Article

Complete genome sequence of the anaerobic, protein-degrading hyperthermophilic crenarchaeon Desulfurococcus kamchatkensis.

Centre "Bioengineering," Russian Academy of Sciences, Moscow, Russia.
Journal of bacteriology (impact factor: 3.94). 01/2009; 191(7):2371-9. DOI:10.1128/JB.01525-08
Source: PubMed

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.

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Keywords

1,474 protein-encoding genes
 
30 peptidases
 
anaerobic organotrophic hyperthermophilic crenarchaeon
 
competitive natural environment
 
crenarchaeon-type origin recognition boxes
 
D. kamchatkensis
 
Desulfurococcus kamchatkensis
 
eukaryotic initiator proteins Orc1
 
genome structure
 
glucose oxidation
 
modified Embden-Meyerhof pathway
 
multiple copies
 
nucleotide composition disparity curve
 
organism's nutritionally diverse
 
polysaccharide degradation enzymes
 
predicted metabolic enzymes
 
replication origin site
 
single region coinciding
 
spacer sequences matches
 
terrestrial hot spring