenes to sense and adapt to different stressors in the environment enables it to persist in many different niches, including food production facilities and in food products. The present study shows that exposure of L. monocytogenes to low-intensity broad-spectrum visible light reduces its growth and motility and alters its multicellular behavior. Light exposure also caused genome-wide changes in transcript levels, affecting multiple metabolic pathways, which are likely to influence the bacterial physiology and lifestyle. In practical terms, the data presented in this study suggest that broad-spectrum visible light is an important environmental variable to consider as a strategy to improve food safety by reducing L. monocytogenes contamination in food production environments.
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Affiliation(s)
- Kristin Sæbø Pettersen
- Norwegian Veterinary Institute, Oslo, Norway
- Norwegian University of Life Sciences, Oslo, Norway
| | - Arvind Y M Sundaram
- Norwegian Sequencing Centre, Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
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25
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Exploring Listeria monocytogenes Transcriptomes in Correlation with Divergence of Lineages and Virulence as Measured in Galleria mellonella. Appl Environ Microbiol 2019; 85:AEM.01370-19. [PMID: 31471303 DOI: 10.1128/aem.01370-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/25/2019] [Indexed: 12/24/2022] Open
Abstract
As for many opportunistic pathogens, the virulence potential of Listeria monocytogenes is highly heterogeneous between isolates and correlated, to some extent, with phylogeny and gene repertoires. In sharp contrast with copious data on intraspecies genome diversity, little is known about transcriptome diversity despite the role of complex genetic regulation in pathogenicity. The current study implemented RNA sequencing to characterize the transcriptome profiles of 33 isolates under optimal in vitro growth conditions. Transcript levels of conserved single-copy genes were comprehensively explored from several perspectives, including phylogeny, in silico-predicted virulence category based on epidemiological multilocus sequence typing (MLST) data, and in vivo virulence phenotype assessed in Galleria mellonella Comparing baseline transcriptomes between isolates was intrinsically more complex than standard genome comparison because of the inherent plasticity of gene expression in response to environmental conditions. We show that the relevance of correlation analyses and their statistical power can be enhanced by using principal-component analysis to remove the first level of irrelevant, highly coordinated changes linked to growth phase. Our results highlight the major contribution of transcription factors with key roles in virulence to the diversity of transcriptomes. Divergence in the basal transcript levels of a substantial fraction of the transcriptome was observed between lineages I and II, echoing previously reported epidemiological differences. Correlation analysis with in vivo virulence identified numerous sugar metabolism-related genes, suggesting that specific pathways might play roles in the onset of infection in G. mellonella IMPORTANCE Listeria monocytogenes is a multifaceted bacterium able to proliferate in a wide range of environments from soil to mammalian host cells. The accumulated genomic data underscore the contribution of intraspecies variations in gene repertoire to differential adaptation strategies between strains, including infection and stress resistance. It seems very likely that the fine-tuning of the transcriptional regulatory network is also a key component of the phenotypic diversity, albeit more difficult to investigate than genome content. Some studies reported incongruity in the basal transcriptome between isolates, suggesting a putative relationship with phenotypes, but small isolate numbers hampered proper correlation analyses with respect to their characteristics. The present study is the embodiment of the promising approach that consists of analyzing correlations between transcriptomes and various isolate characteristics. Statistically significant correlations were found with phylogenetic groups, epidemiological evidence of virulence potential, and virulence in Galleria mellonella larvae used as an in vivo model.
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26
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Chakravarty S, Massé E. RNA-Dependent Regulation of Virulence in Pathogenic Bacteria. Front Cell Infect Microbiol 2019; 9:337. [PMID: 31649894 PMCID: PMC6794450 DOI: 10.3389/fcimb.2019.00337] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 09/18/2019] [Indexed: 12/19/2022] Open
Abstract
During infection, bacterial pathogens successfully sense, respond and adapt to a myriad of harsh environments presented by the mammalian host. This exquisite level of adaptation requires a robust modulation of their physiological and metabolic features. Additionally, virulence determinants, which include host invasion, colonization and survival despite the host's immune responses and antimicrobial therapy, must be optimally orchestrated by the pathogen at all times during infection. This can only be achieved by tight coordination of gene expression. A large body of evidence implicate the prolific roles played by bacterial regulatory RNAs in mediating gene expression both at the transcriptional and post-transcriptional levels. This review describes mechanistic and regulatory aspects of bacterial regulatory RNAs and highlights how these molecules increase virulence efficiency in human pathogens. As illustrative examples, Staphylococcus aureus, Listeria monocytogenes, the uropathogenic strain of Escherichia coli, Helicobacter pylori, and Pseudomonas aeruginosa have been selected.
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Affiliation(s)
- Shubham Chakravarty
- RNA Group, Department of Biochemistry, Faculty of Medicine and Health Sciences, CRCHUS, University of Sherbrooke, Sherbrooke, QC, Canada
| | - Eric Massé
- RNA Group, Department of Biochemistry, Faculty of Medicine and Health Sciences, CRCHUS, University of Sherbrooke, Sherbrooke, QC, Canada
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Cross Talk between SigB and PrfA in Listeria monocytogenes Facilitates Transitions between Extra- and Intracellular Environments. Microbiol Mol Biol Rev 2019; 83:83/4/e00034-19. [PMID: 31484692 DOI: 10.1128/mmbr.00034-19] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The foodborne pathogen Listeria monocytogenes can modulate its transcriptome and proteome to ensure its survival during transmission through vastly differing environmental conditions. While L. monocytogenes utilizes a large array of regulators to achieve survival and growth in different intra- and extrahost environments, the alternative sigma factor σB and the transcriptional activator of virulence genes protein PrfA are two key transcriptional regulators essential for responding to environmental stress conditions and for host infection. Importantly, emerging evidence suggests that the shift from extrahost environments to the host gastrointestinal tract and, subsequently, to intracellular environments requires regulatory interplay between σB and PrfA at transcriptional, posttranscriptional, and protein activity levels. Here, we review the current evidence for cross talk and interplay between σB and PrfA and their respective regulons and highlight the plasticity of σB and PrfA cross talk and the role of this cross talk in facilitating successful transition of L. monocytogenes from diverse extrahost to diverse extra- and intracellular host environments.
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Hauf S, Herrmann J, Miethke M, Gibhardt J, Commichau FM, Müller R, Fuchs S, Halbedel S. Aurantimycin resistance genes contribute to survival of Listeria monocytogenes during life in the environment. Mol Microbiol 2019; 111:1009-1024. [PMID: 30648305 DOI: 10.1111/mmi.14205] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2019] [Indexed: 12/16/2022]
Abstract
Bacteria can cope with toxic compounds such as antibiotics by inducing genes for their detoxification. A common detoxification strategy is compound excretion by ATP-binding cassette (ABC) transporters, which are synthesized upon compound contact. We previously identified the multidrug resistance ABC transporter LieAB in Listeria monocytogenes, a Gram-positive bacterium that occurs ubiquitously in the environment, but also causes severe infections in humans upon ingestion. Expression of the lieAB genes is strongly induced in cells lacking the PadR-type transcriptional repressor LftR, but compounds leading to relief of this repression in wild-type cells were not known. Using RNA-Seq and promoter-lacZ fusions, we demonstrate highly specific repression of the lieAB and lftRS promoters through LftR. Screening of a natural compound library yielded the depsipeptide aurantimycin A - synthesized by the soil-dwelling Streptomyces aurantiacus - as the first known naturally occurring inducer of lieAB expression. Genetic and phenotypic experiments concordantly show that aurantimycin A is a substrate of the LieAB transporter and thus, lftRS and lieAB represent the first known genetic module conferring and regulating aurantimycin A resistance. Collectively, these genes may support the survival of L. monocytogenes when it comes into contact with antibiotic-producing bacteria in the soil.
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Affiliation(s)
- Samuel Hauf
- FG11 Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, Burgstrasse 37, Wernigerode, 38855, Germany
| | - Jennifer Herrmann
- Department of Microbial Natural Products, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University, Campus E8.1, Saarbrücken, 66123, Germany.,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, 38124, Germany
| | - Marcus Miethke
- Department of Microbial Natural Products, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University, Campus E8.1, Saarbrücken, 66123, Germany.,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, 38124, Germany
| | - Johannes Gibhardt
- Department of General Microbiology, University of Göttingen, Grisebachstrasse 8, Göttingen, 37077, Germany
| | - Fabian M Commichau
- Department of General Microbiology, University of Göttingen, Grisebachstrasse 8, Göttingen, 37077, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University, Campus E8.1, Saarbrücken, 66123, Germany.,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, 38124, Germany
| | - Stephan Fuchs
- FG13 Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Burgstrasse 37, Wernigerode, 38855, Germany
| | - Sven Halbedel
- FG11 Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, Burgstrasse 37, Wernigerode, 38855, Germany
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Abstract
Bacterial regulatory RNAs are key players in adaptation to changing environmental conditions and response to diverse cellular stresses. However, while regulatory RNAs of bacterial pathogens have been intensely studied under defined conditions in vitro, characterization of their role during the infection of eukaryotic host organisms is lagging behind. This review summarizes our current understanding of the contribution of the different classes of regulatory RNAs and RNA-binding proteins to bacterial virulence and illustrates their role in infection by reviewing the mechanisms of some prominent representatives of each class. Emerging technologies are described that bear great potential for global, unbiased studies of virulence-related RNAs in bacterial model and nonmodel pathogens in the future. The review concludes by deducing common principles of RNA-mediated gene expression control of virulence programs in different pathogens, and by defining important open questions for upcoming research in the field.
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30
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Warrier I, Ram-Mohan N, Zhu Z, Hazery A, Echlin H, Rosch J, Meyer MM, van Opijnen T. The Transcriptional landscape of Streptococcus pneumoniae TIGR4 reveals a complex operon architecture and abundant riboregulation critical for growth and virulence. PLoS Pathog 2018; 14:e1007461. [PMID: 30517198 PMCID: PMC6296669 DOI: 10.1371/journal.ppat.1007461] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 12/17/2018] [Accepted: 11/07/2018] [Indexed: 11/21/2022] Open
Abstract
Efficient and highly organized regulation of transcription is fundamental to an organism’s ability to survive, proliferate, and quickly respond to its environment. Therefore, precise mapping of transcriptional units and understanding their regulation is crucial to determining how pathogenic bacteria cause disease and how they may be inhibited. In this study, we map the transcriptional landscape of the bacterial pathogen Streptococcus pneumoniae TIGR4 by applying a combination of high-throughput RNA-sequencing techniques. We successfully map 1864 high confidence transcription termination sites (TTSs), 790 high confidence transcription start sites (TSSs) (742 primary, and 48 secondary), and 1360 low confidence TSSs (74 secondary and 1286 primary) to yield a total of 2150 TSSs. Furthermore, our study reveals a complex transcriptome wherein environment-respondent alternate transcriptional units are observed within operons stemming from internal TSSs and TTSs. Additionally, we identify many putative cis-regulatory RNA elements and riboswitches within 5’-untranslated regions (5’-UTR). By integrating TSSs and TTSs with independently collected RNA-Seq datasets from a variety of conditions, we establish the response of these regulators to changes in growth conditions and validate several of them. Furthermore, to demonstrate the importance of ribo-regulation by 5’-UTR elements for in vivo virulence, we show that the pyrR regulatory element is essential for survival, successful colonization and infection in mice suggesting that such RNA elements are potential drug targets. Importantly, we show that our approach of combining high-throughput sequencing with in vivo experiments can reconstruct a global understanding of regulation, but also pave the way for discovery of compounds that target (ribo-)regulators to mitigate virulence and antibiotic resistance. The canonical relationship between a bacterial operon and the mRNA transcript produced from the operon has become significantly more complex as numerous regulatory mechanisms that impact the stability, translational efficiency, and early termination rates for mRNA transcripts have been described. With the rise of antibiotic resistance, these mechanisms offer new potential targets for antibiotic development. In this study we used a combination of high-throughput sequencing technologies to assess genome-wide transcription start and stop sites, as well as determine condition specific global transcription patterns in the human pathogen Streptococcus pneumoniae. We find that the majority of multi-gene operons have alternative start and stop sites enabling condition specific regulation of genes within the same operon. Furthermore, we identified many putative RNA regulators that are widespread in the S. pneumoniae pan-genome. Finally, we show that separately collected RNA-Seq data enables identification of conditional triggers for regulatory RNAs, and experimentally demonstrate that our approach may be used to identify drug-able RNA targets by establishing that pyrR RNA functionality is critical for successful S. pneumoniae mouse colonization and infection. Thus, our study not only uses genome-wide high-throughput approaches to identify putative RNA regulators, but also establishes the importance of such regulators in S. pneumoniae virulence.
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Affiliation(s)
- Indu Warrier
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Nikhil Ram-Mohan
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Zeyu Zhu
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Ariana Hazery
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Haley Echlin
- Department of Infectious Diseases, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Jason Rosch
- Department of Infectious Diseases, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Michelle M. Meyer
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
- * E-mail: (MMM); (TvO)
| | - Tim van Opijnen
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
- * E-mail: (MMM); (TvO)
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31
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Koomen J, den Besten HM, Metselaar KI, Tempelaars MH, Wijnands LM, Zwietering MH, Abee T. Gene profiling-based phenotyping for identification of cellular parameters that contribute to fitness, stress-tolerance and virulence of Listeria monocytogenes variants. Int J Food Microbiol 2018; 283:14-21. [DOI: 10.1016/j.ijfoodmicro.2018.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/31/2018] [Accepted: 06/06/2018] [Indexed: 10/14/2022]
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32
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Affiliation(s)
- Andrea Barta
- a Max F. Perutz Laboratories, Department of Medical Biochemistry , Medical University of Vienna , Dr. Bohr Gasse 9/3, A-1030 Vienna , Austria
| | - Michael F Jantsch
- b Department of Cell- and Developmental Biology , Center for Anatomy and Cell Biology, Medical University of Vienna , Vienna , Austria
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33
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Abstract
Noncoding RNAs (ncRNAs) regulating virulence have been identified in most pathogens. This review discusses RNA-mediated mechanisms exploited by bacterial pathogens to successfully infect and colonize their hosts. It discusses the most representative RNA-mediated regulatory mechanisms employed by two intracellular [Listeria monocytogenes and Salmonella enterica serovar Typhimurium (S. Typhimurium)] and two extracellular (Vibrio cholerae and Staphylococcus aureus) bacterial pathogens. We review the RNA-mediated regulators (e.g., thermosensors, riboswitches, cis- and trans-encoded RNAs) used for adaptation to the specific niches colonized by these bacteria (intestine, blood, or the intracellular environment, for example) in the framework of the specific pathophysiological aspects of the diseases caused by these microorganisms. A critical discussion of the newest findings in the field of bacterial ncRNAs shows how examples in model pathogens could pave the way for the discovery of new mechanisms in other medically important bacterial pathogens.
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Affiliation(s)
- Juan J Quereda
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Paris F-75015, France; , .,Institut National de la Santé et de la Recherche Médicale, U604, Paris F-75015, France.,Institut National de la Recherche Agronomique, USC2020, Paris F-75015, France
| | - Pascale Cossart
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Paris F-75015, France; , .,Institut National de la Santé et de la Recherche Médicale, U604, Paris F-75015, France.,Institut National de la Recherche Agronomique, USC2020, Paris F-75015, France
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34
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Radoshevich L, Cossart P. Listeria monocytogenes: towards a complete picture of its physiology and pathogenesis. Nat Rev Microbiol 2018; 16:32-46. [PMID: 29176582 DOI: 10.1038/nrmicro.2017.126] [Citation(s) in RCA: 464] [Impact Index Per Article: 77.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Listeria monocytogenes is a food-borne pathogen responsible for a disease called listeriosis, which is potentially lethal in immunocompromised individuals. This bacterium, first used as a model to study cell-mediated immunity, has emerged over the past 20 years as a paradigm in infection biology, cell biology and fundamental microbiology. In this Review, we highlight recent advances in the understanding of human listeriosis and L. monocytogenes biology. We describe unsuspected modes of hijacking host cell biology, ranging from changes in organelle morphology to direct effects on host transcription via a new class of bacterial effectors called nucleomodulins. We then discuss advances in understanding infection in vivo, including the discovery of tissue-specific virulence factors and the 'arms race' among bacteria competing for a niche in the microbiota. Finally, we describe the complexity of bacterial regulation and physiology, incorporating new insights into the mechanisms of action of a series of riboregulators that are critical for efficient metabolic regulation, antibiotic resistance and interspecies competition.
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Affiliation(s)
- Lilliana Radoshevich
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Département de Biologie Cellulaire et Infection, F-75015 Paris, France
- Inserm, U604, F-75015 Paris, France
- French National Institute for Agricultural Research (INRA), Unité sous-contrat 2020, F-75015 Paris, France
- Department of Microbiology and Immunology, University of Iowa Carver College of Medicine, Iowa City, Iowa 52242, USA
| | - Pascale Cossart
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Département de Biologie Cellulaire et Infection, F-75015 Paris, France
- Inserm, U604, F-75015 Paris, France
- French National Institute for Agricultural Research (INRA), Unité sous-contrat 2020, F-75015 Paris, France
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35
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Eshwar AK, Guldimann C, Oevermann A, Tasara T. Cold-Shock Domain Family Proteins (Csps) Are Involved in Regulation of Virulence, Cellular Aggregation, and Flagella-Based Motility in Listeria monocytogenes. Front Cell Infect Microbiol 2017; 7:453. [PMID: 29124040 PMCID: PMC5662587 DOI: 10.3389/fcimb.2017.00453] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/04/2017] [Indexed: 11/13/2022] Open
Abstract
Cold shock-domain family proteins (Csps) are highly conserved nucleic acid binding proteins regulating the expression of various genes including those involved in stress resistance and virulence in bacteria. We show here that Csps are involved in virulence, cell aggregation and flagella-based extracellular motility of Listeria monocytogenes. A L. monocytogenes mutant deleted in all three csp genes (ΔcspABD) is attenuated with respect to human macrophage infection as well as virulence in a zebrafish infection model. Moreover, this mutant is incapable of aggregation and fails to express surface flagella or exhibit swarming motility. An evaluation of double csp gene deletion mutant (ΔcspBD, ΔcspAD and ΔcspAB) strains that produce single csp genes showed that there is redundancy as well as functional differences among the three L. monocytogenes Csps in their contributions to virulence, cellular aggregation, flagella production, and swarming motility. Protein and mRNA expression analysis further showed impaired expression of key virulence and motility genes in the csp mutants. Our observations at protein and mRNA level suggest Csp-dependent expression regulation of these genes at transcriptional and post-transcriptional levels. In a mutant lacking all csp genes (ΔcspABD) as well as those possessing single csp genes (ΔcspBD, ΔcspAD, and ΔcspAB) we detected reduced levels of proteins or activity as well as transcripts from the prfA, hly, mpl, and plcA genes suggesting a Csp-dependent transcriptional regulation of these genes. These csp mutants also had reduced or completely lacked ActA proteins and cell surface flagella but contained elevated actA and flaA mRNA levels compared to the parental wild type strain suggesting Csp involvement in post-transcriptional regulation of these genes. Overall, our results suggest that Csps contribute to the expression regulation of virulence and flagella-associated genes thereby promoting host pathogenicity, cell aggregation and flagella-based motility processes in L. monocytogenes.
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Affiliation(s)
- Athmanya K. Eshwar
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Claudia Guldimann
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Anna Oevermann
- Neuropathology—Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Taurai Tasara
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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36
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David DJV, Cossart P. Recent advances in understanding Listeria monocytogenes infection: the importance of subcellular and physiological context. F1000Res 2017; 6. [PMID: 28781746 PMCID: PMC5516218 DOI: 10.12688/f1000research.11363.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/10/2017] [Indexed: 01/04/2023] Open
Abstract
The bacterial pathogen
Listeria monocytogenes (
Lm) is the causative agent of listeriosis, a rare but fatal foodborne disease. During infection,
Lm can traverse several host barriers and enter the cytosol of a variety of cell types. Thus, consideration of the extracellular and intracellular niches of
Lm is critical for understanding the infection process. Here, we review advances in our understanding of
Lm infection and highlight how the interactions between the host and the pathogen are context dependent. We discuss discoveries of how
Lm senses entry into the host cell cytosol. We present findings concerning how the nature of the various cytoskeleton components subverted by
Lm changes depending on both the stage of infection and the subcellular context. We present discoveries of critical components required for
Lm traversal of physiological barriers. Interactions between the host gut microbiota and
Lm will be briefly discussed. Finally, the importance of
Lm biodiversity and post-genomics approaches as a promising way to discover novel virulence factors will be highlighted.
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Affiliation(s)
- Daryl J V David
- Unité des Interactions Bactéries-Cellules, Department of Cell Biology and Infection, Institut Pasteur, Paris, France
| | - Pascale Cossart
- Unité des Interactions Bactéries-Cellules, Department of Cell Biology and Infection, Institut Pasteur, Paris, France
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37
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Schroeder M, Brooks BD, Brooks AE. The Complex Relationship between Virulence and Antibiotic Resistance. Genes (Basel) 2017; 8:E39. [PMID: 28106797 PMCID: PMC5295033 DOI: 10.3390/genes8010039] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/21/2016] [Accepted: 01/07/2017] [Indexed: 12/17/2022] Open
Abstract
Antibiotic resistance, prompted by the overuse of antimicrobial agents, may arise from a variety of mechanisms, particularly horizontal gene transfer of virulence and antibiotic resistance genes, which is often facilitated by biofilm formation. The importance of phenotypic changes seen in a biofilm, which lead to genotypic alterations, cannot be overstated. Irrespective of if the biofilm is single microbe or polymicrobial, bacteria, protected within a biofilm from the external environment, communicate through signal transduction pathways (e.g., quorum sensing or two-component systems), leading to global changes in gene expression, enhancing virulence, and expediting the acquisition of antibiotic resistance. Thus, one must examine a genetic change in virulence and resistance not only in the context of the biofilm but also as inextricably linked pathologies. Observationally, it is clear that increased virulence and the advent of antibiotic resistance often arise almost simultaneously; however, their genetic connection has been relatively ignored. Although the complexities of genetic regulation in a multispecies community may obscure a causative relationship, uncovering key genetic interactions between virulence and resistance in biofilm bacteria is essential to identifying new druggable targets, ultimately providing a drug discovery and development pathway to improve treatment options for chronic and recurring infection.
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Affiliation(s)
- Meredith Schroeder
- Department of Microbiological Sciences; North Dakota State University, Fargo, ND 58105, USA.
| | - Benjamin D Brooks
- Department of Electrical and Computer Engineering; North Dakota State University, Fargo, ND 58105, USA.
| | - Amanda E Brooks
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND 58105, USA.
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Popitsch N, Bilusic I, Rescheneder P, Schroeder R, Lybecker M. Temperature-dependent sRNA transcriptome of the Lyme disease spirochete. BMC Genomics 2017; 18:28. [PMID: 28056764 PMCID: PMC5216591 DOI: 10.1186/s12864-016-3398-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 12/07/2016] [Indexed: 01/05/2023] Open
Abstract
Background Transmission of Borrelia burgdorferi from its tick vector to a vertebrate host requires extensive reprogramming of gene expression. Small regulatory RNAs (sRNA) have emerged in the last decade as important regulators of bacterial gene expression. Despite the widespread observation of sRNA-mediated gene regulation, only one sRNA has been characterized in the Lyme disease spirochete B. burgdorferi. We employed an sRNA-specific deep-sequencing approach to identify the small RNA transcriptome of B. burgdorferi at both 23 °C and 37 °C, which mimics in vitro the transmission from the tick vector to the mammalian host. Results We identified over 1000 sRNAs in B. burgdorferi revealing large amounts of antisense and intragenic sRNAs, as well as characteristic intergenic and 5′ UTR-associated sRNAs. A large fraction of the novel sRNAs (43%) are temperature-dependent and differentially expressed at the two temperatures, suggesting a role in gene regulation for adaptation during transmission. In addition, many genes important for maintenance of Borrelia during its enzootic cycle are associated with antisense RNAs or 5′ UTR sRNAs. RNA-seq data were validated for twenty-two of the sRNAs via Northern blot analyses. Conclusions Our study demonstrates that sRNAs are abundant and differentially expressed by environmental conditions suggesting that gene regulation via sRNAs is a common mechanism utilized in B. burgdorferi. In addition, the identification of antisense and intragenic sRNAs impacts the broadly used loss-of-function genetic approach used to study gene function and increases the coding potential of a small genome. To facilitate access to the analyzed RNA-seq data we have set-up a website at http://www.cibiv.at/~niko/bbdb/ that includes a UCSC browser track hub. By clicking on the respective link, researchers can interactively inspect the data in the UCSC genome browser (Kent et al., Genome Res 12:996-1006, 2002). Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3398-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Niko Popitsch
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ivana Bilusic
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Philipp Rescheneder
- Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, Medical University of Vienna, University of Vienna, Vienna, Austria
| | - Renée Schroeder
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Meghan Lybecker
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, USA.
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Lebreton A, Stavru F, Brisse S, Cossart P. 1926-2016: 90 Years of listeriology. Microbes Infect 2016; 18:711-723. [PMID: 27876526 DOI: 10.1016/j.micinf.2016.10.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 10/26/2016] [Indexed: 01/28/2023]
Abstract
ISOPOL - for "International Symposium on Problems of Listeria and Listeriosis" - meetings gather every three years since 1957 participants from all over the world and allow exchange and update on a wide array of topics concerning Listeria and listeriosis, ranging from epidemiology, diagnostic and typing methods, to genomics, post-genomics, fundamental microbiology, cell biology and pathogenesis. The XIXth ISOPOL meeting took place in Paris from June 14th to 17th, 2016 at Institut Pasteur. We provide here a report of the talks that were given during the meeting, which represents an up-to-date overview of ongoing research on this important pathogen and biological model.
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Affiliation(s)
- Alice Lebreton
- École normale supérieure, PSL Research University, CNRS, Inserm, Institut de Biologie de l'École Normale Supérieure (IBENS), Équipe Infection et Devenir de l'ARN, 75005 Paris, France; INRA, IBENS, 75005 Paris, France
| | - Fabrizia Stavru
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, 75015 Paris, France; Inserm, U604, 75015 Paris, France; INRA, USC2020, 75015 Paris, France; CNRS, SNC5101, Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Molecular Prevention and Therapy of Human Diseases, 75724 Paris, France; Institut Pasteur, Microbial Evolutionary Genomics, 75724 Paris, France; CNRS, UMR 3525, Paris, France
| | - Pascale Cossart
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, 75015 Paris, France; Inserm, U604, 75015 Paris, France; INRA, USC2020, 75015 Paris, France.
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