Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1

Nitin S. Baliga, Sarah J. Bjork, Richard Bonneau, Min Pan, Chika Iloanusi, Molly C H Kottemann, Leroy Hood, Jocelyne DiRuggiero

Research output: Contribution to journalArticle

Abstract

We report a remarkably high UV-radiation resistance in the extremely halophilic archaeon Halobacterium NRC-I withstanding up to 110 J/m2 with no loss of viability. Gene knockout analysis in two putative photolyase-like genes (phr1 and phr2) implicated only phr2 in photoreactivation. The UV-response was further characterized by analyzing simultaneously, along with gene function and protein interactions inferred through comparative genomics approaches, mRNA changes for all 2400 genes during light and dark repair. In addition to photoreactivation, three other putative repair mechanisms were identified including d(CTAG) methylation-directed mismatch repair, four oxidative damage repair enzymes, and two proteases for eliminating damaged proteins. Moreover, a UV-induced down-regulation of many important metabolic functions was observed during light repair and seems to be a phenomenon shared by all three domains of life. The systems analysis has facilitated the assignment of putative functions to 26 of 33 key proteins in the UV response through sequence-based methods and/or similarities of their predicted three-dimensional structures to known structures in the PDB. Finally, the systems analysis has raised, through the integration of experimentally determined and computationally inferred data, many experimentally testable hypotheses that describe the metabolic and regulatory networks of Halobacterium NRC-I.

Original languageEnglish (US)
Pages (from-to)1025-1035
Number of pages11
JournalGenome Research
Volume14
Issue number6
DOIs
StatePublished - Jun 2004

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Halobacterium
Archaea
Radiation
Systems Analysis
Deoxyribodipyrimidine Photo-Lyase
Light
Gene Knockout Techniques
Proteins
DNA Mismatch Repair
Genomics
Metabolic Networks and Pathways
Methylation
Genes
Peptide Hydrolases
Down-Regulation
Messenger RNA
Enzymes

ASJC Scopus subject areas

  • Genetics

Cite this

Baliga, N. S., Bjork, S. J., Bonneau, R., Pan, M., Iloanusi, C., Kottemann, M. C. H., ... DiRuggiero, J. (2004). Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. Genome Research, 14(6), 1025-1035. https://doi.org/10.1101/gr.1993504

Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. / Baliga, Nitin S.; Bjork, Sarah J.; Bonneau, Richard; Pan, Min; Iloanusi, Chika; Kottemann, Molly C H; Hood, Leroy; DiRuggiero, Jocelyne.

In: Genome Research, Vol. 14, No. 6, 06.2004, p. 1025-1035.

Research output: Contribution to journalArticle

Baliga, NS, Bjork, SJ, Bonneau, R, Pan, M, Iloanusi, C, Kottemann, MCH, Hood, L & DiRuggiero, J 2004, 'Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1', Genome Research, vol. 14, no. 6, pp. 1025-1035. https://doi.org/10.1101/gr.1993504
Baliga, Nitin S. ; Bjork, Sarah J. ; Bonneau, Richard ; Pan, Min ; Iloanusi, Chika ; Kottemann, Molly C H ; Hood, Leroy ; DiRuggiero, Jocelyne. / Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. In: Genome Research. 2004 ; Vol. 14, No. 6. pp. 1025-1035.
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