1
|
Serrano M, Martins D, Henriques AO. Clostridioides difficile Sporulation. Adv Exp Med Biol 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
2
|
Razim A, Górska S, Gamian A. Non-Toxin-Based Clostridioides difficile Vaccination Approaches. Pathogens 2023; 12. [PMID: 36839507 DOI: 10.3390/pathogens12020235] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/02/2023] [Accepted: 01/05/2023] [Indexed: 02/05/2023] Open
Abstract
Clostridioides difficile (CD) is a Gram-positive, anaerobic bacterium that infects mainly hospitalized and elderly people who have been treated with long-term antibiotic therapy leading to dysbiosis. The deteriorating demographic structure and the increase in the number of antibiotics used indicate that the problem of CD infections (CDI) will continue to increase. Thus far, there is no vaccine against CD on the market. Unfortunately, clinical trials conducted using the CD toxin-based antigens did not show sufficiently high efficacy, because they did not prevent colonization and transmission between patients. It seems that the vaccine should also include antigens found in the bacterium itself or its spores in order not only to fight the effects of toxins but also to prevent the colonization of the patient. This literature review summarizes the latest advances in research into vaccine antigens that do not contain CD toxins.
Collapse
|
3
|
Haft DH, Gwadz M. Eight Unexpected Selenoprotein Families in Organometallic Biochemistry in Clostridium difficile, in ABC Transport, and in Methylmercury Biosynthesis. J Bacteriol 2023; 205:e0025922. [PMID: 36598231 DOI: 10.1128/jb.00259-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The bioinformatics of a nine-gene locus, designated selenocysteine-assisted organometallic (SAO), was investigated after identifying six new selenoprotein families and constructing hidden Markov models (HMMs) that find and annotate members of those families. Four are selenoproteins in most SAO loci, including Clostridium difficile. They include two ABC transporter subunits, namely, permease SaoP, with selenocysteine (U) at the channel-gating position, and substrate-binding subunit SaoB. Cytosolic selenoproteins include SaoL, homologous to MerB organomercurial lyases from mercury resistance loci, and SaoT, related to thioredoxins. SaoL, SaoB, and surface protein SaoC (an occasional selenoprotein) share an unusual CU dipeptide motif, which is something rare in selenoproteins but found in selenoprotein variants of mercury resistance transporter subunit MerT. A nonselenoprotein, SaoE, shares homology with Cu/Zn efflux and arsenical efflux pumps. The organization of the SAO system suggests substrate interaction with surface-exposed selenoproteins, followed by import, metabolism that may cleave a carbon-to-heavy metal bond, and finally metal efflux. A novel type of mercury resistance is possible, but SAO instead may support fermentative metabolism, with selenocysteine-mediated formation of organometallic intermediates, followed by import, degradation, and metal efflux. Phylogenetic profiling shows SOA loci consistently co-occur with Stickland fermentation markers but even more consistently with 8Fe-9S cofactor-type double-cubane proteins. Hypothesizing that the SAO system forms organometallic intermediates, we investigated the known methylmercury formation protein families HgcA and HgcB. Both families contained overlooked selenoproteins. Most HgcAs have a CU motif N terminal to their previously accepted start sites. Seeking additional rare and overlooked selenoproteins may help reveal more cryptic aspects of microbial biochemistry. IMPORTANCE This work adds 8 novel prokaryotic selenoproteins to the 80 or so families previously known. It describes the SAO (selenocysteine-assisted organometallic) locus, with the most selenoproteins of any known system. The rare CU motif recurs throughout, suggesting the formation and degradation of organometallic compounds. That suggestion triggered a reexamination of HgcA and HcgB, which are methylmercury formation proteins that can adversely impact food safety. Both are selenoproteins, once corrected, with HgcA again showing a CU motif. The SAO system is plausibly a mercury resistance locus for selenium-dependent anaerobes. But instead, it may exploit heavy metals as cofactors in organometallic intermediate-forming pathways that circumvent high activation energies and facilitate the breakdown of otherwise poorly accessible nutrients. SAO could provide an edge that helps Clostridium difficile, an important pathogen, establish disease.
Collapse
|
4
|
Yu B, Kanaan J, Shames H, Wicander J, Aryal M, Li Y, Korza G, Brul S, Kramer G, Li YQ, Nichols FC, Hao B, Setlow P. Identification and characterization of new proteins crucial for bacterial spore resistance and germination. Front Microbiol 2023; 14:1161604. [PMID: 37113233 PMCID: PMC10126465 DOI: 10.3389/fmicb.2023.1161604] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/17/2023] [Indexed: 04/29/2023] Open
Abstract
2Duf, named after the presence of a transmembrane (TM) Duf421 domain and a small Duf1657 domain in its sequence, is likely located in the inner membrane (IM) of spores in some Bacillus species carrying a transposon with an operon termed spoVA 2mob. These spores are known for their extreme resistance to wet heat, and 2Duf is believed to be the primary contributor to this trait. In this study, we found that the absence of YetF or YdfS, both Duf421 domain-containing proteins and found only in wild-type (wt) B. subtilis spores with YetF more abundant, leads to decreased resistance to wet heat and agents that can damage spore core components. The IM phospholipid compositions and core water and calcium-dipicolinic acid levels of YetF-deficient spores are similar to those of wt spores, but the deficiency could be restored by ectopic insertion of yetF, and overexpression of YetF increased wt spore resistance to wet heat. In addition, yetF and ydfS spores have decreased germination rates as individuals and populations with germinant receptor-dependent germinants and increased sensitivity to wet heat during germination, potentially due to damage to IM proteins. These data are consistent with a model in which YetF, YdfS and their homologs modify IM structure to reduce IM permeability and stabilize IM proteins against wet heat damage. Multiple yetF homologs are also present in other spore forming Bacilli and Clostridia, and even some asporogenous Firmicutes, but fewer in asporogenous species. The crystal structure of a YetF tetramer lacking the TM helices has been reported and features two distinct globular subdomains in each monomer. Sequence alignment and structure prediction suggest this fold is likely shared by other Duf421-containing proteins, including 2Duf. We have also identified naturally occurring 2duf homologs in some Bacilli and Clostridia species and in wt Bacillus cereus spores, but not in wt B. subtilis. Notably, the genomic organization around the 2duf gene in most of these species is similar to that in spoVA 2mob, suggesting that one of these species was the source of the genes on this operon in the extremely wet heat resistant spore formers.
Collapse
Affiliation(s)
- Benjamin Yu
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Julia Kanaan
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Hannah Shames
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - James Wicander
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Makunda Aryal
- Department of Physics, East Carolina University, Greenville, NC, United States
| | - Yunfeng Li
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - George Korza
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Stanley Brul
- Molecular Biology and Microbial Food Safety, University of Amsterdam, Amsterdam, Netherlands
| | - Gertjan Kramer
- Laboratory for Mass Spectrometry of Biomolecules, Swammerdam Institute for Life Science, University of Amsterdam, Amsterdam, Netherlands
| | - Yong-qing Li
- Department of Physics, East Carolina University, Greenville, NC, United States
| | - Frank C. Nichols
- Division of Periodontology, UConn Health, Farmington, CT, United States
| | - Bing Hao
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
- Bing Hao,
| | - Peter Setlow
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
- *Correspondence: Peter Setlow,
| |
Collapse
|
5
|
Loskutov SI, Proshin SN, Ryabukhin DS. Evolutionary aspects of gastrointestinal tract microbiome-host interaction underlying gastrointestinal barrier integrity. Russian Journal of Infection and Immunity 2022. [DOI: 10.15789/2220-7619-eao-1633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In the host sustenance and homeostasis, the microbiome is a key component in the functional system. Throughout ontogenetic development, microbiome including that of the gastrointestinal tract (GIT) is the vital factor that ensures not only host functioning, but also its interaction with environment. To uncover the mechanisms underlying GIT microbiome showing a decisive influence on host organism, a systematic approach is needed, because diverse microorganisms are predominantly localized in different parts of the GIT. Recently, a new interdisciplinary direction of science, nanobioinformatics that has been extensively developed considers gene networks as the major object of study representing a coordinated group of genes that functionally account for formation and phenotypic disclosure of various host traits. Here, an important place should be provided to the genetically determined level of the gastrointestinal tract microbiome, its interaction at the level of the host food systems. There have been increasing evidence indicating that the microbiome is directly involved in the pathogenesis of host diseases showing a multi-layered interaction with host metabolic and immune systems. At the same time, the microbial community is unevenly distributed throughout the gastrointestinal tract, and its different portions are variously active while interacting with the host immune system. The architecture of interaction between the microbiome and host cells is extremely complex, and the interaction of individual cells, at the same time, varies greatly. Bacteria colonizing the crypts of the small intestine regulate enterocyte proliferation by affecting DNA replication and gene expression, while bacteria at the tip of the intestinal villi mediate gene expression responsible for metabolism and immune response. Enterocytes and Paneth cells, in turn, regulate the vital activity of the community of microorganisms through the production of polysaccharides (carbohydrates) and antibacterial factors on their surface. Thus, the integrity of the gastrointestinal barrier (GIB) is maintained, which protects the body from infections and inflammation, while violation of its integrity leads to a number of diseases. It has been shown that depending on the dominance of certain types of bacteria the microbiome can maintain or disrupt GIB integrity. The structural and functional GIB integrity is important for body homeostasis. To date, at least 50 proteins have been characterized as being involved in the structural and functional integrability of tight junctions between gastrointestinal tract epithelial cells. The current review comprehensively discusses such issues and presents original research carried out at various facilities of translational biomedicine.
Collapse
|
6
|
Trautwein-Schult A, Bartel J, Maaß S, Becher D. Metabolic Labeling of Clostridioides difficile Proteins. Methods Mol Biol 2021; 2228:271-82. [PMID: 33950497 DOI: 10.1007/978-1-0716-1024-4_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The introduction of stable isotopes in vivo via metabolic labeling approaches (SILAC or 15N-labeling) allows, after combination of differentially treated labeled and unlabeled cells or protein extracts, for correction of protein quantification errors implemented during elaborated sample preparation workflows. The SILAC-based approach uses heavy arginine and lysine to incorporate the label into bacterial strains and cell lines, whereas 15N-metabolic labeling is achieved by cultivation in 15N-salt containing media. In case of Clostridioides difficile, the lack in arginine and lysine auxotrophy as well as the Stickland dominated metabolism makes metabolic labeling challenging. Here, a step-by-step guideline for the metabolic labeling of C. difficile is described, which combines cultivation in liquid 15N-substituted medium followed by cultivation steps on solid 15N-substituted medium. The described procedure results in a label incorporation rate higher than 97%. Cells prepared by the following method can be used as standard for relative quantification approaches of, e.g., the membrane or surface proteome of C. difficile.
Collapse
|
7
|
Chiu PJ, Rathod J, Hong YP, Tsai PJ, Hung YP, Ko WC, Chen JW, Paredes-Sabja D, Huang IH. Clostridioides difficile spores stimulate inflammatory cytokine responses and induce cytotoxicity in macrophages. Anaerobe 2021; 70:102381. [PMID: 34082120 DOI: 10.1016/j.anaerobe.2021.102381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/30/2021] [Accepted: 05/04/2021] [Indexed: 02/08/2023]
Abstract
Clostridioides difficile is a gram-positive, spore-forming anaerobic bacterium, and the leading cause of antibiotic-associated diarrhea worldwide. During C. difficile infection, spores germinate in the presence of bile acids into vegetative cells that subsequently colonize the large intestine and produce toxins. In this study, we demonstrated that C. difficile spores can universally adhere to, and be phagocytosed by, murine macrophages. Only spores from toxigenic strains were able to significantly stimulate the production of inflammatory cytokines by macrophages and subsequently induce significant cytotoxicity. Spores from the isogenic TcdA and TcdB double mutant induced significantly lower inflammatory cytokines and cytotoxicity in macrophages, and these activities were restored by pre-exposure of the spores to either toxins. These findings suggest that during sporulation, spores might be coated with C. difficile toxins from the environment, which could affect C. difficile pathogenesis in vivo.
Collapse
Affiliation(s)
- Po-Jung Chiu
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jagat Rathod
- Department of Earth Sciences National Cheng Kung University, Tainan, Taiwan
| | - Yu-Ping Hong
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Pei-Jane Tsai
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, Taiwan; Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
| | - Yuan-Pin Hung
- Department of Internal Medicine, Tainan Hospital, Ministry of Health and Welfare, Tainan, Taiwan
| | - Wen-Chien Ko
- Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Jenn-Wei Chen
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
| | - Daniel Paredes-Sabja
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA; Millennium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile
| | - I-Hsiu Huang
- Department of Biochemistry and Microbiology, Oklahoma State University Center for Health Sciences, Tulsa, OK, USA; Oklahoma State University College of Osteopathic Medicine at Cherokee Nation, Tahlequah, OK, USA.
| |
Collapse
|
8
|
Abstract
Outbreaks and deaths related to Foodborne Diseases (FBD) occur constantly in the world, as a result of the consumption of contaminated foodstuffs with pathogens such as Listeria monocytogenes, Escherichia coli, Staphylococcus aureus, Salmonella spp, Clostridium spp. and Campylobacter spp. The purpose of this review is to discuss the main omic techniques applied in foodborne pathogen and to demonstrate their functionalities through the food chain and to guarantee the food safety. The main techniques presented are genomic, transcriptomic, secretomic, proteomic, and metabolomic, which together, in the field of food and nutrition, are known as "Foodomics." This review had highlighted the potential of omics to integrate variables that contribute to food safety and to enable us to understand their application on foodborne diseases. The appropriate use of these techniques had driven the definition of critical parameters to achieve successful results in the improvement of consumers health, costs and to obtain safe and high-quality products.
Collapse
Affiliation(s)
| | | | | | - Emmanuel Barboza
- Health Sciences Faculty, University of Western Sao Paulo, Presidente Prudente, Sao Paulo, Brazil
| | | |
Collapse
|