Difference between revisions of "Halobacterium sp. NRC-1"

From MicrobeWiki, the student-edited microbiology resource
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==References==
 
==References==
[Sample reference] [http://ijs.sgmjournals.org/cgi/reprint/50/2/489 Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "''Palaeococcus ferrophilus'' gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". ''International Journal of Systematic and Evolutionary Microbiology''. 2000. Volume 50. p. 489-500.]
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[http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi?view=1 McCready, S., Marcello, L. "''Repair of UV damage in Halobacterium salinarum.''" ''Biochem Soc Trans'' 2003 June. p. 31(Pt 3):694-8.]
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[http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi?view=1 Shukla, HD., DasSarma, S. "Complexity of gas vesicle biogenesis in Halobacterium sp. strain NRC-1: identification of five new proteins." ''J Bacteriol''. 2004 May. p. 186(10):3182-6.]
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[http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi?view=1 Kottemann, M., Kish, A., Iloanusi, C., Bjork, S., DiRuggiero, J. "''Physiological responses of the halophilic archaeon Halobacterium sp. strain NRC1 to desiccation and gamma irradiation.''" ''Extremophiles''. 2005 Jun;9(3):219-27. Epub 2005 Apr 21.]
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[http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi?view=1 Muller, JA., DasSarma, S. "''Genomic analysis of anaerobic respiration in the archaeon Halobacterium sp. strain NRC-1: dimethyl sulfoxide and trimethylamine N-oxide as terminal electron acceptors.''" ''J Bacteriol''. 2005 Mar;187(5):1659-67.]
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[http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi?view=1 Gruber, C., Legat, A., Pfaffenhuemer, M., Radax, C., Weidler, G., Busse, HJ., Stan-Lotter, H. "''Halobacterium noricense sp. nov., an archaeal isolate from a bore core of an alpine Permian salt deposit, classification of Halobacterium sp. NRC-1 as a strain of H. salinarum and emended description of H. salinarum.''" ''Extremophiles''. 2004 Dec. p. 8(6):431-9. ''Epub''. 2004 Jul 30.]
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[http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi?view=1 Crowley, DJ., Boubriak, I., Berquist, BR., Clark, M., Richard, E., Sullivan, L., Dassarma, S., McCready, S. "''The uvrA, uvrB and uvrC genes are required for repair of ultraviolet light induced DNA photoproducts in Halobacterium sp. NRC-1.''" ''Saline Systems''. 2006 Sep. p. 13;2:11.]  
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Edited by Sung-Hee Hong, a student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano
 
Edited by Sung-Hee Hong, a student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano

Revision as of 11:04, 2 May 2007

A Microbial Biorealm page on the genus Halobacterium sp. NRC-1

Classification

Higher order taxa

Archaea; Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Halobacterium; Halobacterium sp. NRC-1

Species

Halobacterium, salinarum


NCBI: Taxonomy

Description and significance

Halobacterium sp. NRC-1 is an exceptionally halophilic archaeon that has given us much insight on elemental cellular processes common to all life forms because of its extreme lifestyle. Because Halobacterium sp. NRC-1 can be easily cultured and is genetically well-behaved, studies of genetic, transcriptomic, proteomic and bioinformatics as well as archaea in general have been helpful during its research in laboratories. Its genome sequence has also been completed in the year of 2000 helping to give research on DNA replication and repair systems, phototrophic, anaerobic, as well as lateral gene transfer over time.

Genome structure

Halobacterium sp. NRC-1 or strain ATCC 700922 is adapted to grow under extreme high salinity conditions. This mesophilic microbe is depicted as a Gram negative, rod shaped into a single arrangement. It has a size of 2 Mb, consisting of 1 chromosome and 2 plasmids. They have no endospores, therefore prone to ultraviolet and gamma rays, temperature and starvation. Its motility consists of tufts of polar flagella and intracellular gas vesicles that are used for buoyancy. Its optimal growth temperature is known to be 42ºC, with NaCl optimum of 4.3 M.

The complete sequence of Halobacterium sp. NRC-1 harbors 2,571,010 bp (base pairs) containing 91 insertion sequences on behalf of 12 families. These are organized into a fairly large chromosome and 2 related minichromosomes-- pNRC100 (200 kb) and pNRC200 (365,425 bp). These two plasmids are mostly responsible for the 91 insertion sequences. The Halobacterium sp. NRC-1 genome codes for about 2,630 proteins. Studies of the genome sequence depict pathways for uptake and use of amino acids, active sodium-proton antiporter and potassium uptake systems, as well as photosensory and signal transduction pathways and DNA replication, transcription/translation systems.

Cell structure and metabolism

Halobacterium sp. NRC-1 is found to grow on either dimethyl sulfoxide (DMSO) or trimethylamine N-oxide (TMAO), which act as the sole terminal electron acceptor. Its doubling time is said to be 1 day. By reverse transcriptase PCR analysis and bioinformatics, an operon, dmsREABCD, which encodes DmsR a regulatory protein, DmsEABC, a part of the DMSO reductase family and a molecular chaperone DmsD were discovered. Further analysis showed that DmsR, DmsA and DmsD are required for anaerobic respiration on DMSO and TMAO for the growth of Halobacterium sp. NRC-1.

Because of its tolerance to high levels of solar radiation in its hypersaline environment, results show that homologous recombination plays a key role in cellular response of Halobacterium sp. NRC-1 to UV damage and repair. NRC-1 has had many studies conducted for its adaptation to extreme conditions. Halobacterium sp. NRC-1 possesses nucleotide excision repair genes uvrA, uvrB and uvrC as well as multiple DNA repair pathways which probably explains for its high UV resistance. Further studies explain that these three nucleotide excision repair genes are required for the removal of UV damage in Halobacterium sp. NRC-1. High salt environments were also found to protect the cells and DNA against gamma irradiation. Thus, the hypersaline environment in which Halobacterium sp. NRC-1 can survive is a crucial factor for its resistance to desiccation, damaging radiation and high vacuum. All these may be due to efficient damage tolerance mechanisms such as recombinational lesion bypass, bypass DNA polymerases and the existence of multiple genomes in Halobacterium.

Halobacterium sp. NRC-1 shows that it has two replication origins, oriC1 and oriC2.

The genome of Halobacterium sp. NRC-1 contains a large gene cluster—gvpMLKJIHGFEDACNO, which is necessary for the production of buoyant gas-filled vesicles (GVs) for the cell. The presence of five new gas vesicle proteins, GvpF, GvpG, GvpJ, GvpL and GvpM, were discovered recently which brings the total number of proteins to seven. GvpJ and GvpM were found to be similar to the old GvpA protein. GvpF and GvpL proteins were found to contain coiled-coil domains. Cloning of the major GV protein has led to the discovery of pNRC100, which is important for GV synthesis. By using pulsed-field gel electrophoresis showed a large inverted repeat (IR) sequence in the pNRC100. By Southern hybridization analysis using two restriction enzymes AFlII and SfiI, the inversion isomers of pNRC100 were demonstrated. This was done by cutting asymmetrically in between the single-copy region of AfiII region and the large single-copy region of SfiI, but not within the large IRs. By doing so, no inversion isomers were detected, which concluded that both copies were required for inversion to occur.

An interesting study from a salt mine in Austria, shows two rod-shaped haloarchaeal strains, A1 and A2 that were isolated. The evidence of the salt is predicted to have been grown during the Permian period—about 225 to 280 million years ago. Surprisingly, the 16S rDNA sequences of the two strains were 97.1% similar to Halobacterium sp. NRC-1. This raises questions and theories on the evolutionary factors of this genome.

Ecology

Describe any interactions with other organisms (included eukaryotes), contributions to the environment, effect on environment, etc.

Pathology

How does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.

Application to Biotechnology

Does this organism produce any useful compounds or enzymes? What are they and how are they used?

Current Research

Enter summaries of the most recent research here--at least three required

References

McCready, S., Marcello, L. "Repair of UV damage in Halobacterium salinarum." Biochem Soc Trans 2003 June. p. 31(Pt 3):694-8.

Shukla, HD., DasSarma, S. "Complexity of gas vesicle biogenesis in Halobacterium sp. strain NRC-1: identification of five new proteins." J Bacteriol. 2004 May. p. 186(10):3182-6.

Kottemann, M., Kish, A., Iloanusi, C., Bjork, S., DiRuggiero, J. "Physiological responses of the halophilic archaeon Halobacterium sp. strain NRC1 to desiccation and gamma irradiation." Extremophiles. 2005 Jun;9(3):219-27. Epub 2005 Apr 21.

Muller, JA., DasSarma, S. "Genomic analysis of anaerobic respiration in the archaeon Halobacterium sp. strain NRC-1: dimethyl sulfoxide and trimethylamine N-oxide as terminal electron acceptors." J Bacteriol. 2005 Mar;187(5):1659-67.

Gruber, C., Legat, A., Pfaffenhuemer, M., Radax, C., Weidler, G., Busse, HJ., Stan-Lotter, H. "Halobacterium noricense sp. nov., an archaeal isolate from a bore core of an alpine Permian salt deposit, classification of Halobacterium sp. NRC-1 as a strain of H. salinarum and emended description of H. salinarum." Extremophiles. 2004 Dec. p. 8(6):431-9. Epub. 2004 Jul 30.

Crowley, DJ., Boubriak, I., Berquist, BR., Clark, M., Richard, E., Sullivan, L., Dassarma, S., McCready, S. "The uvrA, uvrB and uvrC genes are required for repair of ultraviolet light induced DNA photoproducts in Halobacterium sp. NRC-1." Saline Systems. 2006 Sep. p. 13;2:11.




Edited by Sung-Hee Hong, a student of Rachel Larsen and Kit Pogliano