title: Comparative genomics of DNA fragments from six Antarctic marine planktonic bacteria.
abstract: Six environmental fosmid clones from Antarctic coastal water bacterioplankton were completely sequenced. The genome fragments harbored small-subunit rRNA genes that were between 85 and 91% similar to those of their nearest cultivated relatives. The six fragments span four phyla, including the Gemmatimonadetes, Proteobacteria (alpha and gamma), Bacteroidetes, and high-G+C gram-positive bacteria. Gene-finding and annotation analyses identified 244 total open reading frames. Amino acid comparisons of 123 and 113 Antarctic bacterial amino acid sequences to mesophilic homologs from G+C-specific and SwissProt/UniProt databases, respectively, revealed widespread adaptation to the cold. The most significant changes in these Antarctic bacterial protein sequences included a reduction in salt-bridge-forming residues such as arginine, glutamic acid, and aspartic acid, reduced proline contents, and a reduction in stabilizing hydrophobic clusters. Stretches of disordered amino acids were significantly longer in the Antarctic sequences than in the mesophilic sequences. These characteristics were not specific to any one phylum, COG role category, or G+C content and imply that underlying genotypic and biochemical adaptations to the cold are inherent to life in the permanently subzero Antarctic waters.
authors.affiliation: Desert Research Institute, 2215 Raggio Parkway, Reno, NV 89512, USA.
authors.forename: Joseph J
authors.initials: JJ
authors.lastname: Grzymski
authors.forename: Brandon J
authors.initials: BJ
authors.lastname: Carter
authors.forename: Edward F
authors.initials: EF
authors.lastname: DeLong
authors.forename: Robert A
authors.initials: RA
authors.lastname: Feldman
authors.forename: Amir
authors.initials: A
authors.lastname: Ghadiri
authors.forename: Alison E
authors.initials: AE
authors.lastname: Murray
mesh_terms: D000064:Acclimatization; D000596:Amino Acids / Q000378:metabolism; D000864:Antarctic Regions; D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics; D001482:Base Composition; D003081:Cold Climate; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics* / Q000302:isolation & purification; D005798:Genes, Bacterial; D015698:Genomic Library; D023281:Genomics; D008386:Marine Biology; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D010933:Plankton / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D012623:Seawater / Q000382:microbiology
chemical_list: D000596:Amino Acids; D001426:Bacterial Proteins; D004269:DNA, Bacterial