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Sum R, Lim SJM, Sundaresan A, Samanta S, Swaminathan M, Low W, Ayyappan M, Lim TW, Choo MD, Huang GJ, Cheong I. Clostridium septicum manifests a bile salt germinant response mediated by Clostridioides difficile csp gene orthologs. Commun Biol 2024; 7:947. [PMID: 39103440 DOI: 10.1038/s42003-024-06617-4] [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: 05/09/2023] [Accepted: 07/23/2024] [Indexed: 08/07/2024] Open
Abstract
Clostridium septicum infections are highly predictive of certain malignancies in human patients. To initiate infections, C. septicum spores must first germinate and regain vegetative growth. Yet, what triggers the germination of C. septicum spores is still unknown. Here, we observe that C. septicum germinates in response to specific bile salts. Putative bile salt recognition genes are identified in C. septicum based on their similarity in sequence and organization to bile salt-responsive csp genes in Clostridioides difficile. Inactivating two of these csp orthologs (cspC-82 and cspC-1718) results in mutant spores that no longer germinate in the presence of their respective cognate bile salts. Additionally, inactivating the putative cspBA or sleC genes in C. septicum abrogates the germination response to all bile salt germinants, suggesting that both act at a convergent point downstream of cspC-82 and cspC-1718. Molecular dynamics simulations show that both CspC-82 and CspC-1718 bear a strong structural congruence with C. difficile's CspC. The existence of functional bile salt germination sensors in C. septicum may be relevant to the association between infection and malignancy.
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Affiliation(s)
- Rongji Sum
- Temasek Life Sciences Laboratory, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Sylvester Jian Ming Lim
- Temasek Life Sciences Laboratory, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Ajitha Sundaresan
- Temasek Life Sciences Laboratory, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | | | | | - Wayne Low
- Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Madhumitha Ayyappan
- Temasek Life Sciences Laboratory, Singapore, Singapore
- NUS High School of Mathematics and Sciences, Singapore, Singapore
| | - Ting Wei Lim
- Temasek Life Sciences Laboratory, Singapore, Singapore
- NUS High School of Mathematics and Sciences, Singapore, Singapore
| | - Marvin Dragon Choo
- Temasek Life Sciences Laboratory, Singapore, Singapore
- NUS High School of Mathematics and Sciences, Singapore, Singapore
| | | | - Ian Cheong
- Temasek Life Sciences Laboratory, Singapore, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
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Osborne MS, Brehm JN, Olivença C, Cochran AM, Serrano M, Henriques AO, Sorg JA. The impact of YabG mutations on C. difficile spore germination and processing of spore substrates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598338. [PMID: 38915615 PMCID: PMC11195116 DOI: 10.1101/2024.06.10.598338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
YabG is a sporulation-specific protease that is conserved among sporulating bacteria. C. difficile YabG processes cortex destined proteins preproSleC into proSleC and CspBA to CspB and CspA. YabG also affects synthesis of spore coat/exosporium proteins CotA and CdeM. In prior work that identified CspA as the co-germinant receptor, mutations in yabG were found which altered the co-germinants required to initiate spore germination. To understand how these mutations in the yabG locus contribute to C. difficile spore germination, we introduced these mutations into an isogenic background. Spores derived from C. difficile yabG C207A (catalytically inactive), C. difficile yabG A46D, C. difficile yabG G37E, and C. difficile yabG P153L strains germinated in response to TA alone. Recombinantly expressed and purified preproSleC incubated with E. coli lysate expressing wild type YabG resulted in the removal of the pre sequence from preproSleC. Interestingly, only YabGA46D showed any activity towards purified preproSleC. Mutation of the YabG processing site in preproSleC (R119A) led to YabG shifting its processing to R115 or R112. Finally, changes in yabG expression under the mutant promoters were analyzed using a SNAP-tag and revealed expression differences at early and late stages of sporulation. Overall, our results support and expand upon the hypothesis that YabG is important for germination and spore assembly and, upon mutation of the processing site, can shift where it cleaves substrates.
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Affiliation(s)
- Morgan S. Osborne
- Department of Biology, Texas A&M University, College Station, TX 77845, USA
| | - Joshua N. Brehm
- Department of Biology, Texas A&M University, College Station, TX 77845, USA
| | - Carmen Olivença
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Alicia M. Cochran
- Department of Biology, Texas A&M University, College Station, TX 77845, USA
| | - Mónica Serrano
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Adriano O. Henriques
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Joseph A. Sorg
- Department of Biology, Texas A&M University, College Station, TX 77845, USA
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Sundaresan A, Le Ngoc M, Wew MU, Ramkumar V, Raninga P, Sum R, Cheong I. A design of experiments screen reveals that Clostridium novyi-NT spore germinant sensing is stereoflexible for valine and its analogs. Commun Biol 2023; 6:118. [PMID: 36709236 PMCID: PMC9884283 DOI: 10.1038/s42003-023-04496-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 01/17/2023] [Indexed: 01/30/2023] Open
Abstract
Although Clostridium novyi-NT is an anti-cancer bacterial therapeutic which germinates within hypoxic tumors to kill cancer cells, the actual germination triggers for C. novyi-NT are still unknown. In this study, we screen candidate germinants using combinatorial experimental designs and discover by serendipity that D-valine is a potent germinant, inducing 50% spore germination at 4.2 mM concentration. Further investigation revealed that five D-valine analogs are also germinants and four of these analogs are enantiomeric pairs. This stereoflexible effect of L- and D-amino acids shows that spore germination is a complex process where enantiomeric interactions can be confounders. This study also identifies L-cysteine as a germinant, and hypoxanthine and inosine as co-germinants. Several other amino acids promote (L-valine, L-histidine, L-threonine and L-alanine) or inhibit (L-arginine, L-glycine, L-lysine, L-tryptophan) germination in an interaction-dependent manner. D-alanine inhibits all germination, even in complex growth media. This work lays the foundation for improving the germination efficacy of C. novyi-NT spores in tumors.
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Affiliation(s)
- Ajitha Sundaresan
- grid.226688.00000 0004 0620 9198Temasek Life Sciences Laboratory, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Mai Le Ngoc
- grid.4280.e0000 0001 2180 6431NUS High School of Mathematics and Sciences, Singapore, Singapore
| | - Marvell Ung Wew
- grid.4280.e0000 0001 2180 6431NUS High School of Mathematics and Sciences, Singapore, Singapore
| | - Varsha Ramkumar
- grid.4280.e0000 0001 2180 6431NUS High School of Mathematics and Sciences, Singapore, Singapore
| | - Prahlad Raninga
- grid.226688.00000 0004 0620 9198Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Rongji Sum
- grid.226688.00000 0004 0620 9198Temasek Life Sciences Laboratory, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Ian Cheong
- grid.226688.00000 0004 0620 9198Temasek Life Sciences Laboratory, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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Song M, Lei Y, Ali A, Xu Y, Sheng K, Huang T, Huang J, Huang M. Inhibitory effect of licorice extract on the germination and outgrowth of Paraclostridium bifermentans spores. Front Microbiol 2022; 13:1076144. [PMID: 36532483 PMCID: PMC9755857 DOI: 10.3389/fmicb.2022.1076144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/09/2022] [Indexed: 03/26/2024] Open
Abstract
INTRODUCTION Paraclostridium bifermentans is responsible for spoilage properties in vacuum-packaged meat. Ordinary heat treatment techniques are ineffective to control the extremely heat-resistant spores of P. bifermentans. Therefore, finding a new strategy to prevent the contamination of P. bifermentans spores in vacuum-packaged meat is challenging. METHODS In this study, P. bifermentans was isolated from the vacuum-packaged chicken, and the inhibitory effects of licorice extract on the germination and outgrowth of P. bifermentans spores, as well as the key bioactive components in the licorice extract involved in inhibiting spore activity, were investigated. RESULTS The spores induced by combination-nutrient-germinant (150 mmol/L L-alanine and 20 mmol/L inosine, co-AI) did not germinate when the concentration of licorice extract was ≥ 3.13 mg/ml. The germination of P. bifermentans spores induced by non-nutrient-germinant (8 mmol/L dipicolinic acid, DPA) was completely prevented by licorice extract at least 1.56 mg/ml. While the outgrowth of P. bifermentans spores was inhibited at a concentration of 0.39 mg/ml. Licorice extract did not seem to damage the non-germinated spores but blocked the germinant sensing. Licorice extract prevented the outgrowing spores from becoming vegetable cells by disrupting the inner membrane. Furthermore, the results obtained from LC-MS data analysis exhibited 15 key bioactive compounds in licorice extract, such as glycyrrhizic acid, liquiritin, etc. Among them, glycyrrhizic acid and liquiritin apioside exerted efficient inhibitory properties on the germination and outgrowth of P. bifermentans spores. DISCUSSION This present study demonstrated that licorice extract can be used as a promising inhibitor of spores and provides a new method to control the residual P. bifermentans spores in meat products. Meanwhile, this study exhibits a baseline for the better understanding of the potential application of licorice extracts to control the P. bifermentans spores in meat products.
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Affiliation(s)
- Mengmeng Song
- Key Laboratory of Meat Processing and Quality Control, Ministry of Education, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yang Lei
- Key Laboratory of Meat Processing and Quality Control, Ministry of Education, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Ahtisham Ali
- Key Laboratory of Meat Processing and Quality Control, Ministry of Education, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yan Xu
- Key Laboratory of Meat Processing and Quality Control, Ministry of Education, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Kairan Sheng
- Key Laboratory of Meat Processing and Quality Control, Ministry of Education, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Tianran Huang
- Jiangsu Research Center for Livestock and Poultry Products Processing Engineering Technology, Nanjing Huangjiaoshou Food Science and Technology Co., Ltd., Nanjing, China
| | - Jichao Huang
- College of Engineering, Nanjing Agricultural University, Nanjing, China
| | - Ming Huang
- Key Laboratory of Meat Processing and Quality Control, Ministry of Education, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
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Calatayud M, Duysburgh C, Van den Abbeele P, Franckenstein D, Kuchina-Koch A, Marzorati M. Long-Term Lactulose Administration Improves Dysbiosis Induced by Antibiotic and C. difficile in the PathoGut TM SHIME Model. Antibiotics (Basel) 2022; 11:1464. [PMID: 36358119 PMCID: PMC9686563 DOI: 10.3390/antibiotics11111464] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 09/28/2023] Open
Abstract
Clostridioides difficile infection (CDI) is the leading cause of antibiotic-associated diarrhea and an important nosocomial infection with different severity degrees. Disruption of the gut microbiota by broad-spectrum antibiotics creates a proper environment for C. difficile colonization, proliferation, and clinical disease onset. Restoration of the gut microbial ecosystem through prebiotic interventions can constitute an effective complementary treatment of CDI. Using an adapted simulator of the human gut microbial ecosystem, the PathoGutTM SHIME, the effect of different long-term and repeated dose lactulose treatments was tested on C. difficile germination and growth in antibiotic-induced dysbiotic gut microbiota environments. The results showed that lactulose reduced the growth of viable C. difficile cells following clindamycin treatment, shifted the antibiotic-induced dysbiotic microbial community, and stimulated the production of health-promoting metabolites (especially butyrate). Recovery of the gut microenvironment by long-term lactulose administration following CDI was also linked to lactate production, decrease in pH and modulation of bile salt metabolism. At a structural level, lactulose showed a significant bifidogenic potential and restored key commensal members of the gut ecosystem such as Lactobacillaceae, Veillonellaceae and Lachnospiraceae. These results support further human intervention studies aiming to validate the in vitro beneficial effects of lactulose on gut microbiome recovery during antibiotic exposure and CDI.
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Affiliation(s)
- Marta Calatayud
- ProDigest BV, Technologiepark 82, 9052 Ghent, Belgium
- Center of Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | | | | | | | | | - Massimo Marzorati
- ProDigest BV, Technologiepark 82, 9052 Ghent, Belgium
- Center of Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
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Baloh M, Sorg JA. Clostridioides difficile spore germination: initiation to DPA release. Curr Opin Microbiol 2022; 65:101-107. [PMID: 34808546 PMCID: PMC8792321 DOI: 10.1016/j.mib.2021.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/01/2021] [Accepted: 11/04/2021] [Indexed: 02/03/2023]
Abstract
Germination by Clostridioides difficile spores is an essential step in pathogenesis. Spores are metabolically dormant forms of bacteria that resist severe conditions. Work over the last 10 years has elucidated that C. difficile spores germinate thorough a novel pathway. This review summarizes our understanding of C. difficile spore germination and the factors involved in germinant recognition, cortex degradation and DPA release.
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Affiliation(s)
- Marko Baloh
- Department of Biology, Texas A&M University, College Station, TX 77843
| | - Joseph A. Sorg
- Department of Biology, Texas A&M University, College Station, TX 77843,Corresponding author: ph: 979-845-6299,
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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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Christie G, Setlow P. Bacillus spore germination: Knowns, unknowns and what we need to learn. Cell Signal 2020; 74:109729. [PMID: 32721540 DOI: 10.1016/j.cellsig.2020.109729] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/18/2020] [Accepted: 07/21/2020] [Indexed: 01/06/2023]
Abstract
How might a microbial cell that is entirely metabolically dormant - and which has the ability to remain so for extended periods of time - irreversibly commit itself to resuming vegetative growth within seconds of being exposed to certain amino acids or sugars? That this process takes place in the absence of any detectable ATP or de novo protein synthesis, and relies upon a pre-formed apparatus that is immobilised, respectively, in a semi-crystalline membrane or multi-layered proteinaceous coat, only exacerbates the challenge facing spores of Bacillales species when stimulated to germinate. Whereas the process by which spores are formed in response to nutrient starvation - sporulation - involves the orchestrated interplay between hundreds of distinct proteins, the process by which spores return to life - germination - is a much simpler affair, requiring a handful of receptor and channel proteins complemented with specialized peptidoglycan lysins. Despite this relative simplicity, and research effort spanning many decades, comprehensive understanding of key molecular and biochemical details and, in particular signal transduction mechanisms associated with spore germination, has remained elusive. In this review we provide an up to date overview of the field while identifying what we consider to be the key gaps in knowledge associated with germination of Bacillales spores, suggesting also technical approaches that may provide fresh insight to this unique biological process.
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Affiliation(s)
- Graham Christie
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 OAS, United Kingdom.
| | - Peter Setlow
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030-3305, USA.
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Abstract
Understanding the underlying biology of pathogens is essential to develop novel treatment options. To drive this understanding, genetic tools are essential. In recent years, the genetic toolbox available to Clostridioides difficile researchers has expanded significantly but still requires the conjugal transfer of DNA from a donor strain into C. difficile. Here we describe an electroporation-based transformation protocol that was effective at introducing existing genetic tools into different C. difficile strains. An important risk factor for acquiring Clostridioides difficile infection is antibiotic use. Therefore, a detailed knowledge of the physiology and the virulence factors can help drive the development of new diagnostic tools and nonantibiotic therapeutic agents to combat these organisms. Several genetic systems are available to study C. difficile in the laboratory environment, and all rely on stably replicating or segregationally unstable plasmids. Currently, the transfer of plasmids into C. difficile can only be performed by conjugation using Escherichia coli or Bacillus subtilis as conjugal donors. Here we report a method to introduce plasmid DNA into C. difficile using electroporation and test factors that might contribute to higher transformation efficiencies: osmolyte used to stabilize weakened cells, DNA concentration, and recovery time postelectroporation. Depending on the C. difficile strain and plasmid used, this transformation protocol achieves between 20 and 200 colonies per microgram of DNA and is mostly influenced by the recovery time postelectroporation. Based on our findings, we recommend that each strain be tested for the optimum recovery time in each lab. IMPORTANCE Understanding the underlying biology of pathogens is essential to develop novel treatment options. To drive this understanding, genetic tools are essential. In recent years, the genetic toolbox available to Clostridioides difficile researchers has expanded significantly but still requires the conjugal transfer of DNA from a donor strain into C. difficile. Here we describe an electroporation-based transformation protocol that was effective at introducing existing genetic tools into different C. difficile strains.
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