Genomic survey of sequence features for ultraviolet tolerance in haloarchaea (family Halobacteriaceae)

Peng Zhou; Ji Wen; Aharon Oren; Ming Chen; Min Wu

doi:10.1016/j.ygeno.2007.03.015

Genomic survey of sequence features for ultraviolet tolerance in haloarchaea (family Halobacteriaceae)

Peng Zhou, Ji Wen, Aharon Oren, Ming Chen, Min Wu^*

^*Corresponding author for this work

Department of Plant and Environmental Sciences (Natural Sciences)

Research output: Contribution to journal › Article › peer-review

8 Scopus citations

Abstract

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.

Original language	English
Pages (from-to)	103-109
Number of pages	7
Journal	Genomics
Volume	90
Issue number	1
DOIs	https://doi.org/10.1016/j.ygeno.2007.03.015
State	Published - Jul 2007

Bibliographical note

Funding 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.

Keywords

Amino acid composition
CTAG pattern
Dipyrimidine composition
Genomic structure
Halobacterium
UV tolerance

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10.1016/j.ygeno.2007.03.015

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title = "Genomic survey of sequence features for ultraviolet tolerance in haloarchaea (family Halobacteriaceae)",

abstract = "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.",

keywords = "Amino acid composition, CTAG pattern, Dipyrimidine composition, Genomic structure, Halobacterium, UV tolerance",

author = "Peng Zhou and Ji Wen and Aharon Oren and Ming Chen and Min Wu",

note = "Funding 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. ",

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AU - Zhou, Peng

AU - Wen, Ji

AU - Oren, Aharon

AU - Chen, Ming

AU - Wu, Min

N1 - Funding 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.

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N2 - 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.

AB - 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.

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KW - Genomic structure

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Genomic survey of sequence features for ultraviolet tolerance in haloarchaea (family Halobacteriaceae)

Abstract

Bibliographical note

Keywords

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