title: Genome-directed analysis of prophage excision, host defence systems, and central fermentative metabolism in Clostridium pasteurianum.
abstract: Clostridium pasteurianum is emerging as a prospective host for the production of biofuels and chemicals, and has recently been shown to directly consume electric current. Despite this growing biotechnological appeal, the organism's genetics and central metabolism remain poorly understood. Here we present a concurrent genome sequence for the C. pasteurianum type strain and provide extensive genomic analysis of the organism's defence mechanisms and central fermentative metabolism. Next generation genome sequencing produced reads corresponding to spontaneous excision of a novel phage, designated φ6013, which could be induced using mitomycin C and detected using PCR and transmission electron microscopy. Methylome analysis of sequencing reads provided a near-complete glimpse into the organism's restriction-modification systems. We also unveiled the chief C. pasteurianum Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) locus, which was found to exemplify a Type I-B system. Finally, we show that C. pasteurianum possesses a highly complex fermentative metabolism whereby the metabolic pathways enlisted by the cell is governed by the degree of reductance of the substrate. Four distinct fermentation profiles, ranging from exclusively acidogenic to predominantly alcohologenic, were observed through redox consideration of the substrate. A detailed discussion of the organism's central metabolism within the context of metabolic engineering is provided.
authors.affiliation: Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Pyne
authors.affiliation: Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada.
authors.forename: Xuejia
authors.initials: X
authors.lastname: Liu
authors.affiliation: Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada.
authors.forename: Murray
authors.initials: M
authors.lastname: Moo-Young
authors.affiliation: Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada.|Department of Pathology and Molecular Medicine, McMaster University, Ontario, Canada.|Algaeneers Inc. and Neemo Inc., Hamilton, Ontario, Canada.
authors.forename: Duane A
authors.initials: DA
authors.lastname: Chung
authors.affiliation: Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada.
authors.forename: C Perry
authors.initials: CP
authors.lastname: Chou
mesh_terms: D003013:Clostridium / Q000187:drug effects / Q000235:genetics / Q000378:metabolism* / Q000821:virology*; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D015280:DNA Restriction-Modification Enzymes; D005285:Fermentation; D059014:High-Throughput Nucleotide Sequencing; D007218:Industrial Microbiology; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D046529:Microscopy, Electron, Transmission; D016685:Mitomycin / Q000378:metabolism; D016133:Polymerase Chain Reaction; D039002:Prophages / Q000235:genetics / Q000502:physiology; D017422:Sequence Analysis, DNA; D014771:Virion / Q000648:ultrastructure; D014775:Virus Activation; D000073336:Whole Genome Sequencing
chemical_list: D015280:DNA Restriction-Modification Enzymes; D016685:Mitomycin