Genome Research

Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
QUICK SEARCH:   [advanced]


     

This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Kennedy, S. P.
Right arrow Articles by DasSarma, S.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Kennedy, S. P.
Right arrow Articles by DasSarma, S.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati  
What's this?

Vol. 11, Issue 10, 1641-1650, October 2001

LETTER
Understanding the Adaptation of Halobacterium Species NRC-1 to Its Extreme Environment through Computational Analysis of Its Genome Sequence

Sean P. Kennedy,1 Wailap Victor Ng,2 Steven L. Salzberg,3 Leroy Hood,2 and Shiladitya DasSarma1,4

1 Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, Maryland 21202, USA; 2 Institute for Systems Biology, Seattle, Washington 98105, USA; 3 The Institute for Genomic Research, Rockville, Maryland 20850, USA

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.

4 Corresponding author.

11:1641-1650 ©2001 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/01 $5.00
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati    What's this?


This article has been cited by other articles:


Home page
 Mol Biol EvolHome page
S. Blanquart and N. Lartillot
A Site- and Time-Heterogeneous Model of Amino Acid Replacement
Mol. Biol. Evol., May 1, 2008; 25(5): 842 - 858.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
S. Hundt, A. Zaigler, C. Lange, J. Soppa, and G. Klug
Global Analysis of mRNA Decay in Halobacterium salinarum NRC-1 at Single-Gene Resolution Using DNA Microarrays
J. Bacteriol., October 1, 2007; 189(19): 6936 - 6944.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
L. Giaquinto, P. M. G. Curmi, K. S. Siddiqui, A. Poljak, E. DeLong, S. DasSarma, and R. Cavicchioli
Structure and Function of Cold Shock Proteins in Archaea
J. Bacteriol., August 1, 2007; 189(15): 5738 - 5748.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
F. Matsunaga, A. Glatigny, M.-H. Mucchielli-Giorgi, N. Agier, H. Delacroix, L. Marisa, P. Durosay, Y. Ishino, L. Aggerbeck, and P. Forterre
Genomewide and biochemical analyses of DNA-binding activity of Cdc6/Orc1 and Mcm proteins in Pyrococcus sp.
Nucleic Acids Res., May 11, 2007; 35(10): 3214 - 3222.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
C. Sun, M. Zhou, Y. Li, and H. Xiang
Molecular Characterization of the Minimal Replicon and the Unidirectional Theta Replication of pSCM201 in Extremely Halophilic Archaea
J. Bacteriol., December 1, 2006; 188(23): 8136 - 8144.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
A. Kaur, M. Pan, M. Meislin, M. T. Facciotti, R. El-Gewely, and N. S. Baliga
A systems view of haloarchaeal strategies to withstand stress from transition metals
Genome Res., July 1, 2006; 16(7): 841 - 854.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
J. Gross, W. K. Cho, L. Lezhneva, J. Falk, K. Krupinska, K. Shinozaki, M. Seki, R. G. Herrmann, and J. Meurer
A Plant Locus Essential for Phylloquinone (Vitamin K1) Biosynthesis Originated from a Fusion of Four Eubacterial Genes
J. Biol. Chem., June 23, 2006; 281(25): 17189 - 17196.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
R. R. Gan, E. C. Yi, Y. Chiu, H. Lee, Y.-c. P. Kao, T. H. Wu, R. Aebersold, D. R. Goodlett, and W. V. Ng
Proteome Analysis of Halobacterium sp. NRC-1 Facilitated by the Biomodule Analysis Tool BMSorter
Mol. Cell. Proteomics, June 1, 2006; 5(6): 987 - 997.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
K. L. Britton, P. J. Baker, M. Fisher, S. Ruzheinikov, D. J. Gilmour, M.-J. Bonete, J. Ferrer, C. Pire, J. Esclapez, and D. W. Rice
Analysis of protein solvent interactions in glucose dehydrogenase from the extreme halophile Haloferax mediterranei
PNAS, March 28, 2006; 103(13): 4846 - 4851.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
E. F. Mongodin, K. E. Nelson, S. Daugherty, R. T. DeBoy, J. Wister, H. Khouri, J. Weidman, D. A. Walsh, R. T. Papke, G. Sanchez Perez, et al.
The genome of Salinibacter ruber: Convergence and gene exchange among hyperhalophilic bacteria and archaea
PNAS, December 13, 2005; 102(50): 18147 - 18152.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
U. Gophna, W. F. Doolittle, and R. L. Charlebois
Weighted Genome Trees: Refinements and Applications
J. Bacteriol., February 15, 2005; 187(4): 1305 - 1316.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
N. S. Baliga, R. Bonneau, M. T. Facciotti, M. Pan, G. Glusman, E. W. Deutsch, P. Shannon, Y. Chiu, R. S. Weng, R. R. Gan, et al.
Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea
Genome Res., November 1, 2004; 14(11): 2221 - 2234.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
N. S. Baliga, S. J. Bjork, R. Bonneau, M. Pan, C. Iloanusi, M. C.H. Kottemann, L. Hood, and J. DiRuggiero
Systems Level Insights Into the Stress Response to UV Radiation in the Halophilic Archaeon Halobacterium NRC-1
Genome Res., June 1, 2004; 14(6): 1025 - 1035.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
L. Brocchieri
Environmental signatures in proteome properties
PNAS, June 1, 2004; 101(22): 8257 - 8258.
[Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
C. G. Knight, R. Kassen, H. Hebestreit, and P. B. Rainey
From The Cover: Global analysis of predicted proteomes: Functional adaptation of physical properties
PNAS, June 1, 2004; 101(22): 8390 - 8395.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
B. R. Berquist and S. DasSarma
An Archaeal Chromosomal Autonomously Replicating Sequence Element from an Extreme Halophile, Halobacterium sp. Strain NRC-1
J. Bacteriol., October 15, 2003; 185(20): 5959 - 5966.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
Y. A. Goo, E. C. Yi, N. S. Baliga, W. A. Tao, M. Pan, R. Aebersold, D. R. Goodlett, L. Hood, and W. V. Ng
Proteomic Analysis of an Extreme Halophilic Archaeon, Halobacterium sp. NRC-1
Mol. Cell. Proteomics, August 1, 2003; 2(8): 506 - 524.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
C. EVILIA, X. MING, S. DASSARMA, and Y.-M. HOU
Aminoacylation of an unusual tRNACys from an extreme halophile
RNA, July 1, 2003; 9(7): 794 - 801.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
N. F.W. Saunders, T. Thomas, P. M.G. Curmi, J. S. Mattick, E. Kuczek, R. Slade, J. Davis, P. D. Franzmann, D. Boone, K. Rusterholtz, et al.
Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii
Genome Res., July 1, 2003; 13(7): 1580 - 1588.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
A. Bolhuis
Protein transport in the halophilic archaeon Halobacterium sp. NRC-1: a major role for the twin-arginine translocation pathway?
Microbiology, November 1, 2002; 148(11): 3335 - 3346.
[Full Text] [PDF]

Home page
 ScienceHome page
J. Yu, S. Hu, J. Wang, G. K.-S. Wong, S. Li, B. Liu, Y. Deng, L. Dai, Y. Zhou, X. Zhang, et al.
A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica)
Science, April 5, 2002; 296(5565): 79 - 92.
[Abstract] [Full Text] [PDF]


Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
Genes Dev. Learn. Mem.
Protein Science RNA Genome Res.