Database Authors
Ron Caspi1, Amanda Mackie2, David S. Weiss3
1SRI International, 2Macquarie University, 3University of Iowa
Summary Clostridioides difficile R20291 is a highly virulent strain of Clostridioides difficile isolated from a 2003 - 2006 outbreak in Stoke Mandeville, UK [Stabler09]. Clostridioides difficile R20291 is a motile, PCR ribotype 027 strain [Stabler06]. When compared to Clostridioides difficile 630 (ribotype 0120), 027 strains show phenotypic differences relating to motility, antibiotic resistance and toxicity; Clostridioides difficile R20291 contains 5 unique genetic regions, including a novel phage island, a two component regulatory system and transcriptional regulators that are absent from both non-epidemic 027 strains and C. difficile 630 [Stabler09].

This Pathway/Genome Database (PGDB) was generated by the PathoLogic [Karp16, Karp11] component of Pathway Tools software version 24.0 and MetaCyc [Caspi18] version beta on 23-Apr-2020 16:54:14.

The curation of multiple enzymes involved in peptidoglycan synthesis was undertaken during 2020 with expert advice from David S. Weiss from the University of Iowa.

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
chromosome3,6103,51857354,191,339RefSeq:NC_013316.1
Ortholog data available?Yes
Database Contents
Genes3,610
Pathways210
Enzymatic Reactions1,001
Transport Reactions82
Polypeptides3,520
Protein Complexes34
Enzymes681
Transporters518
Compounds844
Transcription Units2,256
tRNAs0
Transcriptional Regulation3
Protein Features4,926
GO Terms23,902
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Clostridia
Peptostreptococcales
Peptostreptococcaceae
Clostridioides
Clostridioides difficile
Clostridioides difficile R20291
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMEA3138243
NCBI BioProjectPRJNA38039
NCBI-Taxonomy645463
Geographic LocationUnited Kingdom

References

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

Karp16: Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A, Fulcher C, Keseler IM, Caspi R (2016). "Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform 17(5);877-90. PMID: 26454094

Stabler06: Stabler RA, Gerding DN, Songer JG, Drudy D, Brazier JS, Trinh HT, Witney AA, Hinds J, Wren BW (2006). "Comparative phylogenomics of Clostridium difficile reveals clade specificity and microevolution of hypervirulent strains." J Bacteriol 188(20);7297-305. PMID: 17015669

Stabler09: Stabler RA, He M, Dawson L, Martin M, Valiente E, Corton C, Lawley TD, Sebaihia M, Quail MA, Rose G, Gerding DN, Gibert M, Popoff MR, Parkhill J, Dougan G, Wren BW (2009). "Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium." Genome Biol 10(9);R102. PMID: 19781061

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