Understanding the adaptation of Halobacterium species NRC-1 to its extremeenvironment through computational analysis of its genome sequence

The genome of the halophilic archaeon Halobacterium sp. NRC-I and predicted proteome have been analyzed by computational methods and reveal characteri stics relevant to life in an extreme environment distinguished by hypersali nity and high solar radiation: (1) The proteome is highly acidic, with a me dian pi of 4.9 and mostly lacking basic proteins. This characteristic corre lates with high surface negative charge, determined through homology modeli ng, as the major adaptive mechanism of halophilic proteins to function in n early saturating salinity. (2) Codon usage displays the expected GC bias in the wobble position and is consistent with a highly acidic proteome. (3) D istinct genomic domains of NRC-I with bacterial character are apparent by w hole proteome BL-AST analysis, including two gene clusters coding for a bac terial-type aerobic respiratory chain. This result indicates that the capac ity of halophiles for aerobic respiration may have been acquired through la teral gene transfer. (4) Two regions of the large chromosome were found wit h relatively lower GC composition and overrepresentation of IS elements, si milar to the minichromosomes. These IS-element-rich regions of the genome m ay serve to exchange DNA between the three replicons and promote genome evo lution. (5) GC-skew analysis showed evidence for the existence of two repli cation origins in the large chromosome. This finding and the occurrence of multiple chromosomes indicate a dynamic genome organization with eukaryotic character.