We have investigated the strategy of Halobacterium sp. NRC-1 and other members of the family Halobacteriaceae to survive ultraviolet (UV) irradiation, based on an integrated analysis of various genomic and proteomic features such as dinucleotide composition and distribution of tetranucleotides in the genome and amino acid composition of the proteins. The low dipyrimidine content may help Halobacterium reduce formation of photoproducts in its genome. The usage of residues susceptible to reactive oxygen species attack is reduced significantly in Halobacterium, which helps the organism to minimize protein damage. We then correlated the expression of the zim gene with the genomic structure to reexamine the importance of the putative mismatch repair pathway proposed previously. Our results showed that Halobacterium sp. NRC-1 and other haloarchaea (Haloarcula marismortui, Haloquadratum walsbyi) have optimized their genomic and proteomic structures to reduce damage induced by UV irradiation, often present at high levels in habitats where these organisms thrive.
Bibliographical noteFunding Information:
This work was supported by the National Basic Research Program of China (973 Program, Grant No. 2004CB719604-3) and in part by the National Science Foundation of China (Grant No. 30670048, No. 30370029, No. 30500106). We are grateful to Nitin S. Baliga (Institute for Systems Biology, Seattle, WA, USA), and Wailap Victor Ng (Notional YangMing University, Taipei, China) for suggestions in collecting data.
- Amino acid composition
- CTAG pattern
- Dipyrimidine composition
- Genomic structure
- UV tolerance