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Jaiaue P, Srimongkol P, Thitiprasert S, Piluk J, Thammaket J, Assabumrungrat S, Cheirsilp B, Tanasupawat S, Thongchul N. Inactivation of guanylate kinase in Bacillus sp. TL7-3 cultivated under an optimized ratio of carbon and nitrogen sources influenced GTP regeneration capability and sporulation. Heliyon 2024; 10:e31956. [PMID: 38841476 PMCID: PMC11152743 DOI: 10.1016/j.heliyon.2024.e31956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/07/2024] Open
Abstract
Bacillus sp. TL7-3 has potential as a dietary supplement to promote human and animal health. It produces spores that can survive in harsh environments. Thus, when supplemented with nutrients, these spores can withstand the acidic pH of the stomach and resume vegetative development in the gut when exposed to growth-promoting conditions. Spores are formed as a cellular defense mechanism when a culture experiences stress and process optimization to achieve high spore production in a typical batch process remains challenging. Existing literature on the manipulation of gene expression and enzyme activity during batch cultivation is limited. Studies on the growth patterns, morphological changes, and relevant gene expression have aided in enhancing spore production. The present study used the response surface methodology for medium optimization. The model suggested that yeast extract and NH4Cl were significant factors controlling spore production. A comparison between the high weight ratio of carbon and nitrogen (C:N) substrates (8.57:1) in the optimized and basal media (0.52:1) showed an 8.76-fold increase in the final spore concentration. The expression of major genes, including codY, spo0A, kinA, and spo0F, involved in the sporulation was compared when cultivating Bacillus sp. TL7-3 in media with varying C:N ratios. At high C:N ratios, spo0A, kinA, and spo0F were upregulated, whereas codY was downregulated. This led to decreased guanylate kinase activity, resulting in a low guanosine triphosphate concentration and inactivation of CodY, thereby reducing the repression of spo0A and CodY-repressed genes and stimulating sporulation.
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Affiliation(s)
- Phetcharat Jaiaue
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Piroonporn Srimongkol
- Center of Excellence in Bioconversion and Bioseparation for Platform Chemical Production, Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Bangkok, Thailand
- Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Bangkok, Thailand
| | - Sitanan Thitiprasert
- Center of Excellence in Bioconversion and Bioseparation for Platform Chemical Production, Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Bangkok, Thailand
- Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Bangkok, Thailand
| | - Jirabhorn Piluk
- Center of Excellence in Bioconversion and Bioseparation for Platform Chemical Production, Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Bangkok, Thailand
- Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Bangkok, Thailand
| | - Jesnipit Thammaket
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Suttichai Assabumrungrat
- Department of Chemical Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok, Thailand
| | - Benjamas Cheirsilp
- Department of Industrial Biotechnology, Faculty of Agro-Industry, Prince of Songkla University, Songkla, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Nuttha Thongchul
- Center of Excellence in Bioconversion and Bioseparation for Platform Chemical Production, Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Bangkok, Thailand
- Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Bangkok, Thailand
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2
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Kumar K, Barbora L, Moholkar VS. Genomic insights into clostridia in bioenergy production: Comparison of metabolic capabilities and evolutionary relationships. Biotechnol Bioeng 2024; 121:1298-1313. [PMID: 38047471 DOI: 10.1002/bit.28610] [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: 11/15/2022] [Revised: 10/19/2023] [Accepted: 11/16/2023] [Indexed: 12/05/2023]
Abstract
Bacteria from diverse genera, including Acetivibrio, Bacillus, Cellulosilyticum, Clostridium, Desulfotomaculum, Lachnoclostridium, Moorella, Ruminiclostridium, and Thermoanaerobacterium, have attracted significant attention due to their versatile metabolic capabilities encompassing acetogenic, cellulolytic, and C1-metabolic properties, and acetone-butanol-ethanol fermentation. Despite their biotechnological significance, a comprehensive understanding of clostridial physiology and evolution has remained elusive. This study reports an extensive comparative genomic analysis of 48 fully sequenced bacterial genomes from these genera. Our investigation, encompassing pan-genomic analysis, central carbon metabolism comparison, exploration of general genome features, and in-depth scrutiny of Cluster of Orthologous Groups genes, has established a holistic whole-genome-based phylogenetic framework. We have classified these strains into acetogenic, butanol-producing, cellulolytic, CO2-fixating, chemo(litho/organo)trophic, and heterotrophic categories, often exhibiting overlaps. Key outcomes include the identification of misclassified species and the revelation of insights into metabolic features, energy conservation, substrate utilization, stress responses, and regulatory mechanisms. These findings can provide guidance for the development of efficient microbial systems for sustainable bioenergy production. Furthermore, by addressing fundamental questions regarding genetic relationships, conserved genomic features, pivotal enzymes, and essential genes, this study has also contributed to our comprehension of clostridial biology, evolution, and their shared metabolic potential.
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Affiliation(s)
- Karan Kumar
- School of Energy Science and Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Lepakshi Barbora
- School of Energy Science and Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Vijayanand S Moholkar
- School of Energy Science and Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
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3
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Zeng J, Fang S, Guo J, Dong M, Tian G, Tao L. Fight or flee, a vital choice for Clostridioides difficile. MLIFE 2024; 3:14-20. [PMID: 38827507 PMCID: PMC11139204 DOI: 10.1002/mlf2.12102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/17/2023] [Accepted: 10/08/2023] [Indexed: 06/04/2024]
Abstract
Clostridioides difficile is a leading cause of healthcare-associated infections, causing billions of economic losses every year. Its symptoms range from mild diarrhea to life-threatening damage to the colon. Transmission and recurrence of C. difficile infection (CDI) are mediated by the metabolically dormant spores, while the virulence of C. difficile is mainly due to the two large clostridial toxins, TcdA and TcdB. Producing toxins or forming spores are two different strategies for C. difficile to cope with harsh environmental conditions. It is of great significance to understand the molecular mechanisms for C. difficile to skew to either of the cellular processes. Here, we summarize the current understanding of the regulation and connections between toxin production and sporulation in C. difficile and further discuss the potential solutions for yet-to-be-answered questions.
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Affiliation(s)
- Ji Zeng
- School of Biomedical and Pharmaceutical SciencesGuangdong University of TechnologyGuangzhouChina
| | - Shuying Fang
- School of Biomedical and Pharmaceutical SciencesGuangdong University of TechnologyGuangzhouChina
| | - Jinquan Guo
- Department of Brest SurgeryPanyu Central HospitalGuangzhouChina
| | - Min Dong
- Department of MicrobiologyHarvard Medical SchoolBostonMassachusettsUSA
- Department of Urology, Boston Children's HospitalHarvard Medical SchoolBostonMassachusettsUSA
| | - Guo‐Bao Tian
- Department of MicrobiologyZhongshan School of Medicine, Sun Yat‐sen UniversityGuangzhouChina
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University), Ministry of EducationGuangzhouChina
- School of MedicineXizang Minzu UniversityXianyangChina
| | - Liang Tao
- Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and BiomedicineWestlake UniversityHangzhouChina
- Research Center for Industries of the Future, School of Life SciencesWestlake UniversityHangzhouChina
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4
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Serrano M, Martins D, Henriques AO. Clostridioides difficile Sporulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1435:273-314. [PMID: 38175480 DOI: 10.1007/978-3-031-42108-2_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Some members of the Firmicutes phylum, including many members of the human gut microbiota, are able to differentiate a dormant and highly resistant cell type, the endospore (hereinafter spore for simplicity). Spore-formers can colonize virtually any habitat and, because of their resistance to a wide variety of physical and chemical insults, spores can remain viable in the environment for long periods of time. In the anaerobic enteric pathogen Clostridioides difficile the aetiologic agent is the oxygen-resistant spore, while the toxins produced by actively growing cells are the main cause of the disease symptoms. Here, we review the regulatory circuits that govern entry into sporulation. We also cover the role of spores in the infectious cycle of C. difficile in relation to spore structure and function and the main control points along spore morphogenesis.
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Affiliation(s)
- Mónica Serrano
- Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal.
| | - Diogo Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Adriano O Henriques
- Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
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5
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Buddle JE, Fagan RP. Pathogenicity and virulence of Clostridioides difficile. Virulence 2023; 14:2150452. [PMID: 36419222 DOI: 10.1080/21505594.2022.2150452] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/02/2022] [Accepted: 11/17/2022] [Indexed: 11/25/2022] Open
Abstract
Clostridioides difficile is the most common cause of nosocomial antibiotic-associated diarrhea, and is responsible for a spectrum of diseases characterized by high levels of recurrence, morbidity, and mortality. Treatment is complex, since antibiotics constitute both the main treatment and the major risk factor for infection. Worryingly, resistance to multiple antibiotics is becoming increasingly widespread, leading to the classification of this pathogen as an urgent threat to global health. As a consummate opportunist, C. difficile is well equipped for promoting disease, owing to its arsenal of virulence factors: transmission of this anaerobe is highly efficient due to the formation of robust endospores, and an array of adhesins promote gut colonization. C. difficile produces multiple toxins acting upon gut epithelia, resulting in manifestations typical of diarrheal disease, and severe inflammation in a subset of patients. This review focuses on such virulence factors, as well as the importance of antimicrobial resistance and genome plasticity in enabling pathogenesis and persistence of this important pathogen.
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Affiliation(s)
- Jessica E Buddle
- Molecular Microbiology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Robert P Fagan
- Molecular Microbiology, School of Biosciences, University of Sheffield, Sheffield, UK
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6
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Frost LR, Stark R, Anonye BO, MacCreath TO, Ferreira LRP, Unnikrishnan M. Dual RNA-seq identifies genes and pathways modulated during Clostridioides difficile colonization. mSystems 2023; 8:e0055523. [PMID: 37615437 PMCID: PMC10654110 DOI: 10.1128/msystems.00555-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/11/2023] [Indexed: 08/25/2023] Open
Abstract
IMPORTANCE The initial interactions between the colonic epithelium and the bacterium are likely critical in the establishment of Clostridioides difficile infection, one of the major causes of hospital-acquired diarrhea worldwide. Molecular interactions between C. difficile and human gut cells have not been well defined mainly due to the technical challenges of studying cellular host-pathogen interactions with this anaerobe. Here we have examined transcriptional changes occurring in the pathogen and host cells during the initial 24 hours of infection. Our data indicate several changes in metabolic pathways and virulence-associated factors during the initial bacterium-host cell contact and early stages of infection. We describe canonical pathways enriched based on the expression profiles of a dual RNA sequencing in the host and bacterium, and functions of bacterial factors that are modulated during infection. This study thus provides fresh insight into the early C. difficile infection process.
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Affiliation(s)
- Lucy R. Frost
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Richard Stark
- Bioinformatics Research Technology Platform, University of Warwick, Coventry, United Kingdom
| | - Blessing O. Anonye
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Thomas O. MacCreath
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Ludmila R. P. Ferreira
- RNA Systems Biology Laboratory (RSBL), Department of Morphology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Meera Unnikrishnan
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
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7
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Rizvi A, Vargas-Cuebas G, Edwards AN, DiCandia MA, Carter ZA, Lee CD, Monteiro MP, McBride SM. Glycine fermentation by C. difficile promotes virulence and spore formation, and is induced by host cathelicidin. Infect Immun 2023; 91:e0031923. [PMID: 37754683 PMCID: PMC10580938 DOI: 10.1128/iai.00319-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 09/28/2023] Open
Abstract
Clostridioides difficile is a leading cause of antibiotic-associated diarrheal disease. C. difficile colonization, growth, and toxin production in the intestine is strongly associated with its ability to use amino acids to generate energy, but little is known about the impact of specific amino acids on C. difficile pathogenesis. The amino acid glycine is enriched in the dysbiotic gut and is suspected to contribute to C. difficile infection. We hypothesized that the use of glycine as an energy source contributes to colonization of the intestine and pathogenesis of C. difficile. To test this hypothesis, we deleted the glycine reductase (GR) genes grdAB, rendering C. difficile unable to ferment glycine, and investigated the impact on growth and pathogenesis. Our data show that the grd pathway promotes growth, toxin production, and sporulation. Glycine fermentation also had a significant impact on toxin production and pathogenesis of C. difficile in the hamster model of disease. Furthermore, we determined that the grd locus is regulated by host cathelicidin (LL-37) and the cathelicidin-responsive regulator, ClnR, indicating that the host peptide signals to control glycine catabolism. The induction of glycine fermentation by LL-37 demonstrates a direct link between the host immune response and the bacterial reactions of toxin production and spore formation.
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Affiliation(s)
- Arshad Rizvi
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Germán Vargas-Cuebas
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Adrianne N. Edwards
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Michael A. DiCandia
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Zavier A. Carter
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Cheyenne D. Lee
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Marcos P. Monteiro
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Shonna M. McBride
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
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8
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Edwards AN, McBride SM. The RgaS-RgaR two-component system promotes Clostridioides difficile sporulation through a small RNA and the Agr1 system. PLoS Genet 2023; 19:e1010841. [PMID: 37844084 PMCID: PMC10602386 DOI: 10.1371/journal.pgen.1010841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/26/2023] [Accepted: 10/02/2023] [Indexed: 10/18/2023] Open
Abstract
The ability to form a dormant spore is essential for the survival of the anaerobic pathogen, Clostridioides difficile, outside of the mammalian gastrointestinal tract. The initiation of sporulation is governed by the master regulator of sporulation, Spo0A, which is activated by phosphorylation. Multiple sporulation factors control Spo0A phosphorylation; however, this regulatory pathway is not well defined in C. difficile. We discovered that RgaS and RgaR, a conserved orphan histidine kinase and orphan response regulator, function together as a cognate two-component regulatory system to directly activate transcription of several genes. One of these targets, agrB1D1, encodes gene products that synthesize and export a small quorum-sensing peptide, AgrD1, which positively influences expression of early sporulation genes. Another target, a small regulatory RNA now known as SpoZ, impacts later stages of sporulation through a small hypothetical protein and an additional, unknown regulatory mechanism(s). Unlike Agr systems in many organisms, AgrD1 does not activate the RgaS-RgaR two-component system, and thus, is not responsible for autoregulating its own production. Altogether, we demonstrate that C. difficile utilizes a conserved two-component system that is uncoupled from quorum-sensing to promote sporulation through two distinct regulatory pathways.
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Affiliation(s)
- Adrianne N. Edwards
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, United States of America
| | - Shonna M. McBride
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, United States of America
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Baldassare MA, Bhattacharjee D, Coles JD, Nelson S, McCollum CA, Seekatz AM. Butyrate enhances Clostridioides difficile sporulation in vitro. J Bacteriol 2023; 205:e0013823. [PMID: 37655912 PMCID: PMC10521354 DOI: 10.1128/jb.00138-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/11/2023] [Indexed: 09/02/2023] Open
Abstract
Short-chain fatty acids (SCFAs) are products of bacterial fermentation that help maintain important gut functions such as maintenance of the intestinal barrier, cell signaling, and immune homeostasis. The main SCFAs acetate, propionate, and butyrate have demonstrated beneficial effects for the host, including its importance in alleviating infections caused by pathogens such as Clostridioides difficile. Despite the potential role of SCFAs in mitigating C. difficile infection, their direct effect on C. difficile remains unclear. Through a set of in vitro experiments, we investigated how SCFAs influence C. difficile growth, sporulation, and toxin production. Similar to previous studies, we observed that butyrate decreased growth of C. difficile strain 630 in a dose-dependent manner. The presence of butyrate also increased C. difficile sporulation, with minimal increases in toxin production. RNA-Seq analysis validated our experimental results, demonstrating increased expression of sporulation-related genes in conjunction with changes in metabolic and regulatory genes, such as a putative carbon starvation protein, CstA. Collectively, these data suggest that butyrate may induce alternative C. difficile survival pathways, modifying its growth ability and virulence to persist in the gut environment. IMPORTANCE Several studies suggest that butyrate may modulate gut infections, such as reducing inflammation caused by the healthcare-associated Clostridioides difficile. While studies in both animal models and human studies correlate high levels of butyrate with reduced C. difficile burden, the direct impact of butyrate on C. difficile remains unclear. Our study demonstrates that butyrate directly influences C. difficile by increasing its sporulation and modifying its metabolism, potentially using butyrate as a biomarker to shift survival strategies in a changing gut environment. These data point to additional therapeutic approaches to combat C. difficile in a butyrate-directed manner.
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Affiliation(s)
| | - Disha Bhattacharjee
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Julian D. Coles
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Sydney Nelson
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - C. Alexis McCollum
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Anna M. Seekatz
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
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10
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Wetzel D, Rizvi A, Edwards AN, McBride SM. The predicted acetoin dehydrogenase pathway represses sporulation of Clostridioides difficile. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.28.551048. [PMID: 37546766 PMCID: PMC10402147 DOI: 10.1101/2023.07.28.551048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Clostridioides difficile is a major gastrointestinal pathogen that is transmitted as a dormant spore. As an intestinal pathogen, C. difficile must contend with variable environmental conditions, including fluctuations in pH and nutrient availability. Nutrition and pH both influence growth and spore formation, but how pH and nutrition jointly influence sporulation are not known. In this study, we investigated the dual impact of pH and pH-dependent metabolism on C. difficile sporulation. Specifically, we examined the impacts of pH and the metabolite acetoin on C. difficile growth and sporulation. We found that expression of the predicted acetoin dehydrogenase operon, acoRABCL , was pH-dependent and regulated by acetoin. Regulation of the C. difficile aco locus is distinct from other characterized systems and appears to involve a co-transcribed DeoR-family regulator rather than the sigma 54 -dependent activator. In addition, an acoA null mutant produced significantly more spores and initiated sporulation earlier than the parent strain. However, unlike other Firmicutes, growth and culture density of C. difficile was not increased by acetoin availability or disruption of the aco pathway. Together, these results indicate that acetoin, pH, and the aco pathway play important roles in nutritional repression of sporulation in C. difficile , but acetoin metabolism does not support cell growth as a stationary phase energy source. IMPORTANCE Clostridioides difficile, or C. diff , is an anaerobic bacterium that lives within the gut of many mammals and causes infectious diarrhea. C. difficile is able to survive outside of the gut and transmit to new hosts by forming dormant spores. It is known that the pH of the intestine and the nutrients available both affect the growth and sporulation of C. diffiicile, but the specific conditions that result in sporulation in the host are not clear. In this study, we investigated how pH and the metabolite acetoin affect the ability of C. difficile to grow, proliferate, and form spores. We found that a mutant lacking the predicted acetoin metabolism pathway form more spores, but their growth is not impacted. These results show that C. difficile uses acetoin differently than many other species and that acetoin has an important role as an environmental metabolite that influences spore formation.
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Ouyang Z, Zhao H, Zhao M, Yang Y, Zhao J. Type IV pili are involved in phenotypes associated with Clostridioides difficile pathogenesis. Crit Rev Microbiol 2023:1-9. [PMID: 37452617 DOI: 10.1080/1040841x.2023.2235002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/23/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Abstract
Clostridioides difficile is a Gram-positive, spore-forming, rod-shaped, obligate anaerobe that is the leading cause of antibiotic-associated diarrhea. Type IV pili (T4P) are elongated appendages on the surface of C. difficile that are polymerized from many pilin proteins. T4P play an important role in C. difficile adherence and particularly in its persistence in the host intestine. Recent studies have shown that T4P promote C. difficile aggregation, surface motility, and biofilm formation, which may enhance its pathogenicity. Additionally, the second messenger cyclic diguanylate increases pilA1 transcript abundance, indirectly promoting T4P-mediated aggregation, surface motility, and biofilm formation of C. difficile. This review summarizes recent advances in C. difficile T4P research and the physiological activities of T4P in the context of C. difficile pathogenesis.
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Affiliation(s)
- Zirou Ouyang
- Hebei Provincial Center for Clinical Laboratories, The Second Hospital of Hebei Medical University, Shijiazhuang City, Hebei Province, China
| | - Hanlin Zhao
- Department of Medical Laboratory, Hebei North University, Zhangjiakou, Hebei Province, China
| | - Min Zhao
- Hebei Provincial Center for Clinical Laboratories, The Second Hospital of Hebei Medical University, Shijiazhuang City, Hebei Province, China
| | - Yaxuan Yang
- School of Public Health, The University of Queensland, Brisbane, Queensland, Australia
| | - Jianhong Zhao
- Hebei Provincial Center for Clinical Laboratories, The Second Hospital of Hebei Medical University, Shijiazhuang City, Hebei Province, China
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12
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Edwards AN, McBride SM. The RgaS-RgaR two-component system promotes Clostridioides difficile sporulation through a small RNA and the Agr1 system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546640. [PMID: 37425791 PMCID: PMC10327067 DOI: 10.1101/2023.06.26.546640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The ability to form a dormant spore is essential for the survival of the anaerobic, gastrointestinal pathogen Clostridioides difficile outside of the mammalian gastrointestinal tract. The initiation of sporulation is governed by the master regulator of sporulation, Spo0A, which is activated by phosphorylation. Multiple sporulation factors control Spo0A phosphorylation; however, this regulatory pathway is not well defined in C. difficile. We discovered that RgaS and RgaR, a conserved orphan histidine kinase and orphan response regulator, function together as a cognate two-component regulatory system to directly activate transcription of several genes. One of these targets, agrB1D1, encodes gene products that synthesize and export a small quorum-sensing peptide, AgrD1, which positively influences expression of early sporulation genes. Another target, a small regulatory RNA now known as SrsR, impacts later stages of sporulation through an unknown regulatory mechanism(s). Unlike Agr systems in many organisms, AgrD1 does not activate the RgaS-RgaR two-component system, and thus, is not responsible for autoregulating its own production. Altogether, we demonstrate that C. difficile utilizes a conserved two-component system that is uncoupled from quorum-sensing to promote sporulation through two distinct regulatory pathways.
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Affiliation(s)
- Adrianne N. Edwards
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, GA, USA
| | - Shonna M. McBride
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, GA, USA
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13
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Baldassare MA, Bhattacharjee D, Coles JD, Nelson S, McCollum CA, Seekatz AM. Butyrate enhances Clostridioides difficile sporulation in vitro. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.27.538596. [PMID: 37163089 PMCID: PMC10168334 DOI: 10.1101/2023.04.27.538596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Short chain fatty acids (SCFAs) are products of bacterial fermentation that help maintain important gut functions such as the intestinal barrier, signaling, and immune homeostasis. The main SCFAs acetate, propionate, and butyrate have demonstrated beneficial effects for the host, including importance in combatting infections caused by pathogens such as Clostridioides difficile . Despite the potential role of SCFAs in mitigating C. difficile infection, their direct effect on C. difficile remains unclear. Through a set of in vitro experiments, we investigated how SCFAs influence C. difficile growth, sporulation, and toxin production. Similar to previous studies, we observed that butyrate decreased growth of C. difficile strain 630 in a dose-dependent manner. The presence of butyrate also increased C. difficile sporulation, with minimal increases in toxin production. RNA-Seq analysis validated our experimental results, demonstrating increased expression of sporulation-related genes in conjunction with alternative metabolic and related C. difficile regulatory pathways, such as the carbon catabolite repressor, CcpA. Collectively, these data suggest that butyrate may signal alternative C. difficile metabolic pathways, thus modifying its growth and virulence to persist in the gut environment. IMPORTANCE Several studies suggest that butyrate may be important in alleviating gut infections, such as reducing inflammation caused by the healthcare-associated Clostridioides difficile . While studies in both animal models and human studies correlate high levels of butyrate with reduced C. difficile burden, the direct impact of butyrate on C. difficile remains unclear. Our study demonstrates that butyrate directly influences C. difficile by increasing its sporulation and modifying its metabolism, potentially using butyrate as a biomarker to shift survival strategies in a changing gut environment. These data point to additional therapeutic approaches to combat C. difficile in a butyrate-directed manner.
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Cheng JKJ, Unnikrishnan M. Clostridioides difficile infection: traversing host-pathogen interactions in the gut. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 36848200 DOI: 10.1099/mic.0.001306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
C. difficile is the primary cause for nosocomial infective diarrhoea. For a successful infection, C. difficile must navigate between resident gut bacteria and the harsh host environment. The perturbation of the intestinal microbiota by broad-spectrum antibiotics alters the composition and the geography of the gut microbiota, deterring colonization resistance, and enabling C. difficile to colonize. This review will discuss how C. difficile interacts with and exploits the microbiota and the host epithelium to infect and persist. We provide an overview of C. difficile virulence factors and their interactions with the gut to aid adhesion, cause epithelial damage and mediate persistence. Finally, we document the host responses to C. difficile, describing the immune cells and host pathways that are associated and triggered during C. difficile infection.
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Affiliation(s)
- Jeffrey K J Cheng
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Meera Unnikrishnan
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
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15
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Wu S, Qin B, Deng S, Liu Y, Zhang H, Lei L, Feng G. CodY is modulated by YycF and affects biofilm formation in Staphylococcus aureus. Front Microbiol 2022; 13:967567. [PMID: 36304951 PMCID: PMC9593060 DOI: 10.3389/fmicb.2022.967567] [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: 06/13/2022] [Accepted: 08/30/2022] [Indexed: 11/21/2022] Open
Abstract
Background Staphylococcus aureus (S. aureus) is the leading cause of various infective diseases, including topical soft tissue infections. The goals of this study were to investigate the roles of YycF and CodY in the regulation of biofilm formation and pathogenicity. Methods Electrophoretic mobility shift assay (EMSA) was conducted to validate the bound promoter regions of YycF protein. We constructed the codY up-regulated or down-regulated S. aureus mutants. The biofilm biomass was determined by crystal violet microtiter assay and scanning electron microscopy (SEM). Quantitative RT-PCR analysis was used to detect the transcripts of biofilm-related genes. The live and dead cells of S. aureus biofilm were also investigated by confocal laser scanning microscopy (CLSM). We constructed an abscess infection in Sprague Dawley (SD) rat models to determine the effect of CodY on bacterial pathogenicity. We further used the RAW264.7, which were cocultured with S. aureus, to evaluate the effect of CodY on macrophages apoptosis. Result Quantitative RT-PCR analyses reveled that YycF negatively regulates codY expression. EMSA assays indicated that YycF protein directly binds to the promoter regions of codY gene. Quantitative RT-PCR confirmed the construction of dual- mutant stains codY + ASyycF and codY-ASyycF. The SEM results showed that the biofilm formation in the codY + ASyycF group was sparser than those in the other groups. The crystal violet assays indicated that the codY + ASyycF group formed less biofilms, which was consistent with the immunofluorescence results of the lowest live cell ration in the codY + ASyycF group. The expression levels of biofilm-associated icaA gene were significantly reduced in the codY + strain, indicating codY negatively regulates the biofilm formation. Furthermore, CodY impedes the pathogenicity in a rat-infection model. After cocultured with bacteria or 4-h in vitro, the apoptosis rates of macrophage cells were lowest in the codY + group. Conclusions YycF negatively regulate the expression of codY. By interaction with codY, YycF could modulate S. aureus biofilm formation via both eDNA- dependent and PIA- dependent pathways, which can be a significant target for antibiofilm. CodY not only impedes the pathogenicity but also has a role on immunoregulation. Thus, the current evidence may provide a supplementary strategy for managing biofilm infections.
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Affiliation(s)
- Shizhou Wu
- Department of Orthopedics, Orthopaedic Research Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Boquan Qin
- Department of Orthopedics, Orthopaedic Research Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Shu Deng
- Boston University Henry M. Goldman School of Dental Medicine, Boston, MA, United States
| | - Yunjie Liu
- West China School of Public Health, Sichuan University, Chengdu, China
| | - Hui Zhang
- Department of Orthopedics, Orthopaedic Research Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Lei Lei
- Department of Preventive Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- *Correspondence: Lei Lei,
| | - Guoying Feng
- College of Electronics and Information Engineering, Sichuan University, Chengdu, China
- Guoying Feng,
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16
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Zeng J, Wang H, Dong M, Tian GB. Clostridioides difficile spore: coat assembly and formation. Emerg Microbes Infect 2022; 11:2340-2349. [PMID: 36032037 PMCID: PMC9542656 DOI: 10.1080/22221751.2022.2119168] [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: 11/07/2022]
Abstract
Clostridioides difficile (C. difficile) is a Gram-positive, spore-forming, toxin-producing, obligate anaerobic bacterium. C. difficile infection (CDI) is the leading cause of healthcare-associated infective diarrhoea. The infection is mediated by the spore, a metabolically inactive form of C. difficile. The spore coat acts as a physical barrier to defend against chemical insults from hosts and natural environments. The composition of spore coat has already been revealed; therefore, the interactive networks of spore coat proteins and the dynamic process of coat assembly are the keys to design strategies to control and cure CDI. This review gives a brief discussion of the signal processing and transcriptional regulation of C. difficile sporulation initiation. Following the discussion, the spore formation is also introduced. Finally, this review mainly focuses on the spore coat assembly, a poorly understood process in C. difficile, and important proteins that have been studied.
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Affiliation(s)
- Ji Zeng
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
| | - Hao Wang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
| | - Min Dong
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Department of Urology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Guo-Bao Tian
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangdong 510080, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
- School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China
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17
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Schnizlein MK, Young VB. Capturing the environment of the Clostridioides difficile infection cycle. Nat Rev Gastroenterol Hepatol 2022; 19:508-520. [PMID: 35468953 DOI: 10.1038/s41575-022-00610-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/21/2022] [Indexed: 12/11/2022]
Abstract
Clostridioides difficile (formerly Clostridium difficile) infection is a substantial health and economic burden worldwide. Great strides have been made over the past several years in characterizing the physiology of C. difficile infection, particularly regarding how gut microorganisms and their host work together to provide colonization resistance. As mammalian hosts and their indigenous gut microbiota have co-evolved, they have formed a complex yet stable relationship that prevents invading microorganisms from establishing themselves. In this Review, we discuss the latest advances in our understanding of C. difficile physiology that have contributed to its success as a pathogen, including its versatile survival factors and ability to adapt to unique niches. Using discoveries regarding microorganism-host and microorganism-microorganism interactions that constitute colonization resistance, we place C. difficile within the fiercely competitive gut environment. A comprehensive understanding of these relationships is required to continue the development of precision medicine-based treatments for C. difficile infection.
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Affiliation(s)
- Matthew K Schnizlein
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Vincent B Young
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
- Department of Internal Medicine/Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, MI, USA.
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18
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Response Regulator CD1688 Is a Negative Modulator of Sporulation in Clostridioides difficile. J Bacteriol 2022; 204:e0013022. [PMID: 35852332 PMCID: PMC9380558 DOI: 10.1128/jb.00130-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two-component signal transduction systems (TCSs), consisting of a sensor histidine kinase (HK) and a response regulator (RR), sense environmental stimuli and then modulate cellular responses, typically through changes in gene expression. Our previous work identified the DNA binding motif of CD1586, an RR implicated in Clostridioides difficile strain R20291 sporulation. To determine the role of this RR in the sporulation pathway in C. difficile, we generated a deletion strain of cd1688 in the historical 630 strain, the homolog of cd1586. The C. difficile Δcd1688 strain exhibited a hypersporulation phenotype, suggesting that CD1688 negatively regulates sporulation. Complementation of the C. difficile Δcd1688 strain restored sporulation. In contrast, a nonphosphorylatable copy of cd1688 did not restore sporulation to wild-type (WT) levels, indicating that CD1688 must be phosphorylated to properly modulate sporulation. Expression of the master regulator spo0A, the sporulation-specific sigma factors sigF, sigE, sigG, and sigK, and a signaling protein encoded by spoIIR was increased in the C. difficile Δcd1688 strain compared to WT. In line with the increased spoIIR expression, we detected an increase in mature SigE at an earlier time point, which arises from SpoIIR-mediated processing of pro-SigE. Taken together, our data suggest that CD1688 is a novel negative modulator of sporulation in C. difficile and contributes to mediating progression through the spore developmental pathway. These results add to our growing understanding of the complex regulatory events involved in C. difficile sporulation, insight that could be exploited for novel therapeutic development. IMPORTANCEClostridioides difficile causes severe gastrointestinal illness and is a leading cause of nosocomial infections in the United States. This pathogen produces metabolically dormant spores that are the major vehicle of transmission between hosts. The sporulation pathway involves an intricate regulatory network that controls a succession of morphological changes necessary to produce spores. The environmental signals inducing the sporulation pathway are not well understood in C. difficile. This work identified a response regulator, CD1688, that, when deleted, led to a hypersporulation phenotype, indicating that it typically acts to repress sporulation. Improving our understanding of the regulatory mechanisms modulating sporulation in C. difficile could provide novel strategies to eliminate or reduce spore production, thus decreasing transmission and disease relapse.
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19
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Development of a Dual-Fluorescent-Reporter System in Clostridioides difficile Reveals a Division of Labor between Virulence and Transmission Gene Expression. mSphere 2022; 7:e0013222. [PMID: 35638354 PMCID: PMC9241537 DOI: 10.1128/msphere.00132-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The bacterial pathogen Clostridioides difficile causes gastroenteritis by producing toxins and transmits disease by making resistant spores. Toxin and spore production are energy-expensive processes that are regulated by multiple transcription factors in response to many environmental inputs. While toxin and sporulation genes are both induced in only a subset of C. difficile cells, the relationship between these two subpopulations remains unclear. To address whether C. difficile coordinates the generation of these subpopulations, we developed a dual-transcriptional-reporter system that allows toxin and sporulation gene expression to be simultaneously visualized at the single-cell level using chromosomally encoded mScarlet and mNeonGreen fluorescent transcriptional reporters. We then adapted an automated image analysis pipeline to quantify toxin and sporulation gene expression in thousands of individual cells under different medium conditions and in different genetic backgrounds. These analyses revealed that toxin and sporulation gene expression rarely overlap during growth on agar plates, whereas broth culture increases this overlap. Our results suggest that certain growth conditions promote a “division of labor” between transmission and virulence gene expression, highlighting how environmental inputs influence these subpopulations. Our data further suggest that the RstA transcriptional regulator skews the population to activate sporulation genes rather than toxin genes. Given that recent work has revealed population-wide heterogeneity for numerous cellular processes in C. difficile, we anticipate that our dual-reporter system will be broadly useful for determining the overlap between these subpopulations. IMPORTANCEClostridioides difficile is an important nosocomial pathogen that causes severe diarrhea by producing toxins and transmits disease by producing spores. While both processes are crucial for C. difficile disease, only a subset of cells express toxins and/or undergo sporulation. Whether C. difficile coordinates the subset of cells inducing these energy-expensive processes remains unknown. To address this question, we developed a dual-fluorescent-reporter system coupled with an automated image analysis pipeline to rapidly compare the expression of two genes of interest across thousands of cells. Using this system, we discovered that certain growth conditions, particularly growth on agar plates, induce a “division of labor” between toxin and sporulation gene expression. Since C. difficile exhibits phenotypic heterogeneity for numerous vital cellular processes, this novel dual-reporter system will enable future studies aimed at understanding how C. difficile coordinates various subpopulations throughout its infectious disease cycle.
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20
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Mechanisms and Applications of Bacterial Sporulation and Germination in the Intestine. Int J Mol Sci 2022; 23:ijms23063405. [PMID: 35328823 PMCID: PMC8953710 DOI: 10.3390/ijms23063405] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/15/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023] Open
Abstract
Recent studies have suggested a major role for endospore forming bacteria within the gut microbiota, not only as pathogens but also as commensal and beneficial members contributing to gut homeostasis. In this review the sporulation processes, spore properties, and germination processes will be explained within the scope of the human gut. Within the gut, spore-forming bacteria are known to interact with the host’s immune system, both in vegetative cell and spore form. Together with the resistant nature of the spore, these characteristics offer potential for spores’ use as delivery vehicles for therapeutics. In the last part of the review, the therapeutic potential of spores as probiotics, vaccine vehicles, and drug delivery systems will be discussed.
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21
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Edwards AN, Willams CL, Pareek N, McBride SM, Tamayo R. c-di-GMP Inhibits Early Sporulation in Clostridioides difficile. mSphere 2021; 6:e0091921. [PMID: 34878288 PMCID: PMC8653836 DOI: 10.1128/msphere.00919-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 11/19/2021] [Indexed: 12/02/2022] Open
Abstract
The formation of dormant spores is essential for the anaerobic pathogen Clostridioides difficile to survive outside the host gastrointestinal tract. The regulatory pathways and environmental signals that initiate C. difficile spore formation within the host are not well understood. One second-messenger signaling molecule, cyclic diguanylate (c-di-GMP), modulates several physiological processes important for C. difficile pathogenesis and colonization, but the impact of c-di-GMP on sporulation is unknown. In this study, we investigated the contribution of c-di-GMP to C. difficile sporulation. The overexpression of a gene encoding a diguanylate cyclase, dccA, decreased the sporulation frequency and early sporulation gene transcription in both the epidemic R20291 and historical 630Δerm strains. The expression of a dccA allele encoding a catalytically inactive DccA that is unable to synthesize c-di-GMP no longer inhibited sporulation, indicating that the accumulation of intracellular c-di-GMP reduces C. difficile sporulation. A null mutation in dccA slightly increased sporulation in R20291 and slightly decreased sporulation in 630Δerm, suggesting that DccA contributes to the intracellular pool of c-di-GMP in a strain-dependent manner. However, these data were highly variable, underscoring the complex regulation involved in modulating intracellular c-di-GMP concentrations. Finally, the overexpression of dccA in known sporulation mutants revealed that c-di-GMP is likely signaling through an unidentified regulatory pathway to control early sporulation events in C. difficile. c-di-GMP-dependent regulation of C. difficile sporulation may represent an unexplored avenue of potential environmental and intracellular signaling that contributes to the complex regulation of sporulation initiation. IMPORTANCE Many bacterial organisms utilize the small signaling molecule cyclic diguanylate (c-di-GMP) to regulate important physiological processes, including motility, toxin production, biofilm formation, and colonization. c-di-GMP inhibits motility and toxin production and promotes biofilm formation and colonization in the anaerobic, gastrointestinal pathogen Clostridioides difficile. However, the impact of c-di-GMP on C. difficile spore formation, a critical step in this pathogen's life cycle, is unknown. Here, we demonstrate that c-di-GMP negatively impacts sporulation in two clinically relevant C. difficile strains, the epidemic strain R20291 and the historical strain 630Δerm. The pathway through which c-di-GMP controls sporulation was investigated, and our results suggest that c-di-GMP is likely signaling through an unidentified regulatory pathway to control C. difficile sporulation. This work implicates c-di-GMP metabolism as a mechanism to integrate environmental and intracellular cues through c-di-GMP levels to influence C. difficile sporulation.
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Affiliation(s)
- Adrianne N. Edwards
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Caitlin L. Willams
- Department of Microbiology and Immunology, University of North Carolina—Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nivedita Pareek
- Department of Microbiology and Immunology, University of North Carolina—Chapel Hill, Chapel Hill, North Carolina, USA
| | - Shonna M. McBride
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Rita Tamayo
- Department of Microbiology and Immunology, University of North Carolina—Chapel Hill, Chapel Hill, North Carolina, USA
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22
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Lee CD, Rizvi A, Edwards AN, DiCandia MA, Vargas Cuebas GG, Monteiro MP, McBride SM. Genetic mechanisms governing sporulation initiation in Clostridioides difficile. Curr Opin Microbiol 2021; 66:32-38. [PMID: 34933206 DOI: 10.1016/j.mib.2021.12.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/03/2021] [Accepted: 12/05/2021] [Indexed: 12/15/2022]
Abstract
As an anaerobe, Clostridioides difficile relies on the formation of a dormant spore for survival outside of the mammalian host's gastrointestinal tract. The spore is recalcitrant to desiccation, numerous disinfectants, UV light, and antibiotics, permitting long-term survival against environmental insults and efficient transmission from host to host. Although the morphological stages of spore formation are similar between C. difficile and other well-studied endospore-forming bacteria, the C. difficile genome does not appear to encode many of the known, conserved regulatory factors that are necessary to initiate sporulation in other spore-forming bacteria. The absence of early sporulation-specific orthologs suggests that C. difficile has evolved to control sporulation initiation in response to its unique and specific ecological niche and environmental cues within the host. Here, we review our current understanding and highlight the recent discoveries that have begun to unravel the regulatory pathways and molecular mechanisms by which C. difficile induces spore formation.
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Affiliation(s)
- Cheyenne D Lee
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, GA, USA
| | - Arshad Rizvi
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, GA, USA
| | - Adrianne N Edwards
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, GA, USA
| | - Michael A DiCandia
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, GA, USA
| | - Germán G Vargas Cuebas
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, GA, USA
| | - Marcos P Monteiro
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, GA, USA
| | - Shonna M McBride
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, GA, USA.
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23
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Smith-Peter E, Séguin DL, St-Pierre É, Sekulovic O, Jeanneau S, Tremblay-Tétreault C, Lamontagne AM, Jacques PÉ, Lafontaine DA, Fortier LC. Inactivation of the riboswitch-controlled GMP synthase GuaA in Clostridioides difficile is associated with severe growth defects and poor infectivity in a mouse model of infection. RNA Biol 2021; 18:699-710. [PMID: 34612173 DOI: 10.1080/15476286.2021.1978768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Clostridioides difficile is the main cause of nosocomial antibiotic-associated diarrhoea. There is a need for new antimicrobials to tackle this pathogen. Guanine riboswitches have been proposed as promising new antimicrobial targets, but experimental evidence of their importance in C. difficile is missing. The genome of C. difficile encodes four distinct guanine riboswitches, each controlling a single gene involved in purine metabolism and transport. One of them controls the expression of guaA, encoding a guanosine monophosphate (GMP) synthase. Here, using in-line probing and GusA reporter assays, we show that these riboswitches are functional in C. difficile and cause premature transcription termination upon binding of guanine. All riboswitches exhibit a high affinity for guanine characterized by Kd values in the low nanomolar range. Xanthine and guanosine also bind the guanine riboswitches, although with less affinity. Inactivating the GMP synthase (guaA) in C. difficile strain 630 led to cell death in minimal growth conditions, but not in rich medium. Importantly, the capacity of a guaA mutant to colonize the mouse gut was significantly reduced. Together, these results demonstrate the importance of de novo GMP biosynthesis in C. difficile during infection, suggesting that targeting guanine riboswitches with analogues could be a viable therapeutic strategy.
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Affiliation(s)
- Erich Smith-Peter
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université De Sherbrooke, Sherbrooke, Quebec, Canada.,Department of Biology, Faculty of Science, Université De Sherbrooke, Sherbrooke, Quebec, Canada
| | - David Lalonde Séguin
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université De Sherbrooke, Sherbrooke, Quebec, Canada
| | - Émilie St-Pierre
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université De Sherbrooke, Sherbrooke, Quebec, Canada
| | - Ognjen Sekulovic
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université De Sherbrooke, Sherbrooke, Quebec, Canada
| | - Simon Jeanneau
- Department of Biology, Faculty of Science, Université De Sherbrooke, Sherbrooke, Quebec, Canada
| | | | - Anne-Marie Lamontagne
- Department of Biology, Faculty of Science, Université De Sherbrooke, Sherbrooke, Quebec, Canada
| | - Pierre-Étienne Jacques
- Department of Biology, Faculty of Science, Université De Sherbrooke, Sherbrooke, Quebec, Canada
| | - Daniel A Lafontaine
- Department of Biology, Faculty of Science, Université De Sherbrooke, Sherbrooke, Quebec, Canada
| | - Louis-Charles Fortier
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université De Sherbrooke, Sherbrooke, Quebec, Canada
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Dhungel BA, Govind R. Phase-variable expression of pdcB, a phosphodiesterase, influences sporulation in Clostridioides difficile. Mol Microbiol 2021; 116:1347-1360. [PMID: 34606654 DOI: 10.1111/mmi.14828] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 02/07/2023]
Abstract
Clostridioides difficile is the causative agent of antibiotic-associated diarrhea and is the leading cause of nosocomial infection in developed countries. An increasing number of C. difficile infections are attributed to epidemic strains that produce more toxins and spores. C. difficile spores are the major factor for the transmission and persistence of the organism. Previous studies have identified global regulators that influence sporulation in C. difficile. This study discovers that PdcB, a phosphodiesterase, enhances sporulation in C. difficile strain UK1. Through genetic and biochemical assays, we show that phase-variable expression of pdcB results in hypo- and hyper-sporulation phenotypes. In the "ON" orientation, the identified promotor is in the right orientation to drive the expression of pdcB. Production of the PdcB phosphodiesterase reduces the intracellular cyclic-di-GMP (c-di-GMP) concentration, resulting in a hyper-sporulation phenotype. Loss of PdcB due to the pdcB promoter being in the OFF orientation or mutation of pdcB results in increased c-di-GMP levels and a hypo-sporulation phenotype. Additionally, we demonstrate that CodY binds to the upstream region of pdcB. DNA inversion reorients the CodY binding site so that in the OFF orientation, CodY binds a site that is upstream of the pdcB promoter and can further repress gene expression.
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Affiliation(s)
| | - Revathi Govind
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
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25
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Shen A. Clostridioides difficile Spore Formation and Germination: New Insights and Opportunities for Intervention. Annu Rev Microbiol 2021; 74:545-566. [PMID: 32905755 DOI: 10.1146/annurev-micro-011320-011321] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Spore formation and germination are essential for the bacterial pathogen Clostridioides difficile to transmit infection. Despite the importance of these developmental processes to the infection cycle of C. difficile, the molecular mechanisms underlying how this obligate anaerobe forms infectious spores and how these spores germinate to initiate infection were largely unknown until recently. Work in the last decade has revealed that C. difficile uses a distinct mechanism for sensing and transducing germinant signals relative to previously characterized spore formers. The C. difficile spore assembly pathway also exhibits notable differences relative to Bacillus spp., where spore formation has been more extensively studied. For both these processes, factors that are conserved only in C. difficile or the related Peptostreptococcaceae family are employed, and even highly conserved spore proteins can have differential functions or requirements in C. difficile compared to other spore formers. This review summarizes our current understanding of the mechanisms controlling C. difficile spore formation and germination and describes strategies for inhibiting these processes to prevent C. difficile infection and disease recurrence.
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Affiliation(s)
- Aimee Shen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA;
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Xu X, Luo Y, Chen H, Song X, Bian Q, Wang X, Liang Q, Zhao J, Li C, Song G, Yang J, Sun L, Jiang J, Wang H, Zhu B, Ye G, Chen L, Tang YW, Jin D. Genomic evolution and virulence association of Clostridioides difficile sequence type 37 (ribotype 017) in China. Emerg Microbes Infect 2021; 10:1331-1345. [PMID: 34125660 PMCID: PMC8253194 DOI: 10.1080/22221751.2021.1943538] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Clostridioides difficile sequence type (ST) 37 (ribotype 017) is one of the most prevalent genotypes circulating in China. However, its genomic evolution and virulence determinants were rarely explored. Whole-genome sequencing, phylogeographic and phylogenetic analyses were conducted for C. difficile ST37 isolates. The 325 ST37 genomes from six continents, including North America (n = 66), South America (n = 4), Oceania (n = 7), Africa (n = 9), Europe (n = 138) and Asia (n = 101), were clustered into six major lineages, with region-dependent distributions, harbouring an array of antibiotic-resistance genes. The ST37 strains from China were divided into four distinct sublineages, showing five importation times and international sources. Isolates associated with severe infections exhibited significantly higher toxin productions, tcdB mRNA levels, and sporulation capacities (P < 0.001). Kyoto Encyclopedia of Genes and Genomes analysis showed 10 metabolic pathways were significantly enriched in the mutations among isolates associated with severe CDI (P < 0.05). Gene mutations in glycometabolism, amino acid metabolism and biosynthesis virtually causing instability in protein activity were correlated positively to the transcription of tcdR and negatively to the expression of toxin repressor genes, ccpA and codY. In summary, our study firstly presented genomic insights into genetic characteristics and virulence association of C. difficile ST37 in China. Gene mutations in certain important metabolic pathways are associated with severe symptoms and correlated with higher virulence in C. difficile ST37 isolates.
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Affiliation(s)
- Xingxing Xu
- Department of Clinical Laboratory, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China.,School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Yuo Luo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Huan Chen
- Key Laboratory of Microorganism technology and bioinformatics research of Zhejiang Province, Hangzhou, People's Republic of China.,NMPA Key Laboratory For Testing and Risk Warning of Pharmaceutical Microbiology, Hangzhou, People's Republic of China
| | - Xiaojun Song
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Qiao Bian
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, People's Republic of China
| | - Xianjun Wang
- Department of Laboratory Medicine, Hangzhou First People's Hospital, Hangzhou, People's Republic of China
| | - Qian Liang
- Key Laboratory of Microorganism technology and bioinformatics research of Zhejiang Province, Hangzhou, People's Republic of China.,NMPA Key Laboratory For Testing and Risk Warning of Pharmaceutical Microbiology, Hangzhou, People's Republic of China
| | - Jianhong Zhao
- Department of Clinical Microbiology, Second Hospital of Hebei Medical University, Hebei Provincial Center for Clinical Laboratories, Shijiazhuang, People's Republic of China
| | - Chunhui Li
- Infection Control Center, Xiangya Hospital of Central South University, Changsha, People's Republic of China
| | - Guangzhong Song
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Jun Yang
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Lingli Sun
- Key Laboratory of Microorganism technology and bioinformatics research of Zhejiang Province, Hangzhou, People's Republic of China.,NMPA Key Laboratory For Testing and Risk Warning of Pharmaceutical Microbiology, Hangzhou, People's Republic of China
| | - Jianmin Jiang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, People's Republic of China
| | - Huanying Wang
- Key Laboratory of Microorganism technology and bioinformatics research of Zhejiang Province, Hangzhou, People's Republic of China.,NMPA Key Laboratory For Testing and Risk Warning of Pharmaceutical Microbiology, Hangzhou, People's Republic of China
| | - Bo Zhu
- Department of Clinical Laboratory, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Guangyong Ye
- Department of Clinical Laboratory, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA.,Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, USA
| | - Yi-Wei Tang
- Cepheid, Danaher Diagnostic Platform, Shanghai, People's Republic of China
| | - Dazhi Jin
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, People's Republic of China.,Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, People's Republic of China
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Martins D, DiCandia MA, Mendes AL, Wetzel D, McBride SM, Henriques AO, Serrano M. CD25890, a conserved protein that modulates sporulation initiation in Clostridioides difficile. Sci Rep 2021; 11:7887. [PMID: 33846410 PMCID: PMC8041843 DOI: 10.1038/s41598-021-86878-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/17/2021] [Indexed: 12/16/2022] Open
Abstract
Bacteria that reside in the gastrointestinal tract of healthy humans are essential for our health, sustenance and well-being. About 50-60% of those bacteria have the ability to produce resilient spores that are important for the life cycle in the gut and for host-to-host transmission. A genomic signature for sporulation in the human intestine was recently described, which spans both commensals and pathogens such as Clostridioides difficile and contains several genes of unknown function. We report on the characterization of a signature gene, CD25890, which, as we show is involved in the control of sporulation initiation in C. difficile under certain nutritional conditions. Spo0A is the main regulatory protein controlling entry into sporulation and we show that an in-frame deletion of CD25890 results in increased expression of spo0A per cell and increased sporulation. The effect of CD25890 on spo0A is likely indirect and mediated through repression of the sinRR´ operon. Deletion of the CD25890 gene, however, does not alter the expression of the genes coding for the cytotoxins or the genes involved in biofilm formation. Our results suggest that CD25890 acts to modulate sporulation in response to the nutrients present in the environment.
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Affiliation(s)
- Diogo Martins
- Instituto de Tecnologia Química E Biológica António Xavier, Avenida da República, 2780-157, Oeiras, Portugal
| | - Michael A DiCandia
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Aristides L Mendes
- Instituto de Tecnologia Química E Biológica António Xavier, Avenida da República, 2780-157, Oeiras, Portugal
| | - Daniela Wetzel
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Shonna M McBride
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Adriano O Henriques
- Instituto de Tecnologia Química E Biológica António Xavier, Avenida da República, 2780-157, Oeiras, Portugal
| | - Mónica Serrano
- Instituto de Tecnologia Química E Biológica António Xavier, Avenida da República, 2780-157, Oeiras, Portugal.
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Systematic Evaluation of Parameters Important for Production of Native Toxin A and Toxin B from Clostridioides difficile. Toxins (Basel) 2021; 13:toxins13040240. [PMID: 33801738 PMCID: PMC8066640 DOI: 10.3390/toxins13040240] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/19/2021] [Accepted: 03/25/2021] [Indexed: 12/26/2022] Open
Abstract
In the attempt to improve the purification yield of native toxin A (TcdA) and toxin B (TcdB) from Clostridioides difficile (C. difficile), we systematically evaluated culture parameters for their influence on toxin production. In this study, we showed that culturing C. difficile in a tryptone-yeast extract medium buffered in PBS (pH 7.5) that contained 5 mM ZnCl2 and 10 mM glucose supported the highest TcdB production, measured by the sandwich ELISA. These culture conditions were scalable into 5 L and 15 L dialysis tube cultures, and we were able to reach a TcdB concentration of 29.5 µg/mL of culture. Furthermore, we established a purification protocol for TcdA and TcdB using FPLC column chromatography, reaching purities of >99% for both toxins with a yield around 25% relative to the starting material. Finally, by screening the melting temperatures of TcdA and TcdB in various buffer conditions using differential scanning fluorimetry, we found optimal conditions for improving the protein stability during storage. The results of this study present a complete protocol for obtaining high amounts of highly purified native TcdA and TcdB from C. difficile.
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Abstract
Clostridioides difficile is the leading cause of nosocomial infection and is the causative agent of antibiotic-associated diarrhea. The severity of the disease is directly associated with toxin production, and spores are responsible for the transmission and persistence of the organism. Previously, we characterized sin locus regulators SinR and SinR' (we renamed it SinI), where SinR is the regulator of toxin production and sporulation. The SinI regulator acts as its antagonist. In Bacillus subtilis, Spo0A, the master regulator of sporulation, controls SinR by regulating the expression of its antagonist, sinI However, the role of Spo0A in the expression of sinR and sinI in C. difficile had not yet been reported. In this study, we tested spo0A mutants in three different C. difficile strains, R20291, UK1, and JIR8094, to understand the role of Spo0A in sin locus expression. Western blot analysis revealed that spo0A mutants had increased SinR levels. Quantitative reverse transcription-PCR (qRT-PCR) analysis of its expression further supported these data. By carrying out genetic and biochemical assays, we show that Spo0A can bind to the upstream region of this locus to regulates its expression. This study provides vital information that Spo0A regulates the sin locus, which controls critical pathogenic traits such as sporulation, toxin production, and motility in C. difficile IMPORTANCE Clostridioides difficile is the leading cause of antibiotic-associated diarrheal disease in the United States. During infection, C. difficile spores germinate, and the vegetative bacterial cells produce toxins that damage host tissue. In C. difficile, the sin locus is known to regulate both sporulation and toxin production. In this study, we show that Spo0A, the master regulator of sporulation, controls sin locus expression. Results from our study suggest that Spo0A directly regulates the expression of this locus by binding to its upstream DNA region. This observation adds new detail to the gene regulatory network that connects sporulation and toxin production in this pathogen.
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The Impact of pH on Clostridioides difficile Sporulation and Physiology. Appl Environ Microbiol 2020; 86:AEM.02706-19. [PMID: 31811041 DOI: 10.1128/aem.02706-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 12/03/2019] [Indexed: 12/18/2022] Open
Abstract
Clostridioides difficile is a pathogenic bacterium that infects the human colon to cause diarrheal disease. Growth of the bacterium is known to be dependent on certain bile acids, oxygen levels, and nutrient availability in the intestine, but how the environmental pH can influence C. difficile is mostly unknown. Previous studies indicated that C. difficile modulates the intestinal pH, and prospective cohort studies have found a strong association between a more alkaline fecal pH and C. difficile infection. Based on these data, we hypothesized that C. difficile physiology can be affected by various pH conditions. In this study, we investigated the impact of a range of pH conditions on C. difficile to assess potential effects on growth, sporulation, motility, and toxin production in the strains 630Δerm and R20291. We observed pH-dependent differences in sporulation rate, spore morphology, and viability. Sporulation frequency was lowest under acidic conditions, and differences in cell morphology were apparent at low pH. In alkaline environments, C. difficile sporulation was greater for strain 630Δerm, whereas R20291 produced relatively high levels of spores in a broad range of pH conditions. Rapid changes in pH during exponential growth impacted sporulation similarly among the strains. Furthermore, we observed an increase in C. difficile motility with increases in pH, and strain-dependent differences in toxin production under acidic conditions. The data demonstrate that pH is an important parameter that affects C. difficile physiology and may reveal relevant insights into the growth and dissemination of this pathogen.IMPORTANCE Clostridioides difficile is an anaerobic bacterium that causes gastrointestinal disease. C. difficile forms dormant spores which can survive harsh environmental conditions, allowing their spread to new hosts. In this study, we determine how intestinally relevant pH conditions impact C. difficile physiology in the two divergent strains, 630Δerm and R20291. Our data demonstrate that low pH conditions reduce C. difficile growth, sporulation, and motility. However, toxin production and spore morphology were differentially impacted in the two strains at low pH. In addition, we observed that alkaline environments reduce C. difficile growth, but increase cell motility. When pH was adjusted rapidly during growth, we observed similar impacts on both strains. This study provides new insights into the phenotypic diversity of C. difficile grown under diverse pH conditions present in the intestinal tract, and demonstrates similarities and differences in the pH responses of different C. difficile isolates.
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Strain-Dependent RstA Regulation of Clostridioides difficile Toxin Production and Sporulation. J Bacteriol 2020; 202:JB.00586-19. [PMID: 31659010 DOI: 10.1128/jb.00586-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 10/21/2019] [Indexed: 02/04/2023] Open
Abstract
The anaerobic spore former Clostridioides difficile causes significant diarrheal disease in humans and other mammals. Infection begins with the ingestion of dormant spores, which subsequently germinate within the host gastrointestinal tract. There, the vegetative cells proliferate and secrete two exotoxins, TcdA and TcdB, which cause disease symptoms. Although spore formation and toxin production are critical for C. difficile pathogenesis, the regulatory links between these two physiological processes are not well understood and are strain dependent. Previously, we identified a conserved C. difficile regulator, RstA, that promotes sporulation initiation through an unknown mechanism and directly and indirectly represses toxin and motility gene transcription in the historical isolate 630Δerm To test whether perceived strain-dependent differences in toxin production and sporulation are mediated by RstA, we created an rstA mutant in the epidemic ribotype 027 strain R20291. RstA affected sporulation and toxin gene expression similarly but more robustly in R20291 than in 630Δerm In contrast, no effect on motility gene expression was observed in R20291. Reporter assays measuring transcriptional regulation of tcdR, the sigma factor gene essential for toxin gene expression, identified sequence-dependent effects influencing repression by RstA and CodY, a global nutritional sensor, in four diverse C. difficile strains. Finally, sequence- and strain-dependent differences were evident in RstA negative autoregulation of rstA transcription. Altogether, our data suggest that strain-dependent differences in RstA regulation contribute to the sporulation and toxin phenotypes observed in R20291. Our data establish RstA as an important regulator of C. difficile virulence traits.IMPORTANCE Two critical traits of Clostridioides difficile pathogenesis are toxin production, which causes disease symptoms, and spore formation, which permits survival outside the gastrointestinal tract. The multifunctional regulator RstA promotes sporulation and prevents toxin production in the historical strain 630Δerm Here, we show that RstA exhibits stronger effects on these phenotypes in an epidemic isolate, R20291, and additional strain-specific effects on toxin and rstA expression are evident. Our data demonstrate that sequence-specific differences within the promoter for the toxin regulator TcdR contribute to the regulation of toxin production by RstA and CodY. These sequence differences account for some of the variability in toxin production among isolates and may allow strains to differentially control toxin production in response to a variety of signals.
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Shen A, Edwards AN, Sarker MR, Paredes-Sabja D. Sporulation and Germination in Clostridial Pathogens. Microbiol Spectr 2019; 7:10.1128/microbiolspec.GPP3-0017-2018. [PMID: 31858953 PMCID: PMC6927485 DOI: 10.1128/microbiolspec.gpp3-0017-2018] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Indexed: 12/14/2022] Open
Abstract
As obligate anaerobes, clostridial pathogens depend on their metabolically dormant, oxygen-tolerant spore form to transmit disease. However, the molecular mechanisms by which those spores germinate to initiate infection and then form new spores to transmit infection remain poorly understood. While sporulation and germination have been well characterized in Bacillus subtilis and Bacillus anthracis, striking differences in the regulation of these processes have been observed between the bacilli and the clostridia, with even some conserved proteins exhibiting differences in their requirements and functions. Here, we review our current understanding of how clostridial pathogens, specifically Clostridium perfringens, Clostridium botulinum, and Clostridioides difficile, induce sporulation in response to environmental cues, assemble resistant spores, and germinate metabolically dormant spores in response to environmental cues. We also discuss the direct relationship between toxin production and spore formation in these pathogens.
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Affiliation(s)
- Aimee Shen
- Department of Molecular Biology and Microbiology, Tufts University Medical School, Boston, MA
| | - Adrianne N Edwards
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Mahfuzur R Sarker
- Department of Microbiology, College of Science, Oregon State University, Corvallis, OR
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR
| | - Daniel Paredes-Sabja
- Department of Gut Microbiota and Clostridia Research Group, Departamento de Ciencias Biolo gicas, Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
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Phase variation of a signal transduction system controls Clostridioides difficile colony morphology, motility, and virulence. PLoS Biol 2019; 17:e3000379. [PMID: 31658249 PMCID: PMC6837544 DOI: 10.1371/journal.pbio.3000379] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 11/07/2019] [Accepted: 10/15/2019] [Indexed: 12/20/2022] Open
Abstract
Recent work has revealed that Clostridioides difficile, a major cause of nosocomial diarrheal disease, exhibits phenotypic heterogeneity within a clonal population as a result of phase variation. Many C. difficile strains representing multiple ribotypes develop two colony morphotypes, termed rough and smooth, but the biological implications of this phenomenon have not been explored. Here, we examine the molecular basis and physiological relevance of the distinct colony morphotypes produced by this bacterium. We show that C. difficile reversibly differentiates into rough and smooth colony morphologies and that bacteria derived from the isolates display discrete motility behaviors. We identified an atypical phase-variable signal transduction system consisting of a histidine kinase and two response regulators, named herein colony morphology regulators RST (CmrRST), which mediates the switch in colony morphology and motility behaviors. The CmrRST-regulated surface motility is independent of flagella and type IV pili, suggesting a novel mechanism of cell migration in C. difficile. Microscopic analysis of cell and colony structure indicates that CmrRST promotes the formation of elongated bacteria arranged in bundled chains, which may contribute to bacterial migration on surfaces. In a hamster model of acute C. difficile disease, the CmrRST system is required for disease development. Furthermore, we provide evidence that CmrRST phase varies during infection, suggesting that the intestinal environment impacts the proportion of CmrRST-expressing C. difficile. Our findings indicate that C. difficile employs phase variation of the CmrRST signal transduction system to generate phenotypic heterogeneity during infection, with concomitant effects on bacterial physiology and pathogenesis. In many bacterial species, a genetically clonal population can generate phenotypic heterogeneity to ensure survival of a subpopulation in the face of sudden environmental stressors. This work shows that the intestinal pathogen Clostridioides difficile introduces heterogeneity into the population through the phase-variable expression of a signal transduction system, resulting in broad changes in physiology, motility, and virulence.
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Ciftci Y, Girinathan BP, Dhungel BA, Hasan MK, Govind R. Clostridioides difficile SinR' regulates toxin, sporulation and motility through protein-protein interaction with SinR. Anaerobe 2019; 59:1-7. [PMID: 31077800 PMCID: PMC6785386 DOI: 10.1016/j.anaerobe.2019.05.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 04/10/2019] [Accepted: 05/07/2019] [Indexed: 12/18/2022]
Abstract
Clostridioides difficile is a Gram-positive, anaerobic bacterium. It is known that C. difficile is one of the major causes of antibiotic associated diarrhea. The enhanced antibiotic resistance observed in C. difficile is the result of highly resistant spores produced by the bacterium. In Bacillus subtilis, the sin operon is involved in sporulation inhibition. Two proteins coded within this operon, SinR and SinI, have an antagonistic relationship; SinR acts as an inhibitor to sporulation whereas SinI represses the activity of SinR, thus allowing the bacterium to sporulate. In a previous study, we examined the sin locus in C. difficile and named the two genes associated with this operon sinR and sinR', analogous to sinR and sinI in B. subtilis, respectively. We have shown that SinR and SinR' have pleiotropic roles in pathogenesis pathways and interact antagonistically with each other. Unlike B. subtilis SinI, SinR' in C. difficile carries two domains: the HTH domain and the Multimerization Domain (MD). In this study, we first performed a GST Pull-down experiment to determine the domain within SinR' that interacts with SinR. Second, the effect of these two domains on three phenotypes; sporulation, motility, and toxin production was examined. The findings of this study confirmed the prediction that the Multimerization Domain (MD) of SinR' is responsible for the interaction between SinR and SinR'. It was also discovered that SinR' regulates sporulation, toxin production and motility primarily by inhibiting SinR activity through the Multimerization Domain (MD).
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Affiliation(s)
- Yusuf Ciftci
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Brintha Parasumanna Girinathan
- Division of Biology, Kansas State University, Manhattan, KS, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA
| | | | - Md Kamrul Hasan
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Revathi Govind
- Division of Biology, Kansas State University, Manhattan, KS, USA.
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Edwards AN, Anjuwon-Foster BR, McBride SM. RstA Is a Major Regulator of Clostridioides difficile Toxin Production and Motility. mBio 2019; 10:e01991-18. [PMID: 30862746 PMCID: PMC6414698 DOI: 10.1128/mbio.01991-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 01/25/2019] [Indexed: 01/05/2023] Open
Abstract
Clostridioides difficile infection (CDI) is a toxin-mediated diarrheal disease. Several factors have been identified that influence the production of the two major C. difficile toxins, TcdA and TcdB, but prior published evidence suggested that additional unknown factors were involved in toxin regulation. Previously, we identified a C. difficile regulator, RstA, that promotes sporulation and represses motility and toxin production. We observed that the predicted DNA-binding domain of RstA was required for RstA-dependent repression of toxin genes, motility genes, and rstA transcription. In this study, we further investigated the regulation of toxin and motility gene expression by RstA. DNA pulldown assays confirmed that RstA directly binds the rstA promoter via the predicted DNA-binding domain. Through mutational analysis of the rstA promoter, we identified several nucleotides that are important for RstA-dependent transcriptional regulation. Further, we observed that RstA directly binds and regulates the promoters of the toxin genes tcdA and tcdB, as well as the promoters for the sigD and tcdR genes, which encode regulators of toxin gene expression. Complementation analyses with the Clostridium perfringens RstA ortholog and a multispecies chimeric RstA protein revealed that the C. difficile C-terminal domain is required for RstA DNA-binding activity, suggesting that species-specific signaling controls RstA function. Our data demonstrate that RstA is a transcriptional repressor that autoregulates its own expression and directly inhibits transcription of the two toxin genes and two positive toxin regulators, thereby acting at multiple regulatory points to control toxin production.IMPORTANCEClostridioides difficile is an anaerobic, gastrointestinal pathogen of humans and other mammals. C. difficile produces two major toxins, TcdA and TcdB, which cause the symptoms of the disease, and forms dormant endospores to survive the aerobic environment outside the host. A recently discovered regulatory factor, RstA, inhibits toxin production and positively influences spore formation. Herein, we determine that RstA directly binds its own promoter DNA to repress its own gene transcription. In addition, our data demonstrate that RstA directly represses toxin gene expression and gene expression of two toxin gene activators, TcdR and SigD, creating a complex regulatory network to tightly control toxin production. This study provides a novel regulatory link between C. difficile sporulation and toxin production. Further, our data suggest that C. difficile toxin production is regulated through a direct, species-specific sensing mechanism.
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Affiliation(s)
- Adrianne N Edwards
- Department of Microbiology and Immunology, Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Brandon R Anjuwon-Foster
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Shonna M McBride
- Department of Microbiology and Immunology, Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, Georgia, USA
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Neumann-Schaal M, Jahn D, Schmidt-Hohagen K. Metabolism the Difficile Way: The Key to the Success of the Pathogen Clostridioides difficile. Front Microbiol 2019; 10:219. [PMID: 30828322 PMCID: PMC6384274 DOI: 10.3389/fmicb.2019.00219] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/28/2019] [Indexed: 12/11/2022] Open
Abstract
Strains of Clostridioides difficile cause detrimental diarrheas with thousands of deaths worldwide. The infection process by the Gram-positive, strictly anaerobic gut bacterium is directly related to its unique metabolism, using multiple Stickland-type amino acid fermentation reactions coupled to Rnf complex-mediated sodium/proton gradient formation for ATP generation. Major pathways utilize phenylalanine, leucine, glycine and proline with the formation of 3-phenylproprionate, isocaproate, butyrate, 5-methylcaproate, valerate and 5-aminovalerate. In parallel a versatile sugar catabolism including pyruvate formate-lyase as a central enzyme and an incomplete tricarboxylic acid cycle to prevent unnecessary NADH formation completes the picture. However, a complex gene regulatory network that carefully mediates the continuous adaptation of this metabolism to changing environmental conditions is only partially elucidated. It involves the pleiotropic regulators CodY and SigH, the known carbon metabolism regulator CcpA, the proline regulator PrdR, the iron regulator Fur, the small regulatory RNA CsrA and potentially the NADH-responsive regulator Rex. Here, we describe the current knowledge of the metabolic principles of energy generation by C. difficile and the underlying gene regulatory scenarios.
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Affiliation(s)
- Meina Neumann-Schaal
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,Integrated Centre of Systems Biology (BRICS), Braunschweig University of Technology, Braunschweig, Germany
| | - Dieter Jahn
- Integrated Centre of Systems Biology (BRICS), Braunschweig University of Technology, Braunschweig, Germany.,Institute of Microbiology, Braunschweig University of Technology, Braunschweig, Germany
| | - Kerstin Schmidt-Hohagen
- Integrated Centre of Systems Biology (BRICS), Braunschweig University of Technology, Braunschweig, Germany.,Department of Bioinformatics and Biochemistry, Braunschweig University of Technology, Braunschweig, Germany
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Daou N, Wang Y, Levdikov VM, Nandakumar M, Livny J, Bouillaut L, Blagova E, Zhang K, Belitsky BR, Rhee K, Wilkinson AJ, Sun X, Sonenshein AL. Impact of CodY protein on metabolism, sporulation and virulence in Clostridioides difficile ribotype 027. PLoS One 2019; 14:e0206896. [PMID: 30699117 PMCID: PMC6353076 DOI: 10.1371/journal.pone.0206896] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 09/25/2018] [Indexed: 12/16/2022] Open
Abstract
Toxin synthesis and endospore formation are two of the most critical factors that determine the outcome of infection by Clostridioides difficile. The two major toxins, TcdA and TcdB, are the principal factors causing damage to the host. Spores are the infectious form of C. difficile, permit survival of the bacterium during antibiotic treatment and are the predominant cell form that leads to recurrent infection. Toxin production and sporulation have their own specific mechanisms of regulation, but they share negative regulation by the global regulatory protein CodY. Determining the extent of such regulation and its detailed mechanism is important for understanding the linkage between two apparently independent biological phenomena and raises the possibility of creating new ways of limiting infection. The work described here shows that a codY null mutant of a hypervirulent (ribotype 027) strain is even more virulent than its parent in a mouse model of infection and that the mutant expresses most sporulation genes prematurely during exponential growth phase. Moreover, examining the expression patterns of mutants producing CodY proteins with different levels of residual activity revealed that expression of the toxin genes is dependent on total CodY inactivation, whereas most sporulation genes are turned on when CodY activity is only partially diminished. These results suggest that, in wild-type cells undergoing nutrient limitation, sporulation genes can be turned on before the toxin genes.
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Affiliation(s)
- Nadine Daou
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, United States of America
| | - Yuanguo Wang
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, United States of America
| | - Vladimir M. Levdikov
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Madhumitha Nandakumar
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medical College, New York, NY, United States of America
| | - Jonathan Livny
- Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
| | - Laurent Bouillaut
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, United States of America
| | - Elena Blagova
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Keshan Zhang
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, United States of America
| | - Boris R. Belitsky
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, United States of America
| | - Kyu Rhee
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medical College, New York, NY, United States of America
| | - Anthony J. Wilkinson
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Xingmin Sun
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States of America
| | - Abraham L. Sonenshein
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, United States of America
- * E-mail:
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Characterization of the virulence of a non-RT027, non-RT078 and binary toxin-positive Clostridium difficile strain associated with severe diarrhea. Emerg Microbes Infect 2018; 7:211. [PMID: 30542069 PMCID: PMC6291415 DOI: 10.1038/s41426-018-0211-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/01/2018] [Accepted: 11/11/2018] [Indexed: 02/06/2023]
Abstract
The expression of the Clostridium difficile binary toxin CDT is generally observed in the RT027 (ST1) and RT078 (ST11) C. difficile isolates, which are associated with severe C. difficile infection (CDI). However, we recently reported that the non-RT027 and non-RT078 C. difficile strain LC693 (TcdA+TcdB+ CDT+, ST201) caused severe diarrhea in a patient in Xiangya Hospital in China. C.difficile LC693 is a member of Clade 3, and in this study, we identified LC693 as RT871 and compared its virulence and pathogenicity to those of C.difficile R20291 (TcdA+TcdB+CDT+, ST1/RT027), UK6 (TcdA+TcdB+CDT+, ST35/RT027), CD630 (TcdA+TcdB+CDT−, ST54, RT012), and 1379 (TcdA+TcdB+CDT−, ST54/RT012), with strain 1379 being an epidemic C.difficile isolate from the same hospital. LC693 displayed a higher sporulation rate than R20291, CD630 or strain 1379. LC693 was comparable to R20291 with respect to spore germination, motility, and biofilm formation, but showed a faster germination rate, higher motility and a higher biofilm formation capability compared to CD630 and strain 1379. The adherence of spores to human gut epithelial cells was similar for all strains.The total toxin release of LC693 was lower than that of R20291, but higher than that of CD630 and strain 1379. Finally, in a mouse model of CDI, LC693 was capable of causing moderate to severe disease. Our findings demonstrate the pathogenicity of non-RT027 and non-RT078 binary toxin-positive C. difficile strains. Furthermore, our data indicate that LC693 may be more virulent than strain 1379, an epidemic strain from the same hospital, and provide the first phenotypic characterization of a non-RT027 and non-RT078 binary toxin-positive ST201 isolate.
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Poquet I, Saujet L, Canette A, Monot M, Mihajlovic J, Ghigo JM, Soutourina O, Briandet R, Martin-Verstraete I, Dupuy B. Clostridium difficile Biofilm: Remodeling Metabolism and Cell Surface to Build a Sparse and Heterogeneously Aggregated Architecture. Front Microbiol 2018; 9:2084. [PMID: 30258415 PMCID: PMC6143707 DOI: 10.3389/fmicb.2018.02084] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 08/14/2018] [Indexed: 12/11/2022] Open
Abstract
Clostridium difficile is an opportunistic entero-pathogen causing post-antibiotic and nosocomial diarrhea upon microbiota dysbiosis. Although biofilms could contribute to colonization, little is known about their development and physiology. Strain 630Δerm is able to form, in continuous-flow micro-fermentors, macro-colonies and submersed biofilms loosely adhesive to glass. According to gene expression data, in biofilm/planktonic cells, central metabolism is active and fuels fatty acid biosynthesis rather than fermentations. Consistently, succinate is consumed and butyrate production is reduced. Toxin A expression, which is coordinated to metabolism, is down-regulated, while surface proteins, like adhesins and the primary Type IV pili subunits, are over-expressed. C-di-GMP level is probably tightly controlled through the expression of both diguanylate cyclase-encoding genes, like dccA, and phosphodiesterase-encoding genes. The coordinated expression of genes controlled by c-di-GMP and encoding the putative surface adhesin CD2831 and the major Type IV pilin PilA1, suggests that c-di-GMP could be high in biofilm cells. A Bacillus subtilis SinR-like regulator, CD2214, and/or CD2215, another regulator co-encoded in the same operon as CD2214, control many genes differentially expressed in biofilm, and in particular dccA, CD2831 and pilA1 in a positive way. After growth in micro-titer plates and disruption, the biofilm is composed of robust aggregated structures where cells are embedded into a polymorphic material. The intact biofilm observed in situ displays a sparse, heterogeneous and high 3D architecture made of rods and micro-aggregates. The biofilm is denser in a mutant of both CD2214 and CD2215 genes, but it is not affected by the inactivation of neither CD2831 nor pilA1. dccA, when over-expressed, not only increases the biofilm but also triggers its architecture to become homogeneous and highly aggregated, in a way independent of CD2831 and barely dependent of pilA1. Cell micro-aggregation is shown to play a major role in biofilm formation and architecture. This thorough analysis of gene expression reprogramming and architecture remodeling in biofilm lays the foundation for a deeper understanding of this lifestyle and could lead to novel strategies to limit C. difficile spread.
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Affiliation(s)
- Isabelle Poquet
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.,Laboratoire Pathogenèse des Bacteries Anaerobies, Institut Pasteur, Paris, France
| | - Laure Saujet
- Laboratoire Pathogenèse des Bacteries Anaerobies, Institut Pasteur, Paris, France.,Sorbonne Paris Cité, Université Paris Diderot, Paris, France
| | - Alexis Canette
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Marc Monot
- Laboratoire Pathogenèse des Bacteries Anaerobies, Institut Pasteur, Paris, France.,Sorbonne Paris Cité, Université Paris Diderot, Paris, France
| | | | - Jean-Marc Ghigo
- Unité de Génétique des Biofilms, Institut Pasteur, Paris, France
| | - Olga Soutourina
- Laboratoire Pathogenèse des Bacteries Anaerobies, Institut Pasteur, Paris, France.,Sorbonne Paris Cité, Université Paris Diderot, Paris, France
| | - Romain Briandet
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Isabelle Martin-Verstraete
- Laboratoire Pathogenèse des Bacteries Anaerobies, Institut Pasteur, Paris, France.,Sorbonne Paris Cité, Université Paris Diderot, Paris, France
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bacteries Anaerobies, Institut Pasteur, Paris, France.,Sorbonne Paris Cité, Université Paris Diderot, Paris, France
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40
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Branching Out: Alterations in Bacterial Physiology and Virulence Due to Branched-Chain Amino Acid Deprivation. mBio 2018; 9:mBio.01188-18. [PMID: 30181248 PMCID: PMC6123439 DOI: 10.1128/mbio.01188-18] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The branched-chain amino acids (BCAAs [Ile, Leu, and Val]) represent important nutrients in bacterial physiology, with roles that range from supporting protein synthesis to signaling and fine-tuning the adaptation to amino acid starvation. In some pathogenic bacteria, the adaptation to amino acid starvation includes induction of virulence gene expression: thus, BCAAs support not only proliferation during infection, but also the evasion of host defenses. The branched-chain amino acids (BCAAs [Ile, Leu, and Val]) represent important nutrients in bacterial physiology, with roles that range from supporting protein synthesis to signaling and fine-tuning the adaptation to amino acid starvation. In some pathogenic bacteria, the adaptation to amino acid starvation includes induction of virulence gene expression: thus, BCAAs support not only proliferation during infection, but also the evasion of host defenses. A body of research has accumulated over the years to describe the multifaceted physiological roles of BCAAs and the mechanisms bacteria use to maintain their intracellular levels. More recent studies have focused on understanding how fluctuations in their intracellular levels impact global regulatory pathways that coordinate the adaptation to nutrient limitation, especially in pathogenic bacteria. In this minireview, we discuss how these studies have refined the individual roles of BCAAs, shed light on how BCAA auxotrophy might promote higher sensitivity to exogenous BCAA levels, and revealed pathogen-specific responses to BCAA deprivation. These advancements improve our understanding of how bacteria meet their nutritional requirements for growth while simultaneously remaining responsive to changes in environmental nutrient availability to promote their survival in a range of environments.
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41
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Woods EC, Edwards AN, Childress KO, Jones JB, McBride SM. The C. difficile clnRAB operon initiates adaptations to the host environment in response to LL-37. PLoS Pathog 2018; 14:e1007153. [PMID: 30125334 PMCID: PMC6117091 DOI: 10.1371/journal.ppat.1007153] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/30/2018] [Accepted: 07/16/2018] [Indexed: 01/05/2023] Open
Abstract
To cause disease, Clostridioides (Clostridium) difficile must resist killing by innate immune effectors in the intestine, including the host antimicrobial peptide, cathelicidin (LL-37). The mechanisms that enable C. difficile to adapt to the intestine in the presence of antimicrobial peptides are unknown. Expression analyses revealed an operon, CD630_16170-CD630_16190 (clnRAB), which is highly induced by LL-37 and is not expressed in response to other cell-surface active antimicrobials. This operon encodes a predicted transcriptional regulator (ClnR) and an ABC transporter system (ClnAB), all of which are required for function. Analyses of a clnR mutant indicate that ClnR is a pleiotropic regulator that directly binds to LL-37 and controls expression of numerous genes, including many involved in metabolism, cellular transport, signaling, gene regulation, and pathogenesis. The data suggest that ClnRAB is a novel regulatory mechanism that senses LL-37 as a host signal and regulates gene expression to adapt to the host intestinal environment during infection.
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Affiliation(s)
- Emily C. Woods
- Department of Microbiology and Immunology, and Emory University Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, United States of America
| | - Adrianne N. Edwards
- Department of Microbiology and Immunology, and Emory University Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, United States of America
| | - Kevin O. Childress
- Department of Microbiology and Immunology, and Emory University Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, United States of America
| | - Joshua B. Jones
- Department of Microbiology and Immunology, and Emory University Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, United States of America
| | - Shonna M. McBride
- Department of Microbiology and Immunology, and Emory University Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, United States of America
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42
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Thanissery R, Zeng D, Doyle RG, Theriot CM. A Small Molecule-Screening Pipeline to Evaluate the Therapeutic Potential of 2-Aminoimidazole Molecules Against Clostridium difficile. Front Microbiol 2018; 9:1206. [PMID: 29928268 PMCID: PMC5997789 DOI: 10.3389/fmicb.2018.01206] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/17/2018] [Indexed: 12/19/2022] Open
Abstract
Antibiotics are considered to be the first line of treatment for mild to moderately severe Clostridium difficile infection (CDI) in humans. However, antibiotics are also risk factors for CDI as they decrease colonization resistance against C. difficile by altering the gut microbiota and metabolome. Finding compounds that selectively inhibit different stages of the C. difficile life cycle, while sparing the indigenous gut microbiota is important for the development of alternatives to standard antibiotic treatment. 2-aminoimidazole (2-AI) molecules are known to disrupt bacterial protection mechanisms in antibiotic resistant bacteria such as Pseudomonas aeruginosa, Acinetobacter baumannii, and Staphylococcus aureus, but are yet to be evaluated against C. difficile. A comprehensive small molecule-screening pipeline was developed to investigate how novel small molecules affect different stages of the C. difficile life cycle (growth, toxin, and sporulation) in vitro, and a library of commensal bacteria that are associated with colonization resistance against C. difficile. The initial screening tested the efficacy of eleven 2-AI molecules (compound 1 through 11) against C. difficile R20291 compared to a vancomycin (2 μg/ml) control. Molecules were selected for their ability to inhibit C. difficile growth, toxin activity, and sporulation. Further testing included growth inhibition of other C. difficile strains (CD196, M68, CF5, 630, BI9, M120) belonging to distinct PCR ribotypes, and a commensal panel (Bacteroides fragilis, B. thetaiotaomicron, C. scindens, C. hylemonae, Lactobacillus acidophilus, L. gasseri, Escherichia coli, B. longum subsp. infantis). Three molecules compound 1 and 2, and 3 were microbicidal, whereas compounds 4, 7, 9, and 11 inhibited toxin activity without affecting the growth of C. difficile strains and the commensal microbiota. The antimicrobial and anti-toxin effects of 2-AI molecules need to be further characterized for mode of action and validated in a mouse model of CDI.
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Affiliation(s)
- Rajani Thanissery
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - Daina Zeng
- Agile Sciences, Inc., Raleigh, NC, United States
| | - Raul G Doyle
- Agile Sciences, Inc., Raleigh, NC, United States
| | - Casey M Theriot
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
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43
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Saito R, Talukdar PK, Alanazi SS, Sarker MR. RelA/DTD-mediated regulation of spore formation and toxin production by Clostridium perfringens type A strain SM101. MICROBIOLOGY-SGM 2018; 164:835-847. [PMID: 29624163 DOI: 10.1099/mic.0.000655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
RelA is a global regulator for stationary phase development in the model bacterium Bacillus subtilis. The relA gene forms a bicistronic operon with the downstream dtd gene. In this study, we evaluated the significance of RelA and DTD proteins in spore formation and toxin production by an important gastrointestinal pathogen Clostridium perfringens. Our β-glucuronidase assay showed that in C. perfringens strain SM101, relA forms a bicistronic operon with its downstream dtd gene, and the relA promoter is expressed during both vegetative and sporulation conditions. By constructing double relA dtd and single dtd mutants in C. perfringens SM101, we found that: (1) RelA is required for maintaining the efficient growth capacity of SM101 cells during vegetative conditions; (2) both RelA and DTD are required for spore formation and enterotoxin (CPE) production by SM101; (3) RelA/DTD activate CodY, which is known to activate spore formation and CPE production in SM101 by activating a key sporulation-specific σ factor F; (4) as expected, RelA/DTD activate sporulation-specific σ factors (σE, σF, σG and σK) by positively regulating Spo0A production; and finally (5) RelA, but not DTD, negatively regulates phospholipase C (PLC) production by repressing plc gene expression. Collectively, our results demonstrate that RelA modulates cellular physiology such as growth, spore formation and toxin production by C. perfringens type A strain SM101, although DTD also plays a role in these pleiotropic functions in coordination with RelA during sporulation. These findings have implications for the understanding of the mechanisms involved in the infectious cycle of C. perfringens.
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Affiliation(s)
- Ryoichi Saito
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA.,Department of Microbiology and Immunology, Field of Applied Laboratory Science, Graduate School of Health Care Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Prabhat K Talukdar
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA.,Department of Microbiology, College of Science, Oregon State University, Corvallis, OR, USA.,Present address: School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Saud S Alanazi
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA.,Department of Microbiology, College of Science, Oregon State University, Corvallis, OR, USA
| | - Mahfuzur R Sarker
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA.,Department of Microbiology, College of Science, Oregon State University, Corvallis, OR, USA
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44
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Nawrocki KL, Wetzel D, Jones JB, Woods EC, McBride SM. Ethanolamine is a valuable nutrient source that impacts Clostridium difficile pathogenesis. Environ Microbiol 2018; 20:1419-1435. [PMID: 29349925 PMCID: PMC5903940 DOI: 10.1111/1462-2920.14048] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 01/03/2018] [Accepted: 01/14/2018] [Indexed: 12/12/2022]
Abstract
Clostridium (Clostridioides) difficile is a gastrointestinal pathogen that colonizes the intestinal tract of mammals and can cause severe diarrheal disease. Although C. difficile growth is confined to the intestinal tract, our understanding of the specific metabolites and host factors that are important for the growth of the bacterium is limited. In other enteric pathogens, the membrane-derived metabolite, ethanolamine (EA), is utilized as a nutrient source and can function as a signal to initiate the production of virulence factors. In this study, we investigated the effects of ethanolamine and the role of the predicted ethanolamine gene cluster (CD1907-CD1925) on C. difficile growth. Using targeted mutagenesis, we disrupted genes within the eut cluster and assessed their roles in ethanolamine utilization, and the impact of eut disruption on the outcome of infection in a hamster model of disease. Our results indicate that the eut gene cluster is required for the growth of C. difficile on ethanolamine as a primary nutrient source. Further, the inability to utilize ethanolamine resulted in greater virulence and a shorter time to morbidity in the animal model. Overall, these data suggest that ethanolamine is an important nutrient source within the host and that, in contrast to other intestinal pathogens, the metabolism of ethanolamine by C. difficile can delay the onset of disease.
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Affiliation(s)
- Kathryn L. Nawrocki
- Department of Microbiology and Immunology, and Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Daniela Wetzel
- Department of Microbiology and Immunology, and Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Joshua B. Jones
- Department of Microbiology and Immunology, and Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Emily C. Woods
- Department of Microbiology and Immunology, and Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Shonna M. McBride
- Department of Microbiology and Immunology, and Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, USA
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45
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Abstract
Clostridium difficile is the primary cause of nosocomial diarrhea and pseudomembranous colitis. It produces dormant spores, which serve as an infectious vehicle responsible for transmission of the disease and persistence of the organism in the environment. In Bacillus subtilis, the sin locus coding SinR (113 aa) and SinI (57 aa) is responsible for sporulation inhibition. In B. subtilis, SinR mainly acts as a repressor of its target genes to control sporulation, biofilm formation, and autolysis. SinI is an inhibitor of SinR, so their interaction determines whether SinR can inhibit its target gene expression. The C. difficile genome carries two sinR homologs in the operon that we named sinR and sinR’, coding for SinR (112 aa) and SinR’ (105 aa), respectively. In this study, we constructed and characterized sin locus mutants in two different C. difficile strains R20291 and JIR8094, to decipher the locus’s role in C. difficile physiology. Transcriptome analysis of the sinRR’ mutants revealed their pleiotropic roles in controlling several pathways including sporulation, toxin production, and motility in C. difficile. Through various genetic and biochemical experiments, we have shown that SinR can regulate transcription of key regulators in these pathways, which includes sigD, spo0A, and codY. We have found that SinR’ acts as an antagonist to SinR by blocking its repressor activity. Using a hamster model, we have also demonstrated that the sin locus is needed for successful C. difficile infection. This study reveals the sin locus as a central link that connects the gene regulatory networks of sporulation, toxin production, and motility; three key pathways that are important for C. difficile pathogenesis. In Bacillus subtilis, sporulation, competence and biofilm formation are regulated by a pleiotropic regulator called SinR. Two sinR homologs are present in C. difficile genome as an operon and henceforth labeled as sinR and sinR’. Our detailed investigation revealed that in C. difficile, the SinR and SinR’ are key master regulators needed for the regulation of several pathways including sporulation, toxin production, and motility.
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Affiliation(s)
| | - Junjun Ou
- Department of Agronomy, Kansas State University, Manhattan, KS, United Sates of America
| | - Bruno Dupuy
- Laboratoire Pathogénese des Bactéries Anaérobies, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Revathi Govind
- Division of Biology, Kansas State University, Manhattan, KS, United Sates of America
- * E-mail:
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46
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Zhu D, Sorg JA, Sun X. Clostridioides difficile Biology: Sporulation, Germination, and Corresponding Therapies for C. difficile Infection. Front Cell Infect Microbiol 2018; 8:29. [PMID: 29473021 PMCID: PMC5809512 DOI: 10.3389/fcimb.2018.00029] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/23/2018] [Indexed: 12/18/2022] Open
Abstract
Clostridioides difficile is a Gram-positive, spore-forming, toxin-producing anaerobe, and an important nosocomial pathogen. Due to the strictly anaerobic nature of the vegetative form, spores are the main morphotype of infection and transmission of the disease. Spore formation and their subsequent germination play critical roles in C. difficile infection (CDI) progress. Under suitable conditions, C. difficile spores will germinate and outgrow to produce the pathogenic vegetative form. During CDI, C. difficile produces toxins (TcdA and TcdB) that are required to initiate the disease. Meanwhile, it also produces spores that are responsible for the persistence and recurrence of C. difficile in patients. Recent studies have shed light on the regulatory mechanisms of C. difficile sporulation and germination. This review is to summarize recent advances on the regulation of sporulation/germination in C. difficile and the corresponding therapeutic strategies that are aimed at these important processes.
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Affiliation(s)
- Duolong Zhu
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Joseph A Sorg
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - Xingmin Sun
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
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47
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Dembek M, Willing SE, Hong HA, Hosseini S, Salgado PS, Cutting SM. Inducible Expression of spo0A as a Universal Tool for Studying Sporulation in Clostridium difficile. Front Microbiol 2017; 8:1793. [PMID: 28983286 PMCID: PMC5613124 DOI: 10.3389/fmicb.2017.01793] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 09/05/2017] [Indexed: 01/01/2023] Open
Abstract
Clostridium difficile remains a leading nosocomial pathogen, putting considerable strain on the healthcare system. The ability to form endospores, highly resistant to environmental insults, is key to its persistence and transmission. However, important differences exist between the sporulation pathways of C. difficile and the model Gram-positive organism Bacillus subtilis. Amongst the challenges in studying sporulation in C. difficile is the relatively poor levels of sporulation and high heterogeneity in the sporulation process. To overcome these limitations we placed Ptet regulatory elements upstream of the master regulator of sporulation, spo0A, generating a new strain that can be artificially induced to sporulate by addition of anhydrotetracycline (ATc). We demonstrate that this strain is asporogenous in the absence of ATc, and that ATc can be used to drive faster and more efficient sporulation. Induction of Spo0A is titratable and this can be used in the study of the spo0A regulon both in vitro and in vivo, as demonstrated using a mouse model of C. difficile infection (CDI). Insights into differences between the sporulation pathways in B. subtilis and C. difficile gained by study of the inducible strain are discussed, further highlighting the universal interest of this tool. The Ptet-spo0A strain provides a useful background in which to generate mutations in genes involved in sporulation, therefore providing an exciting new tool to unravel key aspects of sporulation in C. difficile.
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Affiliation(s)
- Marcin Dembek
- Institute for Cell and Molecular Biosciences, Newcastle UniversityNewcastle upon Tyne, United Kingdom
| | - Stephanie E Willing
- School of Biological Sciences, Royal Holloway, University of LondonLondon, United Kingdom
| | - Huynh A Hong
- School of Biological Sciences, Royal Holloway, University of LondonLondon, United Kingdom
| | - Siamand Hosseini
- School of Biological Sciences, Royal Holloway, University of LondonLondon, United Kingdom
| | - Paula S Salgado
- Institute for Cell and Molecular Biosciences, Newcastle UniversityNewcastle upon Tyne, United Kingdom
| | - Simon M Cutting
- School of Biological Sciences, Royal Holloway, University of LondonLondon, United Kingdom
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A Nutrient-Regulated Cyclic Diguanylate Phosphodiesterase Controls Clostridium difficile Biofilm and Toxin Production during Stationary Phase. Infect Immun 2017; 85:IAI.00347-17. [PMID: 28652311 DOI: 10.1128/iai.00347-17] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 06/20/2017] [Indexed: 12/18/2022] Open
Abstract
The signaling molecule cyclic diguanylate (c-di-GMP) mediates physiological adaptation to extracellular stimuli in a wide range of bacteria. The complex metabolic pathways governing c-di-GMP synthesis and degradation are highly regulated, but the specific cues that impact c-di-GMP signaling are largely unknown. In the intestinal pathogen Clostridium difficile, c-di-GMP inhibits flagellar motility and toxin production and promotes pilus-dependent biofilm formation, but no specific biological functions have been ascribed to any of the individual c-di-GMP synthases or phosphodiesterases (PDEs). Here, we report the functional and biochemical characterization of a c-di-GMP PDE, PdcA, 1 of 37 confirmed or putative c-di-GMP metabolism proteins in C. difficile 630. Our studies reveal that pdcA transcription is controlled by the nutrient-regulated transcriptional regulator CodY and accordingly increases during stationary phase. In addition, PdcA PDE activity is allosterically regulated by GTP, further linking c-di-GMP levels to nutrient availability. Mutation of pdcA increased biofilm formation and reduced toxin biosynthesis without affecting swimming motility or global intracellular c-di-GMP. Analysis of the transcriptional response to pdcA mutation indicates that PdcA-dependent phenotypes manifest during stationary phase, consistent with regulation by CodY. These results demonstrate that inactivation of this single PDE gene is sufficient to impact multiple c-di-GMP-dependent phenotypes, including the production of major virulence factors, and suggest a link between c-di-GMP signaling and nutrient availability.
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Jenior ML, Leslie JL, Young VB, Schloss PD. Clostridium difficile Colonizes Alternative Nutrient Niches during Infection across Distinct Murine Gut Microbiomes. mSystems 2017; 2:e00063-17. [PMID: 28761936 PMCID: PMC5527303 DOI: 10.1128/msystems.00063-17] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 07/03/2017] [Indexed: 01/01/2023] Open
Abstract
Clostridium difficile is the largest single cause of hospital-acquired infection in the United States. A major risk factor for Clostridium difficile infection (CDI) is prior exposure to antibiotics, as they disrupt the gut bacterial community which protects from C. difficile colonization. Multiple antibiotic classes have been associated with CDI susceptibility, many leading to distinct community structures stemming from variation in bacterial targets of action. These community structures present separate metabolic challenges to C. difficile. Therefore, we hypothesized that the pathogen adapts its physiology to the nutrients within different gut environments. Utilizing an in vivo CDI model, we demonstrated that C. difficile highly colonized ceca of mice pretreated with any of three antibiotics from distinct classes. Levels of C. difficile spore formation and toxin activity varied between animals based on the antibiotic pretreatment. These physiologic processes in C. difficile are partially regulated by environmental nutrient concentrations. To investigate metabolic responses of the bacterium in vivo, we performed transcriptomic analysis of C. difficile from ceca of infected mice across pretreatments. This revealed heterogeneous expression in numerous catabolic pathways for diverse growth substrates. To assess which resources C. difficile exploited, we developed a genome-scale metabolic model with a transcriptome-enabled metabolite scoring algorithm integrating network architecture. This platform identified nutrients that C. difficile used preferentially between pretreatments, which were validated through untargeted mass spectrometry of each microbiome. Our results supported the hypothesis that C. difficile inhabits alternative nutrient niches across cecal microbiomes with increased preference for nitrogen-containing carbon sources, particularly Stickland fermentation substrates and host-derived glycans. IMPORTANCE Infection by the bacterium Clostridium difficile causes an inflammatory diarrheal disease which can become life threatening and has grown to be the most prevalent nosocomial infection. Susceptibility to C. difficile infection is strongly associated with previous antibiotic treatment, which disrupts the gut microbiota and reduces its ability to prevent colonization. In this study, we demonstrated that C. difficile altered pathogenesis between hosts pretreated with antibiotics from separate classes and exploited different nutrient sources across these environments. Our metabolite score calculation also provides a platform to study nutrient requirements of pathogens during an infection. Our results suggest that C. difficile colonization resistance is mediated by multiple groups of bacteria competing for several subsets of nutrients and could explain why total reintroduction of competitors through fecal microbial transplant currently is the most effective treatment for recurrent CDI. This work could ultimately contribute to the identification of targeted, context-dependent measures that prevent or reduce C. difficile colonization, including pre- and probiotic therapies.
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Affiliation(s)
- Matthew L. Jenior
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jhansi L. Leslie
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Vincent B. Young
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - Patrick D. Schloss
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
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50
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Adenine Addition Restores Cell Viability and Butanol Production in Clostridium saccharoperbutylacetonicum N1-4 (ATCC 13564) Cultivated at 37°C. Appl Environ Microbiol 2017; 83:AEM.02960-16. [PMID: 28130303 DOI: 10.1128/aem.02960-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/20/2017] [Indexed: 12/11/2022] Open
Abstract
We have developed butanol-producing consolidated bioprocessing from cellulosic substrates through coculture of cellulolytic clostridia and butanol-producing Clostridium saccharoperbutylacetonicum strain N1-4. However, the butanol fermentation by strain N1-4 (which has an optimal growth temperature of 30°C) is sensitive to the higher cultivation temperature of 37°C; the nature of this deleterious effect remains unclear. Comparison of the intracellular metabolites of strain N1-4 cultivated at 30°C and 37°C revealed decreased levels of multiple primary metabolites (notably including nucleic acids and cofactors) during growth at the higher temperature. Supplementation of the culture medium with 250 mg/liter adenine enhanced both cell growth (with the optical density at 600 nm increasing from 4.3 to 10.2) and butanol production (increasing from 3.9 g/liter to 9.6 g/liter) at 37°C, compared to those obtained without adenine supplementation, such that the supplemented 37°C culture exhibited growth and butanol production approaching those observed at 30°C in the absence of adenine supplementation. These improved properties were based on the maintenance of cell viability. We further showed that adenine supplementation enhanced cell viability during growth at 37°C by maintaining ATP levels and inhibiting spore formation. This work represents the first demonstration (to our knowledge) of the importance of adenine-related metabolism for clostridial butanol production, suggesting a new means of enhancing target pathways based on metabolite levels.IMPORTANCE Metabolomic analysis revealed decreased levels of multiple primary metabolites during growth at 37°C, compared to 30°C, in C. saccharoperbutylacetonicum strain N1-4. We found that adenine supplementation restored the cell growth and butanol production of strain N1-4 at 37°C. The effects of adenine supplementation reflected the maintenance of cell viability originating from the maintenance of ATP levels and the inhibition of spore formation. Thus, our metabolomic analysis identified the depleted metabolites that were required to maintain cell viability. Our strategy, which is expected to be applicable to a wide range of organisms, permits the identification of the limiting metabolic pathway, which can serve as a new target for molecular breeding. The other novel finding of this work is that adenine supplementation inhibits clostridial spore formation. The mechanism linking spore formation and metabolomic status in butanol-producing clostridia is expected to be the focus of further research.
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