title: Complete genome sequence of the anaerobic, protein-degrading hyperthermophilic crenarchaeon Desulfurococcus kamchatkensis.
abstract: Desulfurococcus kamchatkensis is an anaerobic organotrophic hyperthermophilic crenarchaeon isolated from a terrestrial hot spring. Its genome consists of a single circular chromosome of 1,365,223 bp with no extrachromosomal elements. A total of 1,474 protein-encoding genes were annotated, among which 205 are exclusive for D. kamchatkensis. The search for a replication origin site revealed a single region coinciding with a global extreme of the nucleotide composition disparity curve and containing a set of crenarchaeon-type origin recognition boxes. Unlike in most archaea, two genes encoding homologs of the eukaryotic initiator proteins Orc1 and Cdc6 are located distantly from this site. A number of mobile elements are present in the genome, including seven transposons representing IS607 and IS200/IS605 families and multiple copies of miniature inverted repeat transposable elements. Two large clusters of regularly interspaced repeats are present; none of the spacer sequences matches known archaeal extrachromosomal elements, except one spacer matches the sequence of a resident gene of D. kamchatkensis. Many of the predicted metabolic enzymes are associated with the fermentation of peptides and sugars, including more than 30 peptidases with diverse specificities, a number of polysaccharide degradation enzymes, and many transporters. Consistently, the genome encodes both enzymes of the modified Embden-Meyerhof pathway of glucose oxidation and a set of enzymes needed for gluconeogenesis. The genome structure and content reflect the organism's nutritionally diverse, competitive natural environment, which is periodically invaded by viruses and other mobile elements.
authors.affiliation: Centre "Bioengineering," Russian Academy of Sciences, Moscow, Russia.
authors.forename: Nikolai V
authors.initials: NV
authors.lastname: Ravin
authors.forename: Andrey V
authors.initials: AV
authors.lastname: Mardanov
authors.forename: Alexey V
authors.initials: AV
authors.lastname: Beletsky
authors.forename: Ilya V
authors.initials: IV
authors.lastname: Kublanov
authors.forename: Tatiana V
authors.initials: TV
authors.lastname: Kolganova
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Lebedinsky
authors.forename: Nikolai A
authors.initials: NA
authors.lastname: Chernyh
authors.forename: Elizaveta A
authors.initials: EA
authors.lastname: Bonch-Osmolovskaya
authors.forename: Konstantin G
authors.initials: KG
authors.lastname: Skryabin
mesh_terms: D000596:Amino Acids / Q000378:metabolism; D000693:Anaerobiosis; D019843:Archaeal Proteins / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D004251:DNA Transposable Elements; D019620:Desulfurococcaceae / Q000145:classification / Q000201:enzymology* / Q000235:genetics* / Q000302:isolation & purification; D016680:Genome, Bacterial; D006026:Glycoside Hydrolases / Q000235:genetics / Q000378:metabolism*; D045482:Hot Springs / Q000382:microbiology; D006358:Hot Temperature; D008969:Molecular Sequence Data; D009005:Monosaccharides / Q000378:metabolism; D010447:Peptide Hydrolases / Q000235:genetics / Q000378:metabolism*; D010802:Phylogeny; D020161:Physical Chromosome Mapping; D018741:Replication Origin
chemical_list: D000596:Amino Acids; D019843:Archaeal Proteins; D004251:DNA Transposable Elements; D009005:Monosaccharides; D006026:Glycoside Hydrolases; D010447:Peptide Hydrolases