Halobacterium salinarum R1

Aerobic halophilic chemoorganotroph growing on the degradation products of less halophilic organisms as the salinity reaches near saturation. Halobacterium species have adapted to optimal growth under conditions of extremely high salinity (10 times that of sea water).Halobacterium salinarum (strain ATCC 29341 / DSM 671 / R1) has 1 chromosome and 4 megaplasmids. The chromosome has a very high GC content of 68 % whereas the plasmids have a lower GC content of 58.8 %. The genome contains 2878 protein-coding genes, 68 % of which have been identified by proteomics. The chromosome contains a 60-kb insertion with plasmid-like characteristics such a reduced GC content of 56% and a reduced proteomic protein identification rate. The plasmid pHS3 codes for a number of essential proteins most of them in, or adjacent to, a 67-kb region with chromosome-like features. Thus, it may be considered a second chromosome rather than a plasmid. The three other plasmids pHS1, pHS2 and pHS4 are related to each other through their large-scale duplications. The chromosome of strain R1 is completely collinear and virtually identical to that of strain NRC-1. Besides differences due to insertion elements, there are only 12 other differences: four point mutations, five frameshifts and three insertion/deletion events. Between strain R1 and strain NRC-1 it is possible to match more than 350 kb of plasmid sequence that are virtually identical at the DNA sequence level. This is contrasted sharply by a highly different overall plasmid architecture: the number of plasmids is different, the patterns of the large-scale duplications are highly dissimilar in the two strains, the regions of colinearity are short and all colinearity breakpoints are associated with insertion elements. These differences in plasmid architecture may reflect biological variations among the strains. Alternatively, the excessive duplication may have resulted in sequence assembly errors. Despite the near identity of the DNA sequences of strains R1 and NRC-1, major differences in the protein-coding set have been found. There are 111 CDS that have not been annotated for strain NRC-1. A total of 2375 CDS map to each other in the two strains, among which 475 differ, mainly because of alternative start codon selection. This illustrates the difficulty of a correct ORF prediction in GC-rich genomes.Based on several lines of evidence, it appears that strains R1 and NRC-1 do not represent independent strains but very probably originate from the same cultivation event of a natural isolate. In this view, the differences between the two strains originate from evolution in the laboratory. (HAMAP: HALS3)