Epigenomic characterization of Clostridioides difficile finds a conserved DNA methyltransferase that mediates sporulation and pathogenesis

AbstractClostridioides difficileis a leading cause of health care-associated infections. Although significant progress has been made in the understanding of its genome, the epigenome ofC. difficileand its functional impact has not been systematically explored. Here, we performed the first comprehensive DNA methylome analysis ofC. difficileusing 36 human isolates and observed great epigenomic diversity. We discovered an orphan DNA methyltransferase with a well-defined specificity whose corresponding gene is highly conserved across our dataset and in all ~300 globalC. difficilegenomes examined. Inactivation of the methyltransferase gene negatively impacted sporulation, a key step inC. difficiledisease transmission, consistently supported by multi-omics data, genetic experiments, and a mouse colonization model. Further experimental and transcriptomic analysis also suggested that epigenetic regulation is associated with cell length, biofilm formation, and host colonization. These findings open up a new epigenetic dimension to characterize medically relevant biological processes in this critical pathogen. This work also provides a set of methods for comparative epigenomics and integrative analysis, which we expect to be broadly applicable to bacterial epigenomics studies.

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CD25890, a conserved protein that modulates sporulation initiation in Clostridioides difficile

Scientific Reports ◽

10.1038/s41598-021-86878-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Diogo Martins ◽

Michael A. DiCandia ◽

Aristides L. Mendes ◽

Daniela Wetzel ◽

Shonna M. McBride ◽

...

Keyword(s):

Life Cycle ◽

Biofilm Formation ◽

Regulatory Protein ◽

Well Being ◽

Human Intestine ◽

Healthy Humans ◽

Clostridioides Difficile ◽

Nutritional Conditions ◽

Sporulation Initiation

AbstractBacteria 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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Molecular characterization of Clostridioides difficile ribotype 027 in a major Chinese hospital

Journal of Microbiology Immunology and Infection ◽

10.1016/j.jmii.2021.01.003 ◽

2021 ◽

Author(s):

Ren-feng Zhang ◽

Yu-xia Man ◽

Yuan-yuan Bai ◽

Chun-hong Shao ◽

Chun-mei Liu ◽

...

Keyword(s):

Molecular Characterization ◽

Ribotype 027 ◽

Clostridioides Difficile

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Identification and Characterization of the First Virulent Phages, Including a Novel Jumbo Virus, Infecting Ochrobactrum spp.

International Journal of Molecular Sciences ◽

10.3390/ijms21062096 ◽

2020 ◽

Vol 21 (6) ◽

pp. 2096

Author(s):

Przemyslaw Decewicz ◽

Piotr Golec ◽

Mateusz Szymczak ◽

Monika Radlinska ◽

Lukasz Dziewit

Keyword(s):

Dna Methyltransferase ◽

Wastewater Treatment Plants ◽

Biogas Production ◽

Genome Mining ◽

Sewage Sample ◽

Bacterial Strains ◽

Regulatory Circuits ◽

A Genome ◽

Insightful Analysis

The Ochrobactrum genus consists of an extensive repertoire of biotechnologically valuable bacterial strains but also opportunistic pathogens. In our previous study, a novel strain, Ochrobactrum sp. POC9, which enhances biogas production in wastewater treatment plants (WWTPs) was identified and thoroughly characterized. Despite an insightful analysis of that bacterium, its susceptibility to bacteriophages present in WWTPs has not been evaluated. Using raw sewage sample from WWTP and applying the enrichment method, two virulent phages, vB_OspM_OC and vB_OspP_OH, which infect the POC9 strain, were isolated. These are the first virulent phages infecting Ochrobactrum spp. identified so far. Both phages were subjected to thorough functional and genomic analyses, which allowed classification of the vB_OspM_OC virus as a novel jumbo phage, with a genome size of over 227 kb. This phage encodes DNA methyltransferase, which mimics the specificity of cell cycle regulated CcrM methylase, a component of the epigenetic regulatory circuits in Alphaproteobacteria. In this study, an analysis of the overall diversity of Ochrobactrum-specific (pro)phages retrieved from databases and extracted in silico from bacterial genomes was also performed. Complex genome mining allowed us to build similarity networks to compare 281 Ochrobactrum-specific viruses. Analyses of the obtained networks revealed a high diversity of Ochrobactrum phages and their dissimilarity to the viruses infecting other bacteria.

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Identification, purification, and characterization of Escherichia coli virus T1 DNA methyltransferase.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)48162-8 ◽

1987 ◽

Vol 262 (31) ◽

pp. 15225-15231

Author(s):

E Scherzer ◽

B Auer ◽

M Schweiger

Keyword(s):

Escherichia Coli ◽

Dna Methyltransferase ◽

Purification And Characterization

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Molecular Characterization of Pathogenicity Locus (PaLoc) and tcdC Genetic Diversity Among tcdA+B+ Clostridioides Difficile Clinical Isolates in Tehran, Iran

10.21203/rs.3.rs-56651/v1 ◽

2020 ◽

Author(s):

Mansoor Kodori ◽

Zohreh Ghalavand ◽

Abbas Yadegar ◽

Gita Eslami ◽

Masoumeh Azimirad ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Characterization ◽

Disease Severity ◽

Genetic Variants ◽

Rflp Analysis ◽

Clostridioides Difficile ◽

Pcr Rflp ◽

The Common ◽

Healthcare Associated

Abstract Background: Clostridioides difficile is the main cause of healthcare-associated diarrhea worldwide. It is proposed that certain C. difficile toxinotypes with distinct pathogenicity locus (PaLoc) variants are associated with disease severity and outcomes. Additionally, few studies have described the common C. difficile toxinotypes, and also little is known about the tcdC variants in Iranian isolates. We characterized the toxinotypes and the tcdC genotypes from a collection of Iranian clinical C. difficile tcdA+B+ isolates with known ribotypes (RTs).Methods: Fifty C. difficile isolates with known RTs and carrying the tcdA and tcdB toxin genes were analyzed. Toxinotyping was carried out based on a PCR-RFLP analysis of a 19.6 kb region encompassing the PaLoc. Genetic diversity of the tcdC gene was determined by the sequencing of the gene.Results: Of the 50 C. difficile isolates investigated, five distinct toxinotypes were recognized. Toxinotypes 0 (33/50, 66%) and V (11/50, 22%) were the most frequently found. C. difficile isolates of the toxinotype 0 mostly belonged to RT 001 (12/33, 36.4%), whereas toxinotype V consisted of RT 126 (9/11, 81.8%). The tcdC sequencing showed six variants (35/50, 70%); tcdC-sc3 (24%), tcdC-A (22%), tcdC-sc9 (18%), tcdC-B (2%), tcdC-sc14 (2%), and tcdC-sc15 (2%). The remaining isolates were wild-types (15/50, 30%) in the tcdC gene.Conclusions: The present study demonstrates that the majority of clinical tcdA+B+ isolates of C. difficile frequently harbor tcdC genetic variants. We also found that the RT 001/ toxinotype 0 and the RT 126/ toxinotype V are the most common types among Iranian isolates. Further studies are needed to investigate the putative association of various tcdC genotypes with CDI severity and its recurrence.

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