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Markus V. Gut bacterial quorum sensing molecules and their association with inflammatory bowel disease: Advances and future perspectives. Biochem Biophys Res Commun 2024; 724:150243. [PMID: 38857558 DOI: 10.1016/j.bbrc.2024.150243] [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: 03/07/2024] [Revised: 05/15/2024] [Accepted: 06/06/2024] [Indexed: 06/12/2024]
Abstract
Inflammatory Bowel Disease (IBD) is an enduring inflammatory disease of the gastrointestinal tract (GIT). The complexity of IBD, its profound impact on patient's quality of life, and its burden on healthcare systems necessitate continuing studies to elucidate its etiology, refine care strategies, improve treatment outcomes, and identify potential targets for novel therapeutic interventions. The discovery of a connection between IBD and gut bacterial quorum sensing (QS) molecules has opened exciting opportunities for research into IBD pathophysiology. QS molecules are small chemical messengers synthesized and released by bacteria based on population density. These chemicals are sensed not only by the microbial species but also by host cells and are essential in gut homeostasis. QS molecules are now known to interact with inflammatory pathways, therefore rendering them potential therapeutic targets for IBD management. Given these intriguing developments, the most recent research findings in this area are herein reviewed. First, the global burden of IBD and the disruptions of the gut microbiota and intestinal barrier associated with the disease are assessed. Next, the general QS mechanism and signaling molecules in the gut are discussed. Then, the roles of QS molecules and their connection with IBD are elucidated. Lastly, the review proposes potential QS-based therapeutic targets for IBD, offering insights into the future research trajectory in this field.
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Affiliation(s)
- Victor Markus
- Near East University, Faculty of Medicine, Department of Medical Biochemistry, Nicosia, TRNC Mersin 10, Turkey.
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2
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Yan X, Gu C, Yu Z, Zhao M, He L. Histidine Kinase QseC in Glaesserella parasuis Enhances the Secretion of Proinflammatory Cytokines by Macrophages via the p38 and NF-κB Signaling Pathways. DNA Cell Biol 2024. [PMID: 39049814 DOI: 10.1089/dna.2024.0078] [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: 07/27/2024] Open
Abstract
The qseC gene is a two-component system that encodes a histidine protein kinase and is highly conserved among different Glaesserella parasuis strains. In this study, we used qRT-PCR and enzyme-linked immunosorbent assay to confirm that Toll-like receptor 4 (TLR4) plays a role in the expression of proinflammatory cytokines interleukin (IL)-1β and IL-6 by stimulating RAW 264.7 macrophages with QseC. Furthermore, we revealed that blocking the p38 and NF-κB pathways that regulate signaling can significantly reduce the production of proinflammatory cytokines induced by QseC. In summary, our data suggest that QseC is a novel proinflammatory mediator that induces TLR4-dependent proinflammatory activity in RAW 264.7 macrophages through the p38 and NF-κB pathways.
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Affiliation(s)
- Xuefeng Yan
- School of Physical Education, Southwest Medical University, Luzhou, China
| | - Congwei Gu
- Technology Department, Experimental Animal Center, Southwest Medical University, Luzhou, China
| | - Zehui Yu
- Technology Department, Experimental Animal Center, Southwest Medical University, Luzhou, China
| | - Mingde Zhao
- Technology Department, Experimental Animal Center, Southwest Medical University, Luzhou, China
| | - Lvqin He
- Technology Department, Experimental Animal Center, Southwest Medical University, Luzhou, China
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3
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Yan X, Gu C, Xiao W, Zhou Y, Xiang X, Yu Z, He M, Yang Q, Zhao M, He L. Evaluation of immunoregulation and immunoprotective efficacy of Glaesserella parasuis histidine kinase QseC. Microb Pathog 2024; 192:106685. [PMID: 38750774 DOI: 10.1016/j.micpath.2024.106685] [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: 11/26/2023] [Revised: 05/08/2024] [Accepted: 05/12/2024] [Indexed: 05/19/2024]
Abstract
QseC is a membrane sensor kinase that enables bacteria to perceive autoinducers -3, adrenaline, and norepinephrine to initiate downstream gene transcription. In this study, we found that the QseC protein of Glaesserella parasuis can serve as an effective antigen to activate the host's immune response. Therefore, we investigated the immunogenicity and host protective effect of this protein. ELISA and indirect immunofluorescence results showed that QseC protein can induce high titer levels of humoral immunity in mice and regularly generate specific serum antibodies. We used MTS reagents to detect lymphocyte proliferation levels and found that QseC protein can cause splenic lymphocyte proliferation with memory and specificity. Further immunological analysis of the spleen cell supernatant revealed significant upregulation of levels of IL-1β, IL-4 and IFN-γ in the QseC + adjuvant group. In the mouse challenge experiment, it was found that QseC + adjuvant can provide effective protection. The results of this study demonstrate that QseC protein provides effective protection in a mouse model and has the potential to serve as a candidate antigen for a novel subunit vaccine for further research.
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MESH Headings
- Animals
- Mice
- Interleukin-4/metabolism
- Interleukin-4/immunology
- Antibodies, Bacterial/blood
- Antibodies, Bacterial/immunology
- Haemophilus Infections/immunology
- Haemophilus Infections/prevention & control
- Haemophilus Infections/microbiology
- Interferon-gamma/metabolism
- Histidine Kinase/genetics
- Histidine Kinase/metabolism
- Histidine Kinase/immunology
- Interleukin-1beta/metabolism
- Interleukin-1beta/genetics
- Immunity, Humoral
- Mice, Inbred BALB C
- Spleen/immunology
- Bacterial Proteins/immunology
- Bacterial Proteins/genetics
- Cell Proliferation
- Female
- Adjuvants, Immunologic
- Haemophilus parasuis/immunology
- Haemophilus parasuis/genetics
- Cytokines/metabolism
- Bacterial Vaccines/immunology
- Bacterial Vaccines/genetics
- Disease Models, Animal
- Antigens, Bacterial/immunology
- Antigens, Bacterial/genetics
- Lymphocytes/immunology
- Vaccines, Subunit/immunology
- Vaccines, Subunit/genetics
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Affiliation(s)
- Xuefeng Yan
- School of Physical Education, Southwest Medical University, Luzhou, China
| | - Congwei Gu
- Experimental Animal Center, Technology Department, Southwest Medical University, Luzhou, China
| | - Wudian Xiao
- Experimental Animal Center, Technology Department, Southwest Medical University, Luzhou, China
| | - Yuhong Zhou
- College of Pharmacy, Southwest Medical University, Luzhou, China
| | - Xinyi Xiang
- School of Public Health, Southwest Medical University, Luzhou, China
| | - Zehui Yu
- Experimental Animal Center, Technology Department, Southwest Medical University, Luzhou, China
| | - Manli He
- Experimental Animal Center, Technology Department, Southwest Medical University, Luzhou, China
| | - Qian Yang
- Experimental Animal Center, Technology Department, Southwest Medical University, Luzhou, China
| | - Mingde Zhao
- Experimental Animal Center, Technology Department, Southwest Medical University, Luzhou, China
| | - Lvqin He
- Experimental Animal Center, Technology Department, Southwest Medical University, Luzhou, China.
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4
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Walsh AM, Leech J, Huttenhower C, Delhomme-Nguyen H, Crispie F, Chervaux C, Cotter P. Integrated molecular approaches for fermented food microbiome research. FEMS Microbiol Rev 2023; 47:fuad001. [PMID: 36725208 PMCID: PMC10002906 DOI: 10.1093/femsre/fuad001] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 12/28/2022] [Accepted: 01/09/2023] [Indexed: 02/03/2023] Open
Abstract
Molecular technologies, including high-throughput sequencing, have expanded our perception of the microbial world. Unprecedented insights into the composition and function of microbial communities have generated large interest, with numerous landmark studies published in recent years relating the important roles of microbiomes and the environment-especially diet and nutrition-in human, animal, and global health. As such, food microbiomes represent an important cross-over between the environment and host. This is especially true of fermented food microbiomes, which actively introduce microbial metabolites and, to a lesser extent, live microbes into the human gut. Here, we discuss the history of fermented foods, and examine how molecular approaches have advanced research of these fermented foods over the past decade. We highlight how various molecular approaches have helped us to understand the ways in which microbes shape the qualities of these products, and we summarize the impacts of consuming fermented foods on the gut. Finally, we explore how advances in bioinformatics could be leveraged to enhance our understanding of fermented foods. This review highlights how integrated molecular approaches are changing our understanding of the microbial communities associated with food fermentation, the creation of unique food products, and their influences on the human microbiome and health.
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Affiliation(s)
- Aaron M Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork and APC Microbiome Ireland, P61 C996, Ireland
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - John Leech
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork and APC Microbiome Ireland, P61 C996, Ireland
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork and APC Microbiome Ireland, P61 C996, Ireland
| | - Christian Chervaux
- Danone Nutricia Research, Centre Daniel Carasso, Palaiseau 91120, France
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork and APC Microbiome Ireland, P61 C996, Ireland
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5
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Evidence for a Causal Role for Escherichia coli Strains Identified as Adherent-Invasive (AIEC) in Intestinal Inflammation. mSphere 2023; 8:e0047822. [PMID: 36883813 PMCID: PMC10117065 DOI: 10.1128/msphere.00478-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
Abstract
Enrichment of adherent-invasive Escherichia coli (AIEC) has been consistently detected in subsets of inflammatory bowel disease (IBD) patients. Although some AIEC strains cause colitis in animal models, these studies did not systematically compare AIEC with non-AIEC strains, and causal links between AIEC and disease are still disputed. Specifically, it remains unclear whether AIEC shows enhanced pathogenicity compared to that of commensal E. coli found in the same ecological microhabitat and if the in vitro phenotypes used to classify strains as AIEC are pathologically relevant. Here, we utilized in vitro phenotyping and a murine model of intestinal inflammation to systematically compare strains identified as AIEC with those identified as non-AIEC and relate AIEC phenotypes to pathogenicity. Strains identified as AIEC caused, on average, more severe intestinal inflammation. Intracellular survival/replication phenotypes routinely used to classify AIEC positively correlated with disease, while adherence to epithelial cells and tumor necrosis factor alpha production by macrophages did not. This knowledge was then applied to design and test a strategy to prevent inflammation by selecting E. coli strains that adhered to epithelial cells but poorly survived/replicated intracellularly. Two E. coli strains that ameliorated AIEC-mediated disease were subsequently identified. In summary, our results show a relationship between intracellular survival/replication in E. coli and pathology in murine colitis, suggesting that strains possessing these phenotypes might not only become enriched in human IBD but also contribute to disease. We provide new evidence that specific AIEC phenotypes are pathologically relevant and proof of principle that such mechanistic information can be therapeutically exploited to alleviate intestinal inflammation. IMPORTANCE Inflammatory bowel disease (IBD) is associated with an altered gut microbiota composition, including expansion of Proteobacteria. Many species in this phylum are thought to contribute to disease under certain conditions, including adherent-invasive Escherichia coli (AIEC) strains, which are enriched in some patients. However, whether this bloom contributes to disease or is just a response to IBD-associated physiological changes is unknown. Although assigning causality is challenging, appropriate animal models can test the hypothesis that AIEC strains have an enhanced ability to cause colitis in comparison to other gut commensal E. coli strains and to identify bacterial traits contributing to virulence. We observed that AIEC strains are generally more pathogenic than commensal E. coli and that bacterial intracellular survival/replication phenotypes contributed to disease. We also found that E. coli strains lacking primary virulence traits can prevent inflammation. Our findings provide critical information on E. coli pathogenicity that may inform development of IBD diagnostic tools and therapies.
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6
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Zhu Y, Dou Q, Du L, Wang Y. QseB/QseC: a two-component system globally regulating bacterial behaviors. Trends Microbiol 2023:S0966-842X(23)00046-X. [PMID: 36849330 DOI: 10.1016/j.tim.2023.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 03/01/2023]
Abstract
QseB/QseC is a two-component system that is involved in the regulation of multiple bacterial behaviors by regulating quorum sensing, bacterial pathogenicity, and antibiotic resistance. Thus, QseB/QseC could provide a target for new antibiotic development. Recently, QseB/QseC has been found to confer survival advantages to environmental bacteria under stress conditions. The molecular mechanistic understanding of QseB/QseC has become an active area of research and revealed some emerging themes, including a deeper understanding of QseB/QseC regulation in different pathogens and environmental bacteria, the functional difference of QseB/QseC among species, and the possibility of analyzing QseB/QseC evolution. Here, we discuss the progression of QseB/QseC studies and describe several unresolved issues and future directions. Resolving these issues is among the challenges of future QseB/QseC studies.
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Affiliation(s)
- Yuxiang Zhu
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Qin Dou
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Liangcheng Du
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Yan Wang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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DeSantis TZ, Cardona C, Narayan NR, Viswanatham S, Ravichandar D, Wee B, Chow CE, Iwai S. StrainSelect: A novel microbiome reference database that disambiguates all bacterial strains, genome assemblies and extant cultures worldwide. Heliyon 2023; 9:e13314. [PMID: 36814618 PMCID: PMC9939595 DOI: 10.1016/j.heliyon.2023.e13314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/01/2022] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
Motivation: Microbial metagenomic profiling software and databases are advancing rapidly for development of novel disease biomarkers and therapeutics yet three problems impede analyses: 1) the conflation of "genome assembly" and "strain" in reference databases; 2) difficulty connecting DNA biomarkers to a procurable strain for laboratory experimentation; and 3) absence of a comprehensive and unified strain-resolved reference database for integrating both shotgun metagenomics and 16S rRNA gene data. Results: We demarcated 681,087 strains, the largest collection of its kind, by filtering public data into a knowledge graph of vertices representing contiguous DNA sequences, genome assemblies, strain monikers and bio-resource center (BRC) catalog numbers then adding inter-vertex edges only for synonyms or direct derivatives. Surprisingly, for 10,043 important strains, we found replicate RefSeq genome assemblies obstructing interpretation of database searches. We organized each strain into eight taxonomic ranks with bootstrap confidence inversely correlated with genome assembly contamination. The StrainSelect database is suited for applications where a taxonomic, functional or procurement reference is needed for shotgun or amplicon metagenomics since 636,568 strains have at least one 16S rRNA gene, 245,005 have at least one annotated genome assembly, and 36,671 are procurable from at least one BRC. The database overcomes all three aforementioned problems since it disambiguates strains from assemblies, locates strains at BRCs, and unifies a taxonomic reference for both 16S rRNA and shotgun metagenomics. Availability: The StrainSelect database is available in igraph and tabular vertex-edge formats compatible with Neo4J. Dereplicated MinHash and fasta databases are distributed for sourmash and usearch pipelines at http://strainselect.secondgenome.com. Contact:todd.desantis@gmail.com. Supplementary information: Supplementary data are available online.
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Affiliation(s)
- Todd Z. DeSantis
- Second Genome, Inc., 1000 Marina Blvd, Suite 500, Brisbane, CA, 94005, USA,Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Germany,Corresponding author at: Second Genome, Inc., 1000 Marina Blvd, Suite 500, Brisbane, CA, 94005, USA.
| | - Cesar Cardona
- Second Genome, Inc., 1000 Marina Blvd, Suite 500, Brisbane, CA, 94005, USA
| | - Nicole R. Narayan
- Second Genome, Inc., 1000 Marina Blvd, Suite 500, Brisbane, CA, 94005, USA
| | - Satish Viswanatham
- Second Genome, Inc., 1000 Marina Blvd, Suite 500, Brisbane, CA, 94005, USA
| | - Divya Ravichandar
- Second Genome, Inc., 1000 Marina Blvd, Suite 500, Brisbane, CA, 94005, USA
| | - Brendan Wee
- Second Genome, Inc., 1000 Marina Blvd, Suite 500, Brisbane, CA, 94005, USA
| | | | - Shoko Iwai
- Second Genome, Inc., 1000 Marina Blvd, Suite 500, Brisbane, CA, 94005, USA
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8
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Abstract
This narrative review seeks to examine the relationships between bacterial microbiomes and infectious disease. This is achieved by detailing how different human host microbiomes develop and function, from the earliest infant acquisitions of maternal and environmental species through to the full development of microbiomes by adulthood. Communication between bacterial species or communities of species within and outside of the microbiome is a factor in both maintenance of homeostasis and management of threats from the external environment. Dysbiosis of this homeostasis is key to understanding the development of disease states. Several microbiomes and the microbiota within are used as prime examples of how changes in species composition, particularly at the phylum level, leads to such diverse conditions as inflammatory bowel disease (IBD), type 2 diabetes, psoriasis, Parkinson's disease, reflux oesophagitis and others. The review examines spatial relationships between microbiomes to understand how dysbiosis in the gut microbiome in particular can influence diseases in distant host sites via routes such as the gut-lung, gut-skin and gut-brain axes. Microbiome interaction with host processes such as adaptive immunity is increasingly identified as critical to developing the capacity of the immune system to react to pathogens. Dysbiosis of essential bacteria involved in modification of host substrates such as bile acid components can result in development of Crohn's disease, small intestine bacterial overgrowth, hepatic cancer and obesity. Interactions between microbiomes in distantly located sites are being increasingly being identified, resulting in a 'whole of body' effect by the combined host microbiome.
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Affiliation(s)
- Jim Manos
- Infection, Immunity and InflammationSchool of Medical SciencesFaculty of Medicine and HealthThe Charles Perkins CentreThe University of SydneySydneyNSWAustralia
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Cuesta S, Burdisso P, Segev A, Kourrich S, Sperandio V. Gut colonization by Proteobacteria alters host metabolism and modulates cocaine neurobehavioral responses. Cell Host Microbe 2022; 30:1615-1629.e5. [PMID: 36323315 PMCID: PMC9669251 DOI: 10.1016/j.chom.2022.09.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/22/2022] [Accepted: 09/14/2022] [Indexed: 11/11/2022]
Abstract
Gut-microbiota membership is associated with diverse neuropsychological outcomes, including substance use disorders (SUDs). Here, we use mice colonized with Citrobacter rodentium or the human γ-Proteobacteria commensal Escherichia coli HS as a model to examine the mechanistic interactions between gut microbes and host responses to cocaine. We find that cocaine exposure increases intestinal norepinephrine levels that are sensed through the bacterial adrenergic receptor QseC to promote intestinal colonization of γ-Proteobacteria. Colonized mice show enhanced host cocaine-induced behaviors. The neuroactive metabolite glycine, a bacterial nitrogen source, is depleted in the gut and cerebrospinal fluid of colonized mice. Systemic glycine repletion reversed, and γ-Proteobacteria mutated for glycine uptake did not alter the host response to cocaine. γ-Proteobacteria modulated glycine levels are linked to cocaine-induced transcriptional plasticity in the nucleus accumbens through glutamatergic transmission. The mechanism outline here could potentially be exploited to modulate reward-related brain circuits that contribute to SUDs.
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Affiliation(s)
- Santiago Cuesta
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA; Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Paula Burdisso
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR) and Plataforma Argentina de Biología Estructural y Metabolómica (PLABEM), Rosario, Santa Fe, Argentina
| | - Amir Segev
- Department of Psychiatry, University of Texas Southwestern Medical School, Dallas, TX 75390, USA
| | - Saïd Kourrich
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, Canada; The Center of Excellence in Research on Orphan Diseases - Foundation Courtois, Université du Québec à Montréal, Montréal, QC, Canada; Center for Studies in Behavioral Neurobiology, Concordia University, Montreal, QC, Canada
| | - Vanessa Sperandio
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA; Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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Proctor A, Parvinroo S, Richie T, Jia X, Lee STM, Karp PD, Paley S, Kostic AD, Pierre JF, Wannemuehler MJ, Phillips GJ. Resources to Facilitate Use of the Altered Schaedler Flora (ASF) Mouse Model to Study Microbiome Function. mSystems 2022; 7:e0029322. [PMID: 35968975 PMCID: PMC9600240 DOI: 10.1128/msystems.00293-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/20/2022] [Indexed: 12/24/2022] Open
Abstract
Animals colonized with a defined microbiota represent useful experimental systems to investigate microbiome function. The altered Schaedler flora (ASF) represents a consortium of eight murine bacterial species that have been used for more than 4 decades where the study of mice with a reduced microbiota is desired. In contrast to germ-free mice, or mice colonized with only one or two species, ASF mice show the normal gut structure and immune system development. To further expand the utility of the ASF, we have developed technical and bioinformatic resources to enable a systems-based analysis of microbiome function using this model. Here, we highlighted four distinct applications of these resources that enable and improve (i) measurements of the abundance of each ASF member by quantitative PCR; (ii) exploration and comparative analysis of ASF genomes and the metabolic pathways they encode that comprise the entire gut microbiome; (iii) global transcriptional profiling to identify genes whose expression responds to environmental changes within the gut; and (iv) discovery of genetic changes resulting from the evolutionary adaptation of the microbiota. These resources were designed to be accessible to a broad community of researchers that, in combination with conventionally-reared mice (i.e., with complex microbiome), should contribute to our understanding of microbiome structure and function. IMPORTANCE Improved experimental systems are needed to advance our understanding of how the gut microbiome influences processes of the mammalian host as well as microbial community structure and function. An approach that is receiving considerable attention is the use of animal models that harbor a stable microbiota of known composition, i.e., defined microbiota, which enables control over an otherwise highly complex and variable feature of mammalian biology. The altered Schaedler flora (ASF) consortium is a well-established defined microbiota model, where mice are stably colonized with 8 distinct murine bacterial species. To take better advantage of the ASF, we established new experimental and bioinformatics resources for researchers to make better use of this model as an experimental system to study microbiome function.
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Affiliation(s)
- Alexandra Proctor
- Department of Veterinary Microbiology, Iowa State University, Ames, Iowa, USA
| | - Shadi Parvinroo
- Department of Veterinary Microbiology, Iowa State University, Ames, Iowa, USA
| | - Tanner Richie
- Division of Biology, Kansas State University, Manhattan Kansas, USA
| | - Xinglin Jia
- Department of Veterinary Microbiology, Iowa State University, Ames, Iowa, USA
| | - Sonny T. M. Lee
- Division of Biology, Kansas State University, Manhattan Kansas, USA
| | - Peter D. Karp
- Bioinformatics Research Group, SRI International, Menlo Park, California, USA
| | - Suzanne Paley
- Bioinformatics Research Group, SRI International, Menlo Park, California, USA
| | - Aleksandar D. Kostic
- Department of Microbiology and Immunology, Joslin Diabetes Center, Harvard University, Cambridge Massachusetts, USA
| | - Joseph F. Pierre
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison Wisconsin, USA
| | | | - Gregory J. Phillips
- Department of Veterinary Microbiology, Iowa State University, Ames, Iowa, USA
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11
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Tian Y, Zuo L, Guan B, Wu H, He Y, Xu Z, Shen M, Hu J, Qian J. Microbiota from patients with ulcerative colitis promote colorectal carcinogenesis in mice. Nutrition 2022; 102:111712. [PMID: 35802940 DOI: 10.1016/j.nut.2022.111712] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 02/05/2023]
Abstract
OBJECTIVES Long-term ulcerative colitis (UC) is associated with both dysbiosis in intestinal microbiota and predisposition to colorectal cancer. In this study, we investigated whether microbiota from patients with UC could increase colorectal carcinogenesis in mice, generated by azoxymethane through intraperitoneal injection. METHODS Mice were gavaged twice per week with intestinal microbiota from patients with UC or healthy individuals. Intestinal tissues were collected from mice and compared by histology, immunohistochemistry, expression microarray, quantitative polymerase chain reaction, Western blot, and flow cytometry analyses. Quantification of bacteria in feces was performed using 16 S ribosomal RNA gene selective quantitative polymerase chain reaction. RESULTS Compared with mice fed microbiota from healthy controls, increased tumorigenesis was observed in mice gavaged with microbiota from patients with UC, including a higher number of colon adenoma and a significantly higher proportion of grade dysplasia. Consistent with tumorigenesis, mice gavaged with microbiota from patients with UC showed an increased expression of Ki67 and proliferating cell nuclear antigen. In addition, an increased expression of cytokines and more abundant presence of T helper cells types 1 and 17 was observed in mice receiving microbiota from patients with UC. Moreover, a decrease in the abundance of short-chain fatty acids was detected in the feces, as well as an altered intestinal microbial composition in mice fed with microbiota from patients with UC. CONCLUSIONS Fecal microbiota from patients with UC exacerbate tumorigenesis in mice. The disturbance of intestinal microbiota and activation of T helper cells types 1 and 17 cytokines caused by gavaging microbiota from patients with UC both contributed to intestinal carcinogenesis.
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Affiliation(s)
- Yun Tian
- Department of Oncology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
| | - Lugen Zuo
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
| | - Bing Guan
- Department of Pathology, Shanghai Sixth People's Hospital Jinshan Branch, Shanghai, China
| | - Huatao Wu
- Anhui Key Laboratory of Tissue Transplantation, Bengbu Medical College, Bengbu, Anhui, China
| | - Yifan He
- Anhui Key Laboratory of Tissue Transplantation, Bengbu Medical College, Bengbu, Anhui, China
| | - Zilong Xu
- Anhui Key Laboratory of Tissue Transplantation, Bengbu Medical College, Bengbu, Anhui, China
| | - Mengdi Shen
- Anhui Key Laboratory of Tissue Transplantation, Bengbu Medical College, Bengbu, Anhui, China
| | - Jianguo Hu
- Anhui Key Laboratory of Tissue Transplantation, Bengbu Medical College, Bengbu, Anhui, China; Department of Clinical Laboratory, First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Jun Qian
- Department of Oncology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
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12
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Yang L, Yuan TJ, Wan Y, Li WW, Liu C, Jiang S, Duan JA. Quorum sensing: a new perspective to reveal the interaction between gut microbiota and host. Future Microbiol 2022; 17:293-309. [PMID: 35164528 DOI: 10.2217/fmb-2021-0217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Quorum sensing (QS), a chemical communication process between bacteria, depends on the synthesis, secretion and detection of signal molecules. It can synchronize the gene expression of bacteria to promote cooperation within the population and improve competitiveness among populations. The preliminary exploration of bacterial QS has been completed under ideal and highly controllable conditions. There is an urgent need to investigate the QS of bacteria under natural conditions, especially the QS of intestinal flora, which is closely related to health. Excitingly, growing evidence has shown that QS also exists in the intestinal flora. The crosstalk of QS between gut microbiota and the host is systematically clarified in this review.
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Affiliation(s)
- Lei Yang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, PR China
| | - Tian-Jie Yuan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, PR China
| | - Yue Wan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, PR China
| | - Wen-Wen Li
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, PR China
| | - Chen Liu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, PR China
| | - Shu Jiang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, PR China
| | - Jin-Ao Duan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, PR China
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13
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Iskandar K, Murugaiyan J, Hammoudi Halat D, Hage SE, Chibabhai V, Adukkadukkam S, Roques C, Molinier L, Salameh P, Van Dongen M. Antibiotic Discovery and Resistance: The Chase and the Race. Antibiotics (Basel) 2022; 11:182. [PMID: 35203785 PMCID: PMC8868473 DOI: 10.3390/antibiotics11020182] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/23/2022] [Accepted: 01/26/2022] [Indexed: 12/14/2022] Open
Abstract
The history of antimicrobial resistance (AMR) evolution and the diversity of the environmental resistome indicate that AMR is an ancient natural phenomenon. Acquired resistance is a public health concern influenced by the anthropogenic use of antibiotics, leading to the selection of resistant genes. Data show that AMR is spreading globally at different rates, outpacing all efforts to mitigate this crisis. The search for new antibiotic classes is one of the key strategies in the fight against AMR. Since the 1980s, newly marketed antibiotics were either modifications or improvements of known molecules. The World Health Organization (WHO) describes the current pipeline as bleak, and warns about the scarcity of new leads. A quantitative and qualitative analysis of the pre-clinical and clinical pipeline indicates that few antibiotics may reach the market in a few years, predominantly not those that fit the innovative requirements to tackle the challenging spread of AMR. Diversity and innovation are the mainstays to cope with the rapid evolution of AMR. The discovery and development of antibiotics must address resistance to old and novel antibiotics. Here, we review the history and challenges of antibiotics discovery and describe different innovative new leads mechanisms expected to replenish the pipeline, while maintaining a promising possibility to shift the chase and the race between the spread of AMR, preserving antibiotic effectiveness, and meeting innovative leads requirements.
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Affiliation(s)
- Katia Iskandar
- Department of Mathématiques Informatique et Télécommunications, Université Toulouse III, Paul Sabatier, INSERM, UMR 1295, 31000 Toulouse, France
- INSPECT-LB: Institut National de Santé Publique, d’Épidémiologie Clinique et de Toxicologie-Liban, Beirut 6573, Lebanon;
- Faculty of Pharmacy, Lebanese University, Beirut 6573, Lebanon
| | - Jayaseelan Murugaiyan
- Department of Biological Sciences, SRM University–AP, Amaravati 522502, India; (J.M.); (S.A.)
| | - Dalal Hammoudi Halat
- Department of Pharmaceutical Sciences, School of Pharmacy, Lebanese International University, Bekaa Campus, Beirut 1103, Lebanon
| | - Said El Hage
- Faculty of Medicine, Lebanese University, Beirut 6573, Lebanon;
| | - Vindana Chibabhai
- Division of Clinical Microbiology and Infectious Diseases, School of Pathology, University of the Witwatersrand, Johannesburg 2193, South Africa;
- Microbiology Laboratory, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg 2193, South Africa
| | - Saranya Adukkadukkam
- Department of Biological Sciences, SRM University–AP, Amaravati 522502, India; (J.M.); (S.A.)
| | - Christine Roques
- Laboratoire de Génie Chimique, Department of Bioprocédés et Systèmes Microbiens, Université Paul Sabtier, Toulouse III, UMR 5503, 31330 Toulouse, France;
| | - Laurent Molinier
- Department of Medical Information, Centre Hospitalier Universitaire, INSERM, UMR 1295, Université Paul Sabatier Toulouse III, 31000 Toulouse, France;
| | - Pascale Salameh
- INSPECT-LB: Institut National de Santé Publique, d’Épidémiologie Clinique et de Toxicologie-Liban, Beirut 6573, Lebanon;
- Faculty of Medicine, Lebanese University, Beirut 6573, Lebanon;
- Department of Primary Care and Population Health, University of Nicosia Medical School, Nicosia 2408, Cyprus
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14
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Expression, Purification, and Characterization of the Recombinant, Two-Component, Response Regulator ArlR from Fusobacterium nucleatum. Appl Biochem Biotechnol 2022; 194:2093-2107. [PMID: 35029789 DOI: 10.1007/s12010-021-03785-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2021] [Indexed: 11/02/2022]
Abstract
Fusobacterium nucleatum is associated with the incidence and development of multiple diseases, such as periodontitis and colorectal cancer (CRC). Until now, studies have proved only a few proteins to be associated with such pathogenic diseases. The two-component system is one of the most prevalent forms of bacterial signal transduction related to intestinal diseases. Here, we report a novel, recombinant, two-component, response regulator protein ArlR from the genome of F. nucleatum strain ATCC 25,586. We optimized the expression and purification conditions of ArlR; in addition, we characterized the interaction of this response regulator protein with the corresponding histidine kinase and DNA sequence. The full-length ArlR was successfully expressed in six E. coli host strains. However, optimum expression conditions of ArlR were present only in E. coli strain BL21 CodonPlus (DE3) RIL that was later induced with isopropyl β-D-1-thiogalactopyranoside (IPTG) for 8 h at 25 °C. The SDS-PAGE analysis revealed the molecular weight of the recombinant protein as 27.3 kDa with approximately 90% purity after gel filtration chromatography. Because ArlR was biologically active after its purification, it accepted the corresponding phosphorylated histidine kinase phosphate group and bound to the analogous DNA sequence. The binding constant between ArlR and the corresponding histidine kinase was about 2.1 μM, whereas the binding constant between ArlR and its operon was 6.4 μM. Altogether, these results illustrate an effective expression and purification method for the novel two-component system protein ArlR.
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15
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Giannakara M, Koumandou VL. Evolution of two-component quorum sensing systems. Access Microbiol 2022; 4:000303. [PMID: 35252749 PMCID: PMC8895600 DOI: 10.1099/acmi.0.000303] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 11/15/2021] [Indexed: 12/16/2022] Open
Abstract
Quorum sensing (QS) is a cell-to-cell communication system that enables bacteria to coordinate their gene expression depending on their population density, via the detection of small molecules called autoinducers. In this way bacteria can act collectively to initiate processes like bioluminescence, virulence and biofilm formation. Autoinducers are detected by receptors, some of which are part of two-component signal transduction systems (TCS), which comprise of a (usually membrane-bound) sensor histidine kinase (HK) and a cognate response regulator (RR). Different QS systems are used by different bacterial taxa, and their relative evolutionary relationships have not been extensively studied. To address this, we used the Kyoto Encyclopedia of Genes and Genomes (KEGG) database to identify all the QS HKs and RRs that are part of TCSs and examined their conservation across microbial taxa. We compared the combinations of the highly conserved domains in the different families of receptors and response regulators using the Simple Modular Architecture Research Tool (SMART) and KEGG databases, and we also carried out phylogenetic analyses for each family, and all families together. The distribution of the different QS systems across taxa, indicates flexibility in HK–RR pairing and highlights the need for further study of the most abundant systems. For both the QS receptors and the response regulators, our results indicate close evolutionary relationships between certain families, highlighting a common evolutionary history which can inform future applications, such as the design of novel inhibitors for pathogenic QS systems.
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Affiliation(s)
- Marina Giannakara
- Genetics Laboratory, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Vassiliki Lila Koumandou
- Genetics Laboratory, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
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16
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Sakai K, Sakurai T, De Velasco MA, Nagai T, Chikugo T, Ueshima K, Kura Y, Takahama T, Hayashi H, Nakagawa K, Kudo M, Nishio K. Intestinal Microbiota and Gene Expression Reveal Similarity and Dissimilarity Between Immune-Mediated Colitis and Ulcerative Colitis. Front Oncol 2021; 11:763468. [PMID: 34778085 PMCID: PMC8578892 DOI: 10.3389/fonc.2021.763468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/11/2021] [Indexed: 12/30/2022] Open
Abstract
Immune checkpoint inhibitors (ICIs) have become the standard of care for several cancers. However, ICI therapy has also been associated with various immune-related adverse events (irAEs). Clinical manifestations of immune-related colitis resemble those of inflammatory bowel diseases such as ulcerative colitis (UC). The composition of the bowel microflora is thought to influence the development of inflammatory bowel disease and irAE colitis. We profiled the gene expressions and microbe compositions of colonic mucosa from patients with solid cancers receiving anti-PD-L1 antibody treatment; we then compared the expression profiles associated with irAE colitis with those associated with UC. The pathway enrichment analysis revealed functional similarities between inflamed regions of irAE colitis and UC. The common enriched pathways included leukocyte extravasation and immune responses, whereas non-inflamed mucosa from patients with irAE colitis was distinct from patients with UC and was characterized by the recruitment of immune cells. A similarity between the microbiota profiles was also identified. A decreased abundance of Bacteroides species was observed in inflamed regions from both irAE colitis and UC based on a microbiota composition analysis of 16S rDNA sequencing. Pathways associated with molecule transport systems, including fatty acids, were enriched in inflamed and non-inflamed irAE colitis and inflamed UC, similar to Piphillin-inferred KEGG pathways. While UC is characterized by local regions of inflammation, ICI treatment extends to non-inflammatory regions of the colonial mucosa where immune cells are reconstituted. This analysis of the similarity and heterogeneity of irAE colitis and UC provides important information for the management of irAE colitis.
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Affiliation(s)
- Kazuko Sakai
- Department of Genome Biology, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Toshiharu Sakurai
- Department of Gastroenterology and Hepatology, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Marco A De Velasco
- Department of Genome Biology, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Tomoyuki Nagai
- Department of Gastroenterology and Hepatology, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Takaaki Chikugo
- Department of Diagnostic Pathology, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Kazuomi Ueshima
- Department of Gastroenterology and Hepatology, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Yurie Kura
- Department of Genome Biology, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Takayuki Takahama
- Department of Medical Oncology, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Hidetoshi Hayashi
- Department of Medical Oncology, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Kazuhiko Nakagawa
- Department of Medical Oncology, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Masatoshi Kudo
- Department of Gastroenterology and Hepatology, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Faculty of Medicine, Kindai University, Osaka, Japan
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17
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Ali S, Alam M, Hasan GM, Hassan MI. Potential therapeutic targets of Klebsiella pneumoniae: a multi-omics review perspective. Brief Funct Genomics 2021; 21:63-77. [PMID: 34448478 DOI: 10.1093/bfgp/elab038] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 11/15/2022] Open
Abstract
The multidrug resistance developed in many organisms due to the prolonged use of antibiotics has been an increasing global health crisis. Klebsiella pneumoniae is a causal organism for various infections, including respiratory, urinary tract and biliary diseases. Initially, immunocompromised individuals are primarily affected by K. pneumoniae. Due to the emergence of hypervirulent strains recently, both healthy and immunocompetent individuals are equally susceptible to K. pneumoniae infections. The infections caused by multidrug-resistant and hypervirulent K. pneumoniae strains are complicated to treat, illustrating an urgent need to develop novel and more practical approaches to combat the pathogen. We focused on the previously performed high-throughput analyses by other groups to discover several novel enzymes that may be considered attractive drug targets of K. pneumoniae. These targets qualify most of the selection criteria for drug targeting, including an absence of its homolog's gene in the host. The capsule, lipopolysaccharide, fimbriae, siderophores and essential virulence factors facilitate the pathogen entry, infection and survival inside the host. This review discusses K. pneumoniae pathophysiology, including its virulence determinants and further the potential drug targets that might facilitate the discovery of novel drugs and effective treatment regimens shortly.
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Affiliation(s)
- Sabeeha Ali
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar New Delhi 110025, India
| | - Manzar Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar New Delhi 110025, India
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar New Delhi 110025, India
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18
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Wang Y, Cao Q, Cao Q, Gan J, Sun N, Yang CG, Bae T, Wu M, Lan L. Histamine activates HinK to promote the virulence of Pseudomonas aeruginosa. Sci Bull (Beijing) 2021; 66:1101-1118. [PMID: 36654344 DOI: 10.1016/j.scib.2021.01.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/25/2020] [Accepted: 12/28/2020] [Indexed: 01/20/2023]
Abstract
During infections, bacteria stimulate host cells to produce and release histamine, which is a key mediator of vital cellular processes in animals. However, the mechanisms underlying the bacterial cell's ability to sense and respond to histamine are poorly understood. Herein, we show that HinK, a LysR-type transcriptional regulator, is required to evoke responses to histamine in Pseudomonas aeruginosa, an important human pathogen. HinK directly binds to and activates the promoter of genes involved in histamine uptake and metabolism, iron acquisition, and Pseudomonas quinolone signal (PQS) biosynthesis. The transcriptional regulatory activity of HinK is induced when histamine is present, and it occurs when HinK binds with imidazole-4-acetic acid (ImAA), a histamine metabolite whose production in P. aeruginosa depends on the HinK-activated histamine uptake and utilization operon hinDAC-pa0222. Importantly, the inactivation of HinK inhibits diverse pathogenic phenotypes of P. aeruginosa. These results suggest that histamine acts as an interkingdom signal and provide insights into the mechanism used by pathogenic bacteria to exploit host regulatory signals to promote virulence.
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Affiliation(s)
- Yaya Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Qiao Cao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; College of Life Science, Northwest University, Xi'an 710069, China
| | - Qin Cao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering, Shanghai Public Health Clinical Center, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 201438, China
| | - Ning Sun
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Cai-Guang Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Taeok Bae
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary IN 46408, USA
| | - Min Wu
- Department of Biomedical Sciences, University of North Dakota, Grand Forks ND 58203-9037, USA
| | - Lefu Lan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai 201203, China.
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19
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Oh HY, Jalde SS, Chung IY, Yoo YJ, Jang HJ, Choi HK, Cho YH. An antipathogenic compound that targets the OxyR peroxide sensor in Pseudomonas aeruginosa. J Med Microbiol 2021; 70. [PMID: 33830911 PMCID: PMC8289212 DOI: 10.1099/jmm.0.001341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Introduction Antipathogenic or antivirulence strategy is to target a virulence pathway that is dispensable for growth, in the hope to mitigate the selection for drug resistance. Hypothesis/Gap Statment Peroxide stress responses are one of the conserved virulence pathways in bacterial pathogens and thus good targets for antipathogenic strategy. Aim This study aims to identify a new chemical compound that targets OxyR, the peroxide sensor required for the full virulence of the opportunistic human pathogen, Pseudomonas aeruginosa. Methodology Computer-based virtual screening under consideration of the ‘eNTRy’ rules and molecular docking were conducted on the reduced form of the OxyR regulatory domain (RD). Selected hits were validated by their ability to phenocopy the oxyR null mutant and modulate the redox cycle of OxyR. Results We first isolated three robust chemical hits that inhibit OxyR without affecting prototrophic growth or viability. One (compound 1) of those affected the redox cycle of OxyR in response to H2O2 treatment, in a way to impair its function. Compound 1 displayed selective antibacterial efficacy against P. aeruginosa in Drosophila infection model, without antibacterial activity against Staphylococcus aureus. Conclusion These results suggest that compound 1 could be an antipathogenic hit inhibiting the P. aeruginosa OxyR. More importantly, our study provides an insight into the computer-based discovery of new-paradigm selective antibacterials to treat Gram-negative bacterial infections presumably with few concerns of drug resistance.
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Affiliation(s)
- Hyo-Young Oh
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do 13488, Republic of Korea
| | - Shivakumar S Jalde
- Department of Medicinal Chemistry, Jungwon University, Goesan 28024, Republic of Korea
| | - In-Young Chung
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do 13488, Republic of Korea
| | - Yeon-Ji Yoo
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do 13488, Republic of Korea
| | - Hye-Jeong Jang
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do 13488, Republic of Korea
| | - Hyun-Kyung Choi
- Department of Medicinal Chemistry, Jungwon University, Goesan 28024, Republic of Korea
| | - You-Hee Cho
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do 13488, Republic of Korea
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20
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Elhenawy W, Hordienko S, Gould S, Oberc AM, Tsai CN, Hubbard TP, Waldor MK, Coombes BK. High-throughput fitness screening and transcriptomics identify a role for a type IV secretion system in the pathogenesis of Crohn's disease-associated Escherichia coli. Nat Commun 2021; 12:2032. [PMID: 33795670 PMCID: PMC8016931 DOI: 10.1038/s41467-021-22306-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/05/2021] [Indexed: 02/06/2023] Open
Abstract
Adherent-invasive Escherichia coli (AIEC) are pathogenic bacteria frequently isolated from patients who have Crohn's disease (CD). Despite the phenotypic differences between AIEC and commensal E. coli, comparative genomic approaches have been unable to differentiate these two groups, making the identification of key virulence factors a challenge. Here, we conduct a high-resolution, in vivo genetic screen to map AIEC genes required for intestinal colonization of mice. In addition, we use in vivo RNA-sequencing to define the host-associated AIEC transcriptome. We identify diverse metabolic pathways required for efficient gut colonization by AIEC and show that a type IV secretion system (T4SS) is required to form biofilms on the surface of epithelial cells, thereby promoting AIEC persistence in the gut. E. coli isolated from CD patients are enriched for a T4SS, suggesting a possible connection to disease activity. Our findings establish the T4SS as a principal AIEC colonization factor and highlight the use of genome-wide screens in decoding the infection biology of CD-associated bacteria that otherwise lack a defined genetic signature.
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Affiliation(s)
- Wael Elhenawy
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, Canada
| | - Sarah Hordienko
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Steven Gould
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Alexander M Oberc
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Caressa N Tsai
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Troy P Hubbard
- Division of Infectious Diseases, Brigham & Women's Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Matthew K Waldor
- Division of Infectious Diseases, Brigham & Women's Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Brian K Coombes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, Canada.
- Farncombe Family Digestive Health Research Institute, Hamilton, ON, Canada.
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21
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Yi L, Dong X, Grenier D, Wang K, Wang Y. Research progress of bacterial quorum sensing receptors: Classification, structure, function and characteristics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 763:143031. [PMID: 33129525 DOI: 10.1016/j.scitotenv.2020.143031] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/16/2020] [Accepted: 10/10/2020] [Indexed: 06/11/2023]
Abstract
The microbial community is an important part of the natural ecosystem, and the quorum sensing system is a momentous communication tool for the microbial community to connect to the surrounding environment. Quorum sensing is a process of cell-cell communication that relies on the production, release, and detection of extracellular signaling molecules, which are called autoinducers. Quorum sensing systems in bacteria consist of two main components: a receptor protein and an autoinducer. The binding of autoinducer to its receptor activates the target gene, which then performs the corresponding function in bacteria. In a natural environment, different bacterial species possess quorum sensing receptors that are structurally and functionally different. So far, many bacterial quorum sensing receptors have been identified and the structure and function of some receptors have been characterized. There are many reviews about quorum sensing and quorum sensing receptors, but there are few reviews that describe various types of quorum sensing in different environments with receptors as the core. Therefore, we summarize the well-defined quorum sensing receptors involved in intra-species and inter-species cell-cell communication, and describe the structure, function, and characteristics of typical receptors for different types of quorum sensing. A systematic understanding of quorum sensing receptors will help researchers to further explore the signaling mechanism and regulation mechanism of quorum sensing system, provide help to clarify the role and function of quorum sensing in natural ecosystems, then provide theoretical basis for the discovery or synthesis of new targeted drugs that block quorum sensing.
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Affiliation(s)
- Li Yi
- College of Life Science, Luoyang Normal University, Luoyang, China; Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, Luoyang, China
| | - Xiao Dong
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China; Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, Luoyang, China
| | - Daniel Grenier
- Groupe de Recherche en Écologie Buccale (GREB), Faculté de Médecine Dentaire, Université Laval, Quebec City, QC, Canada
| | - Kaicheng Wang
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Yang Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China; Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, Luoyang, China.
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22
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Braz VS, Melchior K, Moreira CG. Escherichia coli as a Multifaceted Pathogenic and Versatile Bacterium. Front Cell Infect Microbiol 2020; 10:548492. [PMID: 33409157 PMCID: PMC7779793 DOI: 10.3389/fcimb.2020.548492] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 11/17/2020] [Indexed: 12/20/2022] Open
Abstract
Genetic plasticity promotes evolution and a vast diversity in Escherichia coli varying from avirulent to highly pathogenic strains, including the emergence of virulent hybrid microorganism. This ability also contributes to the emergence of antimicrobial resistance. These hybrid pathogenic E. coli (HyPEC) are emergent threats, such as O104:H4 from the European outbreak in 2011, aggregative adherent bacteria with the potent Shiga-toxin. Here, we briefly revisited the details of these E. coli classic and hybrid pathogens, the increase in antimicrobial resistance in the context of a genetically empowered multifaceted and versatile bug and the growing need to advance alternative therapies to fight these infections.
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Affiliation(s)
- Vânia Santos Braz
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, Brazil
| | - Karine Melchior
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, Brazil
| | - Cristiano Gallina Moreira
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, Brazil
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23
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Ellermann M, Pacheco AR, Jimenez AG, Russell RM, Cuesta S, Kumar A, Zhu W, Vale G, Martin SA, Raj P, McDonald JG, Winter SE, Sperandio V. Endocannabinoids Inhibit the Induction of Virulence in Enteric Pathogens. Cell 2020; 183:650-665.e15. [PMID: 33031742 DOI: 10.1016/j.cell.2020.09.022] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 06/30/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022]
Abstract
Endocannabinoids are host-derived lipid hormones that fundamentally impact gastrointestinal (GI) biology. The use of cannabis and other exocannabinoids as anecdotal treatments for various GI disorders inspired the search for mechanisms by which these compounds mediate their effects, which led to the discovery of the mammalian endocannabinoid system. Dysregulated endocannabinoid signaling was linked to inflammation and the gut microbiota. However, the effects of endocannabinoids on host susceptibility to infection has not been explored. Here, we show that mice with elevated levels of the endocannabinoid 2-arachidonoyl glycerol (2-AG) are protected from enteric infection by Enterobacteriaceae pathogens. 2-AG directly modulates pathogen function by inhibiting virulence programs essential for successful infection. Furthermore, 2-AG antagonizes the bacterial receptor QseC, a histidine kinase encoded within the core Enterobacteriaceae genome that promotes the activation of pathogen-associated type three secretion systems. Taken together, our findings establish that endocannabinoids are directly sensed by bacteria and can modulate bacterial function.
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Affiliation(s)
- Melissa Ellermann
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Alline R Pacheco
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Angel G Jimenez
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Regan M Russell
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Santiago Cuesta
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Aman Kumar
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wenhan Zhu
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gonçalo Vale
- Center for Human Nutrition, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sarah A Martin
- Department of Molecular Genetics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Prithvi Raj
- Microbiome Research Lab, Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jeffrey G McDonald
- Center for Human Nutrition, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sebastian E Winter
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vanessa Sperandio
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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24
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Ellermann M, Sperandio V. Bacterial signaling as an antimicrobial target. Curr Opin Microbiol 2020; 57:78-86. [PMID: 32916624 DOI: 10.1016/j.mib.2020.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/29/2020] [Accepted: 08/03/2020] [Indexed: 12/12/2022]
Abstract
Antibiotics profoundly reduced worldwide mortality. However, the emergence of resistance to the growth inhibiting effects of these drugs occurred. New approaches to treat infectious disease that reduce the likelihood for resistance are needed. In bacterial pathogens, complex signaling networks regulate virulence. Anti-virulence therapies aim to disrupt these networks to attenuate virulence without affecting growth. Quorum-sensing, a cell-to-cell communication system, represents an attractive anti-virulence target because it often activates virulence. The challenge is to identify druggable targets that inhibit virulence, while also minimizing the likelihood of mutations promoting resistance. Moreover, given the ubiquity of quorum-sensing systems in commensals, any potential effects of anti-virulence therapies on microbiome function should also be considered. Here we highlight the efficacy and drawbacks of anti-virulence approaches.
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Affiliation(s)
- Melissa Ellermann
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vanessa Sperandio
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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25
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Meng J, Chen H, Lv Q, Luo X, Yang K. The Release of Norepinephrine in C57BL/6J Mice Treated with 6-Hydroxydopamine (6-OHDA) is Associated with Translocations in Enteric Escherichia coli via the QseC Histidine Kinase Receptor. Med Sci Monit 2020; 26:e922986. [PMID: 32764532 PMCID: PMC7433386 DOI: 10.12659/msm.922986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Background We aimed to investigate the effects of norepinephrine (NE) released from endogenous stores on bacterial translocation of Escherichia coli in mice by administration of 6-hydroxydopamine (6-OHDA), which selectively destroys noradrenergic nerve terminals. Material/Methods E. coli strain BW25113 and its derivatives (BW25113ΔqseC and BW25113ΔqseC pQseC) were used in this study. The serum concentrations of endotoxin were analyzed. The strains BW25113, BW25113ΔqseC, and BW25113ΔqseC pQseC were detected respectively in tissue specimens harvested from mice treated with 6-OHDA. Results Mice treated with BW25113ΔqseC showed reduced levels of bacterial translocation following administration of 6-OHDA compared with mice treated with BW25113. The defect of E. coli QseC receptor caused the norepinephrine-QseC signal chain to be interrupted, and the invasiveness and penetrating power of the bacteria on the intestinal mucosa was weakened, eventually leading to a significant decrease in the incidence of bacterial translocation. Conclusions NE modulates the interaction of enteric bacterial pathogens with their hosts via QseC. The blockade of the QseC receptor-mediated effects may be useful to attenuate bacterial translocation.
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Affiliation(s)
- Jun Meng
- Department of Cardiovascular Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China (mainland)
| | - Huamei Chen
- Department of Anesthesiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China (mainland)
| | - Qin Lv
- Department of Anesthesiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China (mainland)
| | - Xiaodan Luo
- Department of Anesthesiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China (mainland)
| | - Kun Yang
- Department of Anesthesiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China (mainland)
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26
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Khan F, Javaid A, Kim YM. Functional Diversity of Quorum Sensing Receptors in Pathogenic Bacteria: Interspecies, Intraspecies and Interkingdom Level. Curr Drug Targets 2020; 20:655-667. [PMID: 30468123 DOI: 10.2174/1389450120666181123123333] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 11/16/2018] [Accepted: 11/16/2018] [Indexed: 01/17/2023]
Abstract
The formation of biofilm by pathogenic bacteria is considered as one of the most powerful mechanisms/modes of resistance against the action of several antibiotics. Biofilm is formed as a structural adherent over the surfaces of host, food and equipments etc. and is further functionally coordinated by certain chemicals produced itself. These chemicals are known as quorum sensing (QS) signaling molecules and are involved in the cross talk at interspecies, intraspecies and interkingdom levels thus resulting in the production of virulence factors leading to pathogenesis. Bacteria possess receptors to sense these chemicals, which interact with the incoming QS molecules. It is followed by the secretion of virulence molecules, regulation of bioluminescence, biofilm formation, antibiotic resistance development and motility behavioral responses. In the natural environment, different bacterial species (Gram-positive and Gram-negative) produce QS signaling molecules that are structurally and functionally different. Recent and past research shows that various antagonistic molecules (naturally and chemically synthesized) are characterized to inhibit the formation of biofilm and attenuation of bacterial virulence by blocking the QS receptors. This review article describes about the diverse QS receptors at their structural, functional and production levels. Thus, by blocking these receptors with inhibitory molecules can be a potential therapeutic approach to control pathogenesis. Furthermore, these receptors can also be used as a structural platform to screen the most potent inhibitors with the help of bioinformatics approaches.
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Affiliation(s)
- Fazlurrahman Khan
- Marine-Integrated Bionics Research Center, Pukyong National University, Busan 48513, South Korea.,Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida 201306, U.P, India
| | - Aqib Javaid
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida 201306, U.P, India
| | - Young-Mog Kim
- Marine-Integrated Bionics Research Center, Pukyong National University, Busan 48513, South Korea.,Department of Food Science and Technology, Pukyong National University, Busan 48513, South Korea
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27
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Alexander EM, Kreitler DF, Guidolin V, Hurben AK, Drake E, Villalta PW, Balbo S, Gulick AM, Aldrich CC. Biosynthesis, Mechanism of Action, and Inhibition of the Enterotoxin Tilimycin Produced by the Opportunistic Pathogen Klebsiella oxytoca. ACS Infect Dis 2020; 6:1976-1997. [PMID: 32485104 PMCID: PMC7354218 DOI: 10.1021/acsinfecdis.0c00326] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Tilimycin is an enterotoxin produced by the opportunistic pathogen Klebsiella oxytoca that causes antibiotic-associated hemorrhagic colitis (AAHC). This pyrrolobenzodiazepine (PBD) natural product is synthesized by a bimodular nonribosomal peptide synthetase (NRPS) pathway composed of three proteins: NpsA, ThdA, and NpsB. We describe the functional and structural characterization of the fully reconstituted NRPS system and report the steady-state kinetic analysis of all natural substrates and cofactors as well as the structural characterization of both NpsA and ThdA. The mechanism of action of tilimycin was confirmed using DNA adductomics techniques through the detection of putative N-2 guanine alkylation after tilimycin exposure to eukaryotic cells, providing the first structural characterization of a PBD-DNA adduct formed in cells. Finally, we report the rational design of small-molecule inhibitors that block tilimycin biosynthesis in whole cell K. oxytoca (IC50 = 29 ± 4 μM) through the inhibition of NpsA (KD = 29 ± 4 nM).
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Affiliation(s)
- Evan M. Alexander
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Dale F. Kreitler
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences University at Buffalo, Buffalo, New York 14203, USA
| | - Valeria Guidolin
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Alexander K. Hurben
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Eric Drake
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences University at Buffalo, Buffalo, New York 14203, USA
| | - Peter W. Villalta
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Silvia Balbo
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Andrew M. Gulick
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences University at Buffalo, Buffalo, New York 14203, USA
| | - Courtney C. Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
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28
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Tsai CN, MacNair CR, Cao MPT, Perry JN, Magolan J, Brown ED, Coombes BK. Targeting Two-Component Systems Uncovers a Small-Molecule Inhibitor of Salmonella Virulence. Cell Chem Biol 2020; 27:793-805.e7. [PMID: 32413287 DOI: 10.1016/j.chembiol.2020.04.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/27/2020] [Accepted: 04/06/2020] [Indexed: 12/27/2022]
Abstract
Salmonella serovars are leading causes of gastrointestinal disease and have become increasingly resistant to fluoroquinolone and cephalosporin antibiotics. Overcoming this healthcare crisis requires new approaches in antibiotic discovery and the identification of unique bacterial targets. In this work, we describe a chemical genomics approach to identify inhibitors of Salmonella virulence. From a cell-based, promoter reporter screen of ∼50,000 small molecules, we identified dephostatin as a non-antibiotic compound that inhibits intracellular virulence factors and polymyxin resistance genes. Dephostatin disrupts signaling through both the SsrA-SsrB and PmrB-PmrA two-component regulatory systems and restores sensitivity to the last-resort antibiotic, colistin. Cell-based experiments and mouse models of infection demonstrate that dephostatin attenuates Salmonella virulence in vitro and in vivo, suggesting that perturbing regulatory networks is a promising strategy for the development of anti-infectives.
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Affiliation(s)
- Caressa N Tsai
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Craig R MacNair
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - My P T Cao
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Jordyn N Perry
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Jakob Magolan
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Brian K Coombes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada.
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29
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Maini Rekdal V, Nol Bernadino P, Luescher MU, Kiamehr S, Le C, Bisanz JE, Turnbaugh PJ, Bess EN, Balskus EP. A widely distributed metalloenzyme class enables gut microbial metabolism of host- and diet-derived catechols. eLife 2020; 9:e50845. [PMID: 32067637 PMCID: PMC7028382 DOI: 10.7554/elife.50845] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/03/2020] [Indexed: 12/23/2022] Open
Abstract
Catechol dehydroxylation is a central chemical transformation in the gut microbial metabolism of plant- and host-derived small molecules. However, the molecular basis for this transformation and its distribution among gut microorganisms are poorly understood. Here, we characterize a molybdenum-dependent enzyme from the human gut bacterium Eggerthella lenta that dehydroxylates catecholamine neurotransmitters. Our findings suggest that this activity enables E. lenta to use dopamine as an electron acceptor. We also identify candidate dehydroxylases that metabolize additional host- and plant-derived catechols. These dehydroxylases belong to a distinct group of largely uncharacterized molybdenum-dependent enzymes that likely mediate primary and secondary metabolism in multiple environments. Finally, we observe catechol dehydroxylation in the gut microbiotas of diverse mammals, confirming the presence of this chemistry in habitats beyond the human gut. These results suggest that the chemical strategies that mediate metabolism and interactions in the human gut are relevant to a broad range of species and habitats.
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Affiliation(s)
- Vayu Maini Rekdal
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Paola Nol Bernadino
- Department of Chemistry and Molecular BiologyUniversity of California, IrvineIrvineUnited States
- Department of Chemistry and Molecular BiochemistryUniversity of California, IrvineIrvineUnited States
| | - Michael U Luescher
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Sina Kiamehr
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Chip Le
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Jordan E Bisanz
- Department of Microbiology and ImmunologyUniversity of California, San FranciscoSan FranciscoUnited States
| | - Peter J Turnbaugh
- Department of Microbiology and ImmunologyUniversity of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Elizabeth N Bess
- Department of Chemistry and Molecular BiologyUniversity of California, IrvineIrvineUnited States
- Department of Chemistry and Molecular BiochemistryUniversity of California, IrvineIrvineUnited States
| | - Emily P Balskus
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
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30
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Kumar A, Ellermann M, Sperandio V. Taming the Beast: Interplay between Gut Small Molecules and Enteric Pathogens. Infect Immun 2019; 87:e00131-19. [PMID: 31262983 PMCID: PMC6704596 DOI: 10.1128/iai.00131-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The overuse of antibiotics has led to the evolution of drug-resistant bacteria that are becoming increasingly dangerous to human health. According to the Centers for Disease Control and Prevention, antibiotic-resistant bacteria cause at least 2 million illnesses and 23,000 deaths in the United States annually. Traditionally, antibiotics are bactericidal or bacteriostatic agents that place selective pressure on bacteria, leading to the expansion of antibiotic-resistant strains. In addition, antibiotics that are effective against some pathogens can also exacerbate their pathogenesis and may lead to severe progression of the disease. Therefore, alternative strategies are needed to treat antibiotic-resistant bacterial infections. One novel approach is to target bacterial virulence to prevent or limit pathogen colonization, while also minimizing tissue damage and disease comorbidities in the host. This review focuses on the interactions between enteric pathogens and naturally occurring small molecules in the human gut as potential therapeutic targets for antivirulence strategies. Individual small molecules in the intestines modulate enteric pathogen virulence and subsequent intestinal fitness and colonization. Targeted interruption of pathogen sensing of these small molecules could therefore attenuate their virulence. This review highlights the paths of discovery for new classes of antimicrobials that could potentially mitigate the urgent problem of antibiotic resistance.
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Affiliation(s)
- Aman Kumar
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Melissa Ellermann
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Vanessa Sperandio
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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31
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QseC Signaling in the Outbreak O104:H4 Escherichia coli Strain Combines Multiple Factors during Infection. J Bacteriol 2019; 201:JB.00203-19. [PMID: 31235511 DOI: 10.1128/jb.00203-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/08/2019] [Indexed: 12/22/2022] Open
Abstract
Enteroaggregative Escherichia coli (EAEC) from the O104:H4 specific serotype caused a large outbreak of bloody diarrhea with some complicated cases of hemolytic-uremic syndrome (HUS) in Europe in 2011. The outbreak strain consisted in an EAEC capable to produce the Shiga toxin (Stx) subtype 2a, a characteristic from enterohemorrhagic E. coli QseBC two-component system detects AI-3/Epi/NE and mediates the chemical signaling between pathogen and mammalian host. This system coordinates a cascade of virulence genes expression in important human enteropathogens. The blocking of QseC of EAEC C227-11 (Stx+) strain by N-phenyl-4-{[(phenylamino) thioxomethyl]amino}-benzenesulfonamide (also known as LED209) in vivo demonstrated a lower efficiency of colonization. The periplasmic protein VisP, which is related to survival mechanisms in a colitis model of infection, bacterial membrane maintenance, and stress resistance, here presented high levels of expression during the initial infection within the host. Under acid stress conditions, visP expression levels were differentiated in an Stx-dependent way. Together, these results emphasize the important role of VisP and the histidine kinase sensor QseC in the C227-11 (Stx+) outbreak strain for the establishment of the infectious niche process in the C57BL/6 mouse model and of LED209 as a promising antivirulence drug strategy against these enteric pathogens.IMPORTANCE EAEC is a remarkable etiologic agent of acute and persistent diarrhea worldwide. The isolates harbor specific subsets of virulence genes and their pathogenesis needs to be better understood. Chemical signaling via histidine kinase sensor QseC has been shown as a potential target to elucidate the orchestration of the regulatory cascade of virulence factors.
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32
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Zhu W, Miyata N, Winter MG, Arenales A, Hughes ER, Spiga L, Kim J, Sifuentes-Dominguez L, Starokadomskyy P, Gopal P, Byndloss MX, Santos RL, Burstein E, Winter SE. Editing of the gut microbiota reduces carcinogenesis in mouse models of colitis-associated colorectal cancer. J Exp Med 2019; 216:2378-2393. [PMID: 31358565 PMCID: PMC6781011 DOI: 10.1084/jem.20181939] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 05/28/2019] [Accepted: 07/09/2019] [Indexed: 12/13/2022] Open
Abstract
Enterobacteriaceae family members such as E. coli exacerbate development of intestinal malignancy. Zhu et al. report that targeting the metabolism of protumoral Enterobacteriaceae by tungstate prevents tumor development in murine models of colitis-associated colorectal cancer. Chronic inflammation and gut microbiota dysbiosis, in particular the bloom of genotoxin-producing E. coli strains, are risk factors for the development of colorectal cancer. Here, we sought to determine whether precision editing of gut microbiota metabolism and composition could decrease the risk for tumor development in mouse models of colitis-associated colorectal cancer (CAC). Expansion of experimentally introduced E. coli strains in the azoxymethane/dextran sulfate sodium colitis model was driven by molybdoenzyme-dependent metabolic pathways. Oral administration of sodium tungstate inhibited E. coli molybdoenzymes and selectively decreased gut colonization with genotoxin-producing E. coli and other Enterobacteriaceae. Restricting the bloom of Enterobacteriaceae decreased intestinal inflammation and reduced the incidence of colonic tumors in two models of CAC, the azoxymethane/dextran sulfate sodium colitis model and azoxymethane-treated, Il10-deficient mice. We conclude that metabolic targeting of protumoral Enterobacteriaceae during chronic inflammation is a suitable strategy to prevent the development of malignancies arising from gut microbiota dysbiosis.
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Affiliation(s)
- Wenhan Zhu
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Naoteru Miyata
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX.,Digestive Disease Center, International University of Health and Welfare, Mita Hospital, Japan
| | - Maria G Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Alexandre Arenales
- Departamento de Clinica e Cirurgia Veterinarias, Escola de Veterinaria, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Elizabeth R Hughes
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Luisella Spiga
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jiwoong Kim
- Department of Clinical Science, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX
| | | | - Petro Starokadomskyy
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX
| | - Purva Gopal
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Mariana X Byndloss
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - Renato L Santos
- Departamento de Clinica e Cirurgia Veterinarias, Escola de Veterinaria, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ezra Burstein
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX .,Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Sebastian E Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX
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33
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Ramakrishnan SK, Zhang H, Ma X, Jung I, Schwartz AJ, Triner D, Devenport SN, Das NK, Xue X, Zeng MY, Hu Y, Mortensen RM, Greenson JK, Cascalho M, Wobus CE, Colacino JA, Nunez G, Rui L, Shah YM. Intestinal non-canonical NFκB signaling shapes the local and systemic immune response. Nat Commun 2019; 10:660. [PMID: 30737385 PMCID: PMC6368617 DOI: 10.1038/s41467-019-08581-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 01/21/2019] [Indexed: 12/13/2022] Open
Abstract
Microfold cells (M-cells) are specialized cells of the intestine that sample luminal microbiota and dietary antigens to educate the immune cells of the intestinal lymphoid follicles. The function of M-cells in systemic inflammatory responses are still unclear. Here we show that epithelial non-canonical NFkB signaling mediated by NFkB-inducing kinase (NIK) is highly active in intestinal lymphoid follicles, and is required for M-cell maintenance. Intestinal NIK signaling modulates M-cell differentiation and elicits both local and systemic IL-17A and IgA production. Importantly, intestinal NIK signaling is active in mouse models of colitis and patients with inflammatory bowel diseases; meanwhile, constitutive NIK signaling increases the susceptibility to inflammatory injury by inducing ectopic M-cell differentiation and a chronic increase of IL-17A. Our work thus defines an important function of non-canonical NFkB and M-cells in immune homeostasis, inflammation and polymicrobial sepsis.
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Affiliation(s)
| | - Huabing Zhang
- Department of Molecular & Integrative Physiology, University of Michigan, Michigan, MI, 48109, USA
| | - Xiaoya Ma
- Department of Molecular & Integrative Physiology, University of Michigan, Michigan, MI, 48109, USA
| | - Inkyung Jung
- Department of Molecular & Integrative Physiology, University of Michigan, Michigan, MI, 48109, USA
| | - Andrew J Schwartz
- Department of Molecular & Integrative Physiology, University of Michigan, Michigan, MI, 48109, USA
| | - Daniel Triner
- Department of Molecular & Integrative Physiology, University of Michigan, Michigan, MI, 48109, USA
| | - Samantha N Devenport
- Department of Molecular & Integrative Physiology, University of Michigan, Michigan, MI, 48109, USA
| | - Nupur K Das
- Department of Molecular & Integrative Physiology, University of Michigan, Michigan, MI, 48109, USA
| | - Xiang Xue
- Department of Molecular & Integrative Physiology, University of Michigan, Michigan, MI, 48109, USA
| | - Melody Y Zeng
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yinling Hu
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Richard M Mortensen
- Department of Molecular & Integrative Physiology, University of Michigan, Michigan, MI, 48109, USA
| | - Joel K Greenson
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Marilia Cascalho
- Transplantation Biology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Surgery, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Christiane E Wobus
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Nutritional Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Gabriel Nunez
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Liangyou Rui
- Department of Molecular & Integrative Physiology, University of Michigan, Michigan, MI, 48109, USA
- Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yatrik M Shah
- Department of Molecular & Integrative Physiology, University of Michigan, Michigan, MI, 48109, USA.
- Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.
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Sudo N. Biogenic Amines: Signals Between Commensal Microbiota and Gut Physiology. Front Endocrinol (Lausanne) 2019; 10:504. [PMID: 31417492 PMCID: PMC6685489 DOI: 10.3389/fendo.2019.00504] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 07/11/2019] [Indexed: 12/20/2022] Open
Abstract
There is increasing interest in the interactions among the gut microbiota, gut, and brain, which is often referred to as the "microbiota-gut-brain" axis. Biogenic amines including dopamine, norepinephrine, serotonin, and histamines are all generated by commensal gut microorganisms and are suggested to play roles as signaling molecules mediating the function of the "microbiota-gut-brain" axis. In addition, such amines generated in the gut have attracted attention in terms of possible clues into the etiologies of depression, anxiety, and even psychosis. This review covers the latest research related to the potential role of microbe-derived amines such as catecholamine, serotonin, histamine, as well as other trace amines, in modulating not only gut physiology but also brain function of the host. Further attention in this field can offer not only insight into expanding the fundamental roles and impacts of the human microbiome, but also further offer new therapeutic strategies for psychological disorders based on regulating the balance of resident bacteria.
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Sun Y, Li L, Xie R, Wang B, Jiang K, Cao H. Stress Triggers Flare of Inflammatory Bowel Disease in Children and Adults. Front Pediatr 2019; 7:432. [PMID: 31709203 PMCID: PMC6821654 DOI: 10.3389/fped.2019.00432] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 10/07/2019] [Indexed: 12/15/2022] Open
Abstract
Inflammatory bowel disease (IBD) is an idiopathic inflammatory disease characterized by chronic and relapsing manifestations. It is noteworthy that the prevalence of IBD is gradually increasing in both children and adults. Currently, the pathogenesis of IBD remains to be completely elucidated. IBD is believed to occur through interactions among genetics, environmental factors, and the gut microbiota. However, the relapsing and remitting course of IBD underlines the importance of other modifiers, such as psychological stress. Growing evidence from clinical and experimental studies suggests that stress acts as a promoting or relapsing factor for IBD. Importantly, recent studies have reported an increasing incidence of anxiety or depression in both children and adults with IBD. In this article, we review the mechanisms by which stress affects IBD, such as via impaired intestinal barrier function, disturbance of the gut microbiota, intestinal dysmotility, and immune and neuroendocrine dysfunction. With regard to both children and adults, we provide recent evidence to describe how stress can affect IBD at various stages. Furthermore, we emphasize the importance of mental healing and discuss the value of approaches targeting stress in clinical management to develop enhanced strategies for the prevention and treatment of IBD.
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Affiliation(s)
- Yue Sun
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China
| | - Lu Li
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China
| | - Runxiang Xie
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China
| | - Bangmao Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China
| | - Kui Jiang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China
| | - Hailong Cao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China
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Palmela C, Chevarin C, Xu Z, Torres J, Sevrin G, Hirten R, Barnich N, Ng SC, Colombel JF. Adherent-invasive Escherichia coli in inflammatory bowel disease. Gut 2018; 67:574-587. [PMID: 29141957 DOI: 10.1136/gutjnl-2017-314903] [Citation(s) in RCA: 320] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 09/20/2017] [Accepted: 10/28/2017] [Indexed: 02/06/2023]
Abstract
Intestinal microbiome dysbiosis has been consistently described in patients with IBD. In the last decades, Escherichia coli, and the adherent-invasive E coli (AIEC) pathotype in particular, has been implicated in the pathogenesis of IBD. Since the discovery of AIEC, two decades ago, progress has been made in unravelling these bacteria characteristics and its interaction with the gut immune system. The mechanisms of adhesion of AIEC to intestinal epithelial cells (via FimH and cell adhesion molecule 6) and its ability to escape autophagy when inside macrophages are reviewed here. We also explore the existing data on the prevalence of AIEC in patients with Crohn's disease and UC, and the association between the presence of AIEC and disease location, activity and postoperative recurrence. Finally, we highlight potential therapeutic strategies targeting AIEC colonisation of gut mucosa, including the use of phage therapy, bacteriocins and antiadhesive molecules. These strategies may open new avenues for the prevention and treatment of IBD in the future.
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Affiliation(s)
- Carolina Palmela
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.,Division of Gastroenterology, Hospital Beatriz Ângelo, Loures, Portugal
| | - Caroline Chevarin
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, F-63000 Clermont-Ferrand, France
| | - Zhilu Xu
- Department of Medicine and Therapeutics, Institute of Digestive Diseases, LKS Institute of Health Science, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China
| | - Joana Torres
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.,Division of Gastroenterology, Hospital Beatriz Ângelo, Loures, Portugal
| | - Gwladys Sevrin
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, F-63000 Clermont-Ferrand, France
| | - Robert Hirten
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Nicolas Barnich
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, F-63000 Clermont-Ferrand, France
| | - Siew C Ng
- Department of Medicine and Therapeutics, Institute of Digestive Diseases, LKS Institute of Health Science, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China
| | - Jean-Frederic Colombel
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
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Anderson CJ, Kendall MM. Salmonella enterica Serovar Typhimurium Strategies for Host Adaptation. Front Microbiol 2017; 8:1983. [PMID: 29075247 PMCID: PMC5643478 DOI: 10.3389/fmicb.2017.01983] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 09/26/2017] [Indexed: 12/21/2022] Open
Abstract
Bacterial pathogens must sense and respond to newly encountered host environments to regulate the expression of critical virulence factors that allow for niche adaptation and successful colonization. Among bacterial pathogens, non-typhoidal serovars of Salmonella enterica, such as serovar Typhimurium (S. Tm), are a primary cause of foodborne illnesses that lead to hospitalizations and deaths worldwide. S. Tm causes acute inflammatory diarrhea that can progress to invasive systemic disease in susceptible patients. The gastrointestinal tract and intramacrophage environments are two critically important niches during S. Tm infection, and each presents unique challenges to limit S. Tm growth. The intestinal tract is home to billions of commensal microbes, termed the microbiota, which limits the amount of available nutrients for invading pathogens such as S. Tm. Therefore, S. Tm encodes strategies to manipulate the commensal population and side-step this nutritional competition. During subsequent stages of disease, S. Tm resists host immune cell mechanisms of killing. Host cells use antimicrobial peptides, acidification of vacuoles, and nutrient limitation to kill phagocytosed microbes, and yet S. Tm is able to subvert these defense systems. In this review, we discuss recently described molecular mechanisms that S. Tm uses to outcompete the resident microbiota within the gastrointestinal tract. S. Tm directly eliminates close competitors via bacterial cell-to-cell contact as well as by stimulating a host immune response to eliminate specific members of the microbiota. Additionally, S. Tm tightly regulates the expression of key virulence factors that enable S. Tm to withstand host immune defenses within macrophages. Additionally, we highlight the chemical and physical signals that S. Tm senses as cues to adapt to each of these environments. These strategies ultimately allow S. Tm to successfully adapt to these two disparate host environments. It is critical to better understand bacterial adaptation strategies because disruption of these pathways and mechanisms, especially those shared by multiple pathogens, may provide novel therapeutic intervention strategies.
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Affiliation(s)
- Christopher J Anderson
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine,, Charlottesville, VA, United States
| | - Melissa M Kendall
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine,, Charlottesville, VA, United States
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38
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Yang Y, Liao Y, Ma Y, Gong W, Zhu G. The role of major virulence factors of AIEC involved in inflammatory bowl disease—a mini-review. Appl Microbiol Biotechnol 2017; 101:7781-7787. [DOI: 10.1007/s00253-017-8507-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/30/2017] [Accepted: 08/30/2017] [Indexed: 02/07/2023]
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39
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Natfji AA, Osborn HM, Greco F. Feasibility of polymer-drug conjugates for non-cancer applications. Curr Opin Colloid Interface Sci 2017. [DOI: 10.1016/j.cocis.2017.07.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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40
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McKay R, Hauk P, Wu HC, Pottash AE, Shang W, Terrell J, Payne GF, Bentley WE. Controlling localization of Escherichia coli populations using a two-part synthetic motility circuit: An accelerator and brake. Biotechnol Bioeng 2017; 114:2883-2895. [PMID: 28755474 DOI: 10.1002/bit.26391] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/21/2017] [Accepted: 07/23/2017] [Indexed: 12/30/2022]
Abstract
Probiotics, whether taken as capsules or consumed in foods, have been regarded as safe for human use by regulatory agencies. Being living cells, they serve as "tunable" factories for the synthesis of a vast array of beneficial molecules. The idea of reprogramming probiotics to act as controllable factories, producing potential therapeutic molecules under user-specified conditions, represents a new and powerful concept in drug synthesis and delivery. Probiotics that serve as drug delivery vehicles pose several challenges, one being targeting (as seen with nanoparticle approaches). Here, we employ synthetic biology to control swimming directionality in a process referred to as "pseudotaxis." Escherichia coli, absent the motility regulator cheZ, swim sporadically, missing the traditional "run" in the run:tumble swimming paradigm. Upon introduction of cheZ in trans and its signal-generated upregulation, engineered bacteria can be "programmed" to swim toward the source of the chemical cue. Here, engineered cells that encounter sufficient levels of the small signal molecule pyocyanin, produce an engineered CheZ and swim with programmed directionality. By incorporating a degradation tag at the C-terminus of CheZ, the cells stop running when they exit spaces containing pyocyanin. That is, the engineered CheZ modified with a C-terminal extension derived from the putative DNA-binding transcriptional regulator YbaQ (RREERAAKKVA) is consumed by the ClpXP protease machine at a rate sufficient to "brake" the cells when pyocyanin levels are too low. Through this process, we demonstrate that over time, these engineered E. coli accumulate in pyocyanin-rich locales. We suggest that such approaches may find utility in engineering probiotics so that their beneficial functions can be focused in areas of principal benefit.
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Affiliation(s)
- Ryan McKay
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland
| | - Pricila Hauk
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland
| | - Hsuan-Chen Wu
- Department of Biochemical Science and Technology, National Taiwan University, Taipei City, Taiwan
| | - Alex Eli Pottash
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland
| | - Wu Shang
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland
| | | | - Gregory F Payne
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland
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Involvement of Two-Component Signaling on Bacterial Motility and Biofilm Development. J Bacteriol 2017; 199:JB.00259-17. [PMID: 28533218 DOI: 10.1128/jb.00259-17] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Two-component signaling is a specialized mechanism that bacteria use to respond to changes in their environment. Nonpathogenic strains of Escherichia coli K-12 harbor 30 histidine kinases and 32 response regulators, which form a network of regulation that integrates many other global regulators that do not follow the two-component signaling mechanism, as well as signals from central metabolism. The output of this network is a multitude of phenotypic changes in response to changes in the environment. Among these phenotypic changes, many two-component systems control motility and/or the formation of biofilm, sessile communities of bacteria that form on surfaces. Motility is the first reversible attachment phase of biofilm development, followed by a so-called swim or stick switch toward surface organelles that aid in the subsequent phases. In the mature biofilm, motility heterogeneity is generated by a combination of evolutionary and gene regulatory events.
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Indole-Induced Reversion of Intrinsic Multiantibiotic Resistance in Lysobacter enzymogenes. Appl Environ Microbiol 2017. [PMID: 28625984 DOI: 10.1128/aem.00995-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Lysobacter species are a group of environmental bacteria that are emerging as a new source of antibiotics. One characteristic of Lysobacter is intrinsic resistance to multiple antibiotics, which had not been studied. To understand the resistance mechanism, we tested the effect of blocking two-component regulatory systems (TCSs) on the antibiotic resistance of Lysobacter enzymogenes, a prolific producer of antibiotics. Upon treatment with LED209, an inhibitor of the widespread TCS QseC/QseB, L. enzymogenes produced a large amount of an unknown metabolite that was barely detectable in the untreated culture. Subsequent structural elucidation by nuclear magnetic resonance (NMR) unexpectedly revealed that the metabolite was indole. Indole production was also markedly induced by adrenaline, a known modulator of QseC/QseB. Next, we identified two TCS genes, L. enzymogenesqseC (Le-qseC) and Le-qseB, in L. enzymogenes and found that mutations of Le-qseC and Le-qseB also led to a dramatic increase in indole production. We then chemically synthesized a fluorescent indole probe that could label the cells. While the Le-qseB (cytoplasmic response regulator) mutant was clearly labeled by the probe, the Le-qseC (membrane sensor) mutant was not labeled. It was reported previously that indole can enhance antibiotic resistance in bacteria. Therefore, we tested if the dramatic increase in the level of indole production in L. enzymogenes upon blocking of Le-qseC and Le-qseB would lead to enhanced antibiotic resistance. Surprisingly, we found that indole caused the intrinsically multiantibiotic-resistant bacterium L. enzymogenes to become susceptible. Point mutations at conserved amino acids in Le-QseC also led to antibiotic susceptibility. Because indole is known as an interspecies signal, these findings may have implications.IMPORTANCE The environmental bacterium Lysobacter is a new source of antibiotic compounds and exhibits intrinsic antibiotic resistance. Here, we found that the inactivation of a two-component regulatory system (TCS) by an inhibitor or by gene deletion led to a remarkable increase in the level of production of a metabolite in L. enzymogenes, and this metabolite was identified to be indole. We chemically synthesized a fluorescent indole probe and found that it could label the wild type and a mutant of the TCS cytoplasmic response regulator but not a mutant of the TCS membrane sensor. Indole treatment caused the intrinsically multidrug-resistant bacterium L. enzymogenes to be susceptible to antibiotics. Mutations of the TCS sensor also led to antibiotic susceptibility. Because indole is known as an interspecies signal between gut microbiota and mammalian hosts, the observation that indole could render intrinsically resistant L. enzymogenes susceptible to common antibiotics may have implications.
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43
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Drug repurposing for antivirulence therapy against opportunistic bacterial pathogens. Emerg Top Life Sci 2017; 1:13-22. [DOI: 10.1042/etls20160018] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 02/21/2017] [Accepted: 02/22/2017] [Indexed: 12/23/2022]
Abstract
Antibiotic resistance is a serious public health concern at the global level. Available antibiotics have saved millions of lives, but are progressively losing their efficacy against many bacterial pathogens, and very few new antibiotics are being developed by the pharmaceutical industry. Over the last few decades, progress in understanding the pathogenic process of bacterial infections has led researchers to focus on bacterial virulence factors as potential targets for ‘antivirulence' drugs, i.e. compounds which inhibit the ability of bacteria to cause damage to the host, as opposed to inhibition of bacterial growth which is typical of antibiotics. Hundreds of virulence inhibitors have been examined to date in vitro and/or in animal models, but only a few were entered into clinical trials and none were approved, thus hindering the clinical validation of antivirulence therapy. To breathe new life into antivirulence research and speed-up its transfer to the clinic, antivirulence activities have also been sought in drugs already approved for different therapeutic purposes in humans. If effective, these drugs could be repositioned for antivirulence therapy and have an easier and faster transfer to the clinic. In this work we summarize the approaches which have led to the identification of repurposing candidates with antivirulence activities, and discuss the challenges and opportunities related to antivirulence therapy and drug repurposing. While this approach undoubtedly holds promise for boosting antivirulence drug research, some important issues remain to be addressed in order to make antivirulence drugs viable alternatives to traditional antibacterials.
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Gomes-Neto JC, Mantz S, Held K, Sinha R, Segura Munoz RR, Schmaltz R, Benson AK, Walter J, Ramer-Tait AE. A real-time PCR assay for accurate quantification of the individual members of the Altered Schaedler Flora microbiota in gnotobiotic mice. J Microbiol Methods 2017; 135:52-62. [PMID: 28189782 DOI: 10.1016/j.mimet.2017.02.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 01/31/2017] [Accepted: 02/07/2017] [Indexed: 01/22/2023]
Abstract
Changes in the gastrointestinal microbial community are frequently associated with chronic diseases such as Inflammatory Bowel Diseases. However, understanding the relationship of any individual taxon within the community to host physiology is made complex due to the diversity and individuality of the gut microbiota. Defined microbial communities such as the Altered Schaedler Flora (ASF) help alleviate the challenges of a diverse microbiota by allowing one to interrogate the relationship between individual bacterial species and host responses. An important aspect of studying these relationships with defined microbial communities is the ability to measure the population abundance and dynamics of each member. Herein, we describe the development of an improved ASF species-specific and sensitive real-time quantitative polymerase chain reaction (qPCR) for use with SYBR Green chemistry to accurately assess individual ASF member abundance. This approach targets hypervariable regions V1 through V3 of the 16S rRNA gene of each ASF taxon to enhance assay specificity. We demonstrate the reproducibility, sensitivity and application of this new method by quantifying each ASF bacterium in two inbred mouse lines. We also used it to assess changes in ASF member abundance before and after acute antibiotic perturbation of the community as well as in mice fed two different diets. Additionally, we describe a nested PCR assay for the detection of lowly abundant ASF members. Altogether, this improved qPCR method will facilitate gnotobiotic research involving the ASF community by allowing for reproducible quantification of its members under various physiological conditions.
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Affiliation(s)
- João Carlos Gomes-Neto
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Sara Mantz
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Kyler Held
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Rohita Sinha
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Rafael R Segura Munoz
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Robert Schmaltz
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Andrew K Benson
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jens Walter
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada; Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Amanda E Ramer-Tait
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA.
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