Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence.
By Sean Kennedy, W. Ng, Steven L. Salzberg, Leroy Hood, S. DasSarma. Genome Research, 2001
338 citations recorded by the source corpus.
The genome of the halophilic archaeon Halobacterium sp. NRC-1 and predicted proteome have been analyzed by computational methods and reveal characteristics relevant to life in an extreme environment distinguished by hypersalinity and high solar radiation: (1) The proteome is highly acidic, with a median pI of 4.9 and mostly lacking basic proteins. This characteristic correlates with high surface negative charge, determined through homology modeling, as the major adaptive mechanism of halophilic proteins to function in nearly saturating salinity. (2) Codon usage displays the expected GC bias in the wobble position and is consistent with a highly acidic proteome. (3) Distinct genomic domains of NRC-1 with bacterial character are apparent by whole proteome BLAST analysis, including two gene clusters coding for a bacterial-type aerobic respiratory chain. This result indicates that the capacity of halophiles for aerobic respiration may have been acquired through lateral gene transfer. (4) Two regions of the large chromosome were found with relatively lower GC composition and overrepresentation of IS elements, similar to the minichromosomes. These IS-element-rich regions of the genome may serve to exchange DNA between the three replicons and promote genome evolution. (5) GC-skew analysis showed evidence for the existence of two replication origins in the large chromosome. This finding and the occurrence of multiple chromosomes indicate a dynamic genome organization with eukaryotic character.
Subfields: Ecology, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/6cc2e47ce76cbbb6528adebdd5821e68cbdf5e1e
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Citations in the corpus
- Microbial life at high salt concentrations: phylogenetic and metabolic diversity (2008, background): “Ng WV, Kennedy SP, Mahairas GG, Berquist B, Pan M, Shukla HD, Lasky SR, Baliga NS, Thorsson V, Sbrogna J, Swartzell S, Weir D, Hall J, Dahl TA, Welti R, Goo YA, Leithausen B, Keller K, Cruz R, Danson MJ, Hough DW, Maddocks DG, Jablonski PE, Krebs MP, Angevine GM, Dale H, Isenbarger TA, Peck RF, Pohl”
- Molecular aspects of bacterial pH sensing and homeostasis (2011, neutral): “Conversely, the surface-exposed proteins of alkaliphiles such as Bacillus pseudofirmus OF4 generally have low p I values relative to those of neutralophiles, potentially contributing to proton capture and surface retention under the proton-scarce conditions of high p”