The pangenome of the genus Clostridium

• Published in: Environmental microbiology Vol. 19; no. 7; pp. 2588 - 2603
• Main Authors: Udaondo, Zulema, Duque, Estrella, Ramos, Juan‐Luis
• Format: Journal Article
• Language: English
• Published: England Wiley Subscription Services, Inc 01.07.2017
• Subjects: Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Biosynthesis; Cell walls; Chemicals; Clostridium; Clostridium - classification; Clostridium - genetics; Clostridium - metabolism; Coenzyme A; Deoxyribonucleic acid; DNA; DNA repair; Energy conservation; Enzymes; Genome, Bacterial; Genomes; Glucose metabolism; Glycerol; Kinases; Metabolic Networks and Pathways; Metabolism; Metabolites; Modules; Multilocus Sequence Typing; Network analysis; Nitrogen; Nitrogen sources; Organic nitrogen; Pathogenicity; Pathogens; Phylogeny; Protein families; Protein-Serine-Threonine Kinases - genetics; Protein-Serine-Threonine Kinases - metabolism; Proteins; Ribonuclease P; S-Adenosylmethionine; S-Adenosylmethionine - metabolism; Transcription
• ISSN: 1462-2912; 1462-2920
• DOI: 10.1111/1462-2920.13732

Summary The pangenome for the genus Clostridium sensu stricto, which was obtained using highly curated and annotated genomes from 16 species is presented; some of these cause disease, while others are used for the production of added‐value chemicals. Multilocus sequencing analysis revealed that species of this genus group into at least two clades that include non‐pathogenic and pathogenic strains, suggesting that pathogenicity is dispersed across the phylogenetic tree. The core genome of the genus includes 546 protein families, which mainly comprise those involved in protein translation and DNA repair. The GS‐GOGAT may represent the central pathway for generating organic nitrogen from inorganic nitrogen sources. Glycerol and glucose metabolism genes are well represented in the core genome together with a set of energy conservation systems. A metabolic network comprising proteins/enzymes, RNAs and metabolites, whose topological structure is a non‐random and scale‐free network with hierarchically structured modules was built. These modules shed light on the interactions between RNAs, proteins and metabolites, revealing biological features of transcription and translation, cell wall biosynthesis, C1 metabolism and N metabolism. Network analysis identified four nodes that function as hubs and bottlenecks, namely, coenzyme A, HPr kinases, S‐adenosylmethionine and the ribonuclease P‐protein, suggesting pivotal roles for them in Clostridium.