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Anderson CJ, Boeckaerts L, Chin P, Cardas JB, Xie W, Gonçalves A, Blancke G, Benson S, Rogatti S, Simpson MS, Davey A, Choi SM, Desmet S, Bushman SD, Goeminne G, Vandenabeele P, Desai MS, Vereecke L, Ravichandran KS. Metabolite-based inter-kingdom communication controls intestinal tissue recovery following chemotherapeutic injury. Cell Host Microbe 2024:S1931-3128(24)00285-3. [PMID: 39197455 DOI: 10.1016/j.chom.2024.07.026] [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: 01/04/2024] [Revised: 06/12/2024] [Accepted: 07/31/2024] [Indexed: 09/01/2024]
Abstract
Cytotoxic chemotherapies have devastating side effects, particularly within the gastrointestinal tract. Gastrointestinal toxicity includes the death and damage of the epithelium and an imbalance in the intestinal microbiota, otherwise known as dysbiosis. Whether dysbiosis is a direct contributor to tissue toxicity is a key area of focus. Here, from both mammalian and bacterial perspectives, we uncover an intestinal epithelial cell death-Enterobacteriaceae signaling axis that fuels dysbiosis. Specifically, our data demonstrate that chemotherapy-induced epithelial cell apoptosis and the purine-containing metabolites released from dying cells drive the inter-kingdom transcriptional re-wiring of the Enterobacteriaceae, including fundamental shifts in bacterial respiration and promotion of purine utilization-dependent expansion, which in turn delays the recovery of the intestinal tract. Inhibition of epithelial cell death or restriction of the Enterobacteriaceae to homeostatic levels reverses dysbiosis and improves intestinal recovery. These findings suggest that supportive therapies that maintain homeostatic levels of Enterobacteriaceae may be useful in resolving intestinal disease.
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Affiliation(s)
- Christopher J Anderson
- VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK.
| | - Laura Boeckaerts
- VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Priscilla Chin
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - Javier Burgoa Cardas
- VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Wei Xie
- VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Amanda Gonçalves
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; VIB BioImaging Core, Ghent, Belgium
| | - Gillian Blancke
- VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Sam Benson
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - Sebastian Rogatti
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - Mariska S Simpson
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - Anna Davey
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - Sze Men Choi
- VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | | | - Summer D Bushman
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-sur-Alzette, Luxembourg
| | | | - Peter Vandenabeele
- VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Mahesh S Desai
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-sur-Alzette, Luxembourg
| | - Lars Vereecke
- VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Kodi S Ravichandran
- VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
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2
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Gonyar LA, Sauder AB, Mortensen L, Willsey GG, Kendall MM. The yad and yeh fimbrial loci influence gene expression and virulence in enterohemorrhagic Escherichia coli O157:H7. mSphere 2024; 9:e0012424. [PMID: 38904402 PMCID: PMC11287998 DOI: 10.1128/msphere.00124-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/15/2024] [Indexed: 06/22/2024] Open
Abstract
Fimbriae are essential virulence factors for many bacterial pathogens. Fimbriae are extracellular structures that attach bacteria to surfaces. Thus, fimbriae mediate a critical step required for any pathogen to establish infection by anchoring a bacterium to host tissue. The human pathogen enterohemorrhagic Escherichia coli (EHEC) O157:H7encodes 16 fimbriae that may be important for EHEC to initiate infection and allow for productive expression of virulence traits important in later stages of infection, including a type III secretion system (T3SS) and Shiga toxin; however, the roles of most EHEC fimbriae are largely uncharacterized. Here, we provide evidence that two EHEC fimbriae, Yad and Yeh, modulate expression of diverse genes including genes encoding T3SS and Shiga toxin and that these fimbriae are required for robust colonization of the gastrointestinal tract. These findings reveal a significant and previously unappreciated role for fimbriae in bacterial pathogenesis as important determinants of virulence gene expression.IMPORTANCEFimbriae are extracellular proteinaceous structures whose defining role is to anchor bacteria to surfaces. This is a fundamental step for bacterial pathogens to establish infection in a host. Here, we show that the contributions of fimbriae to pathogenesis are more complex. Specifically, we demonstrate that fimbriae influence expression of virulence traits essential for disease progression in the intestinal pathogen enterohemorrhagic Escherichia coli. Gram-positive and Gram-negative bacteria express multiple fimbriae; therefore, these findings may have broad implications for understanding how pathogens use fimbriae, beyond adhesion, to initiate infection and coordinate gene expression, which ultimately results in disease.
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Affiliation(s)
- Laura A. Gonyar
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Amber B. Sauder
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Lindsay Mortensen
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Graham G. Willsey
- Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
| | - Melissa M. Kendall
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
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3
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Moreira de Gouveia MI, Bernalier-Donadille A, Jubelin G. Enterobacteriaceae in the Human Gut: Dynamics and Ecological Roles in Health and Disease. BIOLOGY 2024; 13:142. [PMID: 38534413 DOI: 10.3390/biology13030142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/08/2024] [Accepted: 02/21/2024] [Indexed: 03/28/2024]
Abstract
The human gut microbiota plays a crucial role in maintaining host health. Our review explores the prevalence and dynamics of Enterobacteriaceae, a bacterial family within the Proteobacteria phylum, in the human gut which represents a small fraction of the gut microbiota in healthy conditions. Even though their roles are not yet fully understood, Enterobacteriaceae and especially Escherichia coli (E. coli) play a part in creating an anaerobic environment, producing vitamins and protecting against pathogenic infections. The composition and residency of E. coli strains in the gut fluctuate among individuals and is influenced by many factors such as geography, diet and health. Dysbiosis, characterized by alterations in the microbial composition of the gut microbiota, is associated with various diseases, including obesity, inflammatory bowel diseases and metabolic disorders. A consistent pattern in dysbiosis is the expansion of Proteobacteria, particularly Enterobacteriaceae, which has been proposed as a potential marker for intestinal and extra-intestinal inflammatory diseases. Here we develop the potential mechanisms contributing to Enterobacteriaceae proliferation during dysbiosis, including changes in oxygen levels, alterations in mucosal substrates and dietary factors. Better knowledge of these mechanisms is important for developing strategies to restore a balanced gut microbiota and reduce the negative consequences of the Enterobacteriaceae bloom.
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Affiliation(s)
| | | | - Gregory Jubelin
- Université Clermont Auvergne, INRAE, MEDIS UMR454, F-63000 Clermont-Ferrand, France
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4
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Moreira de Gouveia MI, Reuter A, Garrivier A, Daniel J, Bernalier-Donadille A, Jubelin G. Design and validation of a dual-fluorescence reporter system to monitor bacterial gene expression in the gut environment. Appl Microbiol Biotechnol 2023; 107:7301-7312. [PMID: 37750914 DOI: 10.1007/s00253-023-12788-7] [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: 06/22/2023] [Revised: 09/04/2023] [Accepted: 09/10/2023] [Indexed: 09/27/2023]
Abstract
Fluorescence-based reporter systems are valuable tools for studying gene expression dynamics in living cells. However, available strategies to follow gene expression in bacteria within their natural ecosystem that can be typically rich and complex are scarce. In this work, we designed a plasmid-based tool ensuring both the identification of a strain of interest in complex environments and the monitoring of gene expression through the combination of two distinct fluorescent proteins as reporter genes. The tool was validated in Escherichia coli to monitor the expression of eut genes involved in the catabolism of ethanolamine. We demonstrated that the constructed reporter strain gradually responds with a bimodal output to increasing ethanolamine concentrations during in vitro cultures. The reporter strain was next inoculated to mice, and flow cytometry was used to detect the reporter strain among the dense microbiota of intestinal samples and to analyze specifically the expression of eut genes. This novel dual-fluorescent reporter system would be helpful to evaluate transcriptional processes in bacteria within complex environments. KEY POINTS: • A reporter tool was developed to monitor bacterial gene expression in complex environments. • Ethanolamine utilization (eut) genes are expressed by commensal E. coli in the mouse gut. • Expression of eut genes follows a bimodal distribution.
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Affiliation(s)
| | - Audrey Reuter
- Université Clermont Auvergne, INRAE, MEDIS UMR454, F-63000, Clermont-Ferrand, France
| | - Annie Garrivier
- Université Clermont Auvergne, INRAE, MEDIS UMR454, F-63000, Clermont-Ferrand, France
| | - Julien Daniel
- Université Clermont Auvergne, INRAE, MEDIS UMR454, F-63000, Clermont-Ferrand, France
| | | | - Gregory Jubelin
- Université Clermont Auvergne, INRAE, MEDIS UMR454, F-63000, Clermont-Ferrand, France.
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5
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Chen GY, Thorup NR, Miller AJ, Li YC, Ayres JS. Cooperation between physiological defenses and immune resistance produces asymptomatic carriage of a lethal bacterial pathogen. SCIENCE ADVANCES 2023; 9:eadg8719. [PMID: 37352357 PMCID: PMC10289649 DOI: 10.1126/sciadv.adg8719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/18/2023] [Indexed: 06/25/2023]
Abstract
Animals evolved two defense strategies to survive infections. Antagonistic strategies include immune resistance mechanisms that operate to kill invading pathogens. Cooperative or physiological defenses mediate host adaptation to the infected state, limiting physiological damage and disease, without killing the pathogen, and have been shown to cause asymptomatic carriage and transmission of lethal pathogens. Here, we demonstrate that physiological defenses cooperate with the adaptive immune response to generate long-term asymptomatic carriage of the lethal enteric murine pathogen, Citrobacter rodentium. Asymptomatic carriage of genetically virulent C. rodentium provided immune resistance against subsequent infections. Immune protection was dependent on systemic antibody responses and pathogen virulence behavior rather than the recognition of specific virulent antigens. Last, we demonstrate that an avirulent strain of C. rodentium in the field has background mutations in genes that are important for LPS structure. Our work reveals insight into how asymptomatic infections can arise mechanistically with immune resistance, mediating exclusion of phenotypically virulent enteric pathogen to promote asymptomatic carriage.
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Affiliation(s)
- Grischa Y. Chen
- Molecular and Systems Physiology Lab, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- NOMIS Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Natalia R. Thorup
- Molecular and Systems Physiology Lab, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- NOMIS Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Abigail J. Miller
- Molecular and Systems Physiology Lab, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- NOMIS Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Yao-Cheng Li
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Janelle S. Ayres
- Molecular and Systems Physiology Lab, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- NOMIS Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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6
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Chen GY, Thorup NR, Miller AJ, Li YC, Ayres JS. Cooperation between physiological defenses and immune resistance produces asymptomatic carriage of a lethal bacterial pathogen. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.22.525099. [PMID: 36711884 PMCID: PMC9882269 DOI: 10.1101/2023.01.22.525099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Animals have evolved two defense strategies to survive infections. Antagonistic strategies include mechanisms of immune resistance that operate to sense and kill invading pathogens. Cooperative or physiological defenses mediate host adaptation to the infected state, limiting physiological damage and disease, without killing the pathogen, and have been shown to cause asymptomatic carriage and transmission of lethal pathogens. Here we demonstrate that physiological defenses cooperate with the adaptive immune response to generate long-term asymptomatic carriage of the lethal enteric murine pathogen, Citrobacter rodentium. Asymptomatic carriage of genetically virulent C. rodentium provided immune resistance against subsequent infections. Host immune protection was dependent on systemic antibody responses and pathogen virulence behavior, rather than the recognition of specific virulent factor antigens. Finally, we demonstrate that an avirulent strain of C. rodentium in the field has background mutations in two genes that are important for LPS structure. Our work reveals novel insight into how asymptomatic infections can arise mechanistically with immune resistance, mediating exclusion of phenotypically virulent enteric pathogen to promote asymptomatic carriage.
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Affiliation(s)
- Grischa Y. Chen
- Molecular and Systems Physiology Lab, The Salk Institute for Biological Studies, La Jolla, CA 92037
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037
- NOMIS Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Natalia R. Thorup
- Molecular and Systems Physiology Lab, The Salk Institute for Biological Studies, La Jolla, CA 92037
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037
- NOMIS Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Abigail J. Miller
- Molecular and Systems Physiology Lab, The Salk Institute for Biological Studies, La Jolla, CA 92037
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037
- NOMIS Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Yao-Cheng Li
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Janelle S. Ayres
- Molecular and Systems Physiology Lab, The Salk Institute for Biological Studies, La Jolla, CA 92037
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037
- NOMIS Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA 92037
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7
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Moreira de Gouveia MI, Daniel J, Garrivier A, Bernalier-Donadille A, Jubelin G. Diversity of ethanolamine utilization by human commensal Escherichiacoli. Res Microbiol 2023; 174:103989. [PMID: 35988812 DOI: 10.1016/j.resmic.2022.103989] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/03/2022] [Accepted: 08/05/2022] [Indexed: 01/11/2023]
Abstract
Ethanolamine (EA) is a substrate naturally present in the human gut and its catabolism by bacteria relies on the presence of eut genes encoding specific metabolic enzymes and accessory proteins. To date, EA utilization has been mostly investigated in gut bacterial pathogens. The aim of this study was to evaluate the ability of human gut commensal Escherichia coli isolates to utilize EA as a nitrogen and/or carbon sources. Although the capacity to consume EA is heterogeneous between the 40 strains of our collection, we determined that most of them could degrade EA to generate ammonia, a useful nitrogen resource for growth. Three isolates were also able to exploit EA as a carbon source. We also revealed that the inability of some strains to catabolize EA is explained either by mutations in the eut locus or by a defect in gene transcription. Finally, we demonstrated the importance of EA utilization for an optimal fitness of commensal E. coli in vivo. Our study provides new insights on the diversity of commensal E. coli strains to utilize EA as a nutrient in the gut and opens the way for new research in the field of interactions between host, gut microbiota and pathogens.
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Affiliation(s)
| | - Julien Daniel
- Université Clermont Auvergne, INRAE, MEDIS UMR454, F-63000, Clermont-Ferrand, France.
| | - Annie Garrivier
- Université Clermont Auvergne, INRAE, MEDIS UMR454, F-63000, Clermont-Ferrand, France.
| | | | - Gregory Jubelin
- Université Clermont Auvergne, INRAE, MEDIS UMR454, F-63000, Clermont-Ferrand, France.
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8
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Venzon M, Das R, Luciano DJ, Burnett J, Park HS, Devlin JC, Kool ET, Belasco JG, Hubbard EJA, Cadwell K. Microbial byproducts determine reproductive fitness of free-living and parasitic nematodes. Cell Host Microbe 2022; 30:786-797.e8. [PMID: 35413267 PMCID: PMC9187612 DOI: 10.1016/j.chom.2022.03.015] [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: 09/29/2021] [Revised: 02/09/2022] [Accepted: 03/10/2022] [Indexed: 11/03/2022]
Abstract
Trichuris nematodes reproduce within the microbiota-rich mammalian intestine and lay thousands of eggs daily, facilitating their sustained presence in the environment and hampering eradication efforts. Here, we show that bacterial byproducts facilitate the reproductive development of nematodes. First, we employed a pipeline using the well-characterized, free-living nematode C. elegans to identify microbial factors with conserved roles in nematode reproduction. A screen for E. coli mutants that impair C. elegans fertility identified genes in fatty acid biosynthesis and ethanolamine utilization pathways, including fabH and eutN. Additionally, Trichuris muris eggs displayed defective hatching in the presence of fabH- or eutN-deficient E. coli due to reduced arginine or elevated aldehydes, respectively. T. muris reared in gnotobiotic mice colonized with these E. coli mutants displayed morphological defects and failed to lay viable eggs. These findings indicate that microbial byproducts mediate evolutionarily conserved transkingdom interactions that impact the reproductive fitness of distantly related nematodes.
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Affiliation(s)
- Mericien Venzon
- Vilcek Institute of Graduate Biomedical Sciences, New York University Grossman School of Medicine, New York, NY 10016, USA; Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ritika Das
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Daniel J Luciano
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Julia Burnett
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Hyun Shin Park
- Seegene Inc., Ogeum-ro, Songpa-Gu, Seoul 05548, Republic of Korea
| | - Joseph Cooper Devlin
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Eric T Kool
- Department of Chemistry, Stanford Cancer Institute, and ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Joel G Belasco
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - E Jane Albert Hubbard
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Cell Biology, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA.
| | - Ken Cadwell
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA; Division of Gastroenterology, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA.
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9
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Sauder AB, Kendall MM. A pathogen-specific sRNA influences enterohemorrhagic Escherichia coli fitness and virulence in part by direct interaction with the transcript encoding the ethanolamine utilization regulatory factor EutR. Nucleic Acids Res 2021; 49:10988-11004. [PMID: 34591974 PMCID: PMC8565329 DOI: 10.1093/nar/gkab863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 09/09/2021] [Accepted: 09/14/2021] [Indexed: 01/07/2023] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) O157:H7 relies on sRNAs to coordinate expression of metabolic and virulence factors to colonize the host. Here, we focus on the sRNA, named MavR (metabolism and virulence regulator), that is conserved among pathogenic Enterobacteriaceae. MavR is constitutively expressed under in vitro conditions that promote EHEC virulence gene expression. Using MS2-affinity purification coupled with RNA sequencing, the eutR transcript was identified as a putative target of MavR. EutR is a transcription factor that promotes expression of genes required for ethanolamine metabolism as well as virulence factors important for host colonization. MavR binds to the eutR coding sequence to protect the eutR transcript from RNase E-mediated degradation. Ultimately, MavR promotes EutR expression and in turn ethanolamine utilization and ethanolamine-dependent growth. RNAseq analyses revealed that MavR also affected expression of genes important for other metabolic pathways, motility, oxidative stress and attaching and effacing lesion formation, which contribute to EHEC colonization of the gastrointestinal tract. In support of the idea that MavR-dependent gene expression affects fitness during infection, deletion of mavR resulted in significant (∼10- to 100-fold) attenuation in colonization of the mammalian intestine. Altogether, these studies reveal an important, extensive, and robust phenotype for a bacterial sRNA in host-pathogen interactions.
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Affiliation(s)
- Amber B Sauder
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Melissa M Kendall
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
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10
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Liang Q, Vallance BA. What's for dinner? How Citrobacter rodentium's metabolism helps it thrive in the competitive gut. Curr Opin Microbiol 2021; 63:76-82. [PMID: 34243134 DOI: 10.1016/j.mib.2021.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/16/2021] [Accepted: 06/21/2021] [Indexed: 01/04/2023]
Abstract
Enteric bacterial infections impose a significant and global health burden on society, and their threat is increasing in concert with a rise in antibiotic resistance. There is thus a great need to quickly develop new antimicrobial treatments and interest is growing in targeting pathogen nutrition and metabolism. In this review, we highlight recent research on the metabolism of Citrobacter rodentium, a murine-specific relative of enteropathogenic Escherichia coli (EPEC) and enterohemorrhagic E. coli (EHEC). We focus on the mechanisms by which C. rodentium acquires nutrients as well as the distinct metabolic strategies that C. rodentium employs in varying spatiotemporal niches. We propose that identifying and targeting nutrients found essential for bacterial pathogenesis is an attractive anti-microbial approach in the new post-antibiotic era.
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Affiliation(s)
- Qiaochu Liang
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, BC Children's Hospital and University of British Columbia, Vancouver, British Columbia, Canada
| | - Bruce A Vallance
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, BC Children's Hospital and University of British Columbia, Vancouver, British Columbia, Canada.
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11
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Wale KR, Cottam C, Connolly JP, Roe AJ. Transcriptional and metabolic regulation of EHEC and Citrobacter rodentium pathogenesis. Curr Opin Microbiol 2021; 63:70-75. [PMID: 34224961 DOI: 10.1016/j.mib.2021.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/04/2021] [Accepted: 06/16/2021] [Indexed: 11/24/2022]
Abstract
Enterohaemorrhagic Escherichia coli (EHEC) is a gastrointestinal pathogen that colonizes the colonic epithelium of humans and ruminants using a Type Three Secretion System (T3SS). This system is indispensable for disease and is regulated in response to a plethora of host and microbiota derived signals. The murine pathogen, Citrobacter rodentium, has become an instrumental tool in studying EHEC infection mechanisms in vivo, given its natural ability to infect mice and reliance on the same colonisation machinery. Here, we provide a review of the most recent advancements in EHEC infection biology, focusing on transcriptional regulation of the T3SS in response to physiologically relevant signals and how colonisation impacts on the metabolic micro-environment of the host niche. We pay particular attention to studies that have employed the C. rodentium model for elucidation of such mechanisms in vivo.
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Affiliation(s)
- Kabo R Wale
- Institute of Infection, Immunity & Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Curtis Cottam
- Newcastle University Biosciences Institute, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - James Pr Connolly
- Newcastle University Biosciences Institute, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Andrew J Roe
- Institute of Infection, Immunity & Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
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Prentice MB. Bacterial microcompartments and their role in pathogenicity. Curr Opin Microbiol 2021; 63:19-28. [PMID: 34107380 DOI: 10.1016/j.mib.2021.05.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/26/2021] [Accepted: 05/17/2021] [Indexed: 02/08/2023]
Abstract
Catabolic bacterial microcompartments (BMC), or metabolosomes, are self-assembling structures formed by enzymes enclosed by porous protein shells. They provide a specialised environment inside bacterial cells separating a short catabolic pathway with reactive or toxic intermediates from the cytoplasm. Substrates for microcompartment metabolism like ethanolamine and 1,2-propanediol are constantly produced in the human intestine by bacterial metabolism of food or host cell components. Enteric pathogens gain a competitive advantage in the intestine by metabolising these substrates, an advantage enhanced by the host inflammatory response. They exploit the intestinal specificity of signature metabolosome substrates by adopting substrate sensors and regulators encoded by BMC operons for governance of non-metabolic processes in pathogenesis. In turn, products of microcompartment metabolism regulate the host immune system.
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Affiliation(s)
- Michael B Prentice
- Department of Pathology, University College Cork, Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Ireland.
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Pokhrel A, Kang SY, Schmidt-Dannert C. Ethanolamine bacterial microcompartments: from structure, function studies to bioengineering applications. Curr Opin Microbiol 2021; 62:28-37. [PMID: 34034083 DOI: 10.1016/j.mib.2021.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/21/2021] [Accepted: 04/29/2021] [Indexed: 12/15/2022]
Abstract
Two decades of structural and functional studies have revealed functions, structures and diversity of bacterial microcompartments. The protein-based organelles encapsulate diverse metabolic pathways in semipermeable, icosahedral or pseudo-icosahedral shells. One of the first discovered and characterized microcompartments are those involved in ethanolamine degradation. This review will summarize their function and assembly along with shared and unique characteristics with other microcompartment types. The modularity and self-assembling properties of their shell proteins make them valuable targets for bioengineering. Advances and prospects for shell protein engineering in vivo and in vitro for synthetic biology and biotechnology applications will be discussed.
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Affiliation(s)
- Anaya Pokhrel
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
| | - Sun-Young Kang
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
| | - Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA.
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