Halobacterium sp. NRC-1

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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. Halobacterium sp. NRC-1 exists in extreme high concentrations of salt and can be found all over the world. These include salt production facilities, in brine inclusions in salt crystals in salt mines, as well as natural lakes and ponds and in salt marshes. 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 was completed in 2000 helping further 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 a Gram-negative, rod shaped into a single arrangement which is significant in their ability to move and survive in the harsh environment they live in. It has a genome size of 2 Mb, consisting of 1 chromosome and 2 plasmids. (1) They have no endospores, therefore can be harmed by 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. (1)

The complete sequence of Halobacterium sp. NRC-1 harbors 2,571,010 bp (base pairs) containing 91 insertion sequences on behalf of 12 families. (1) These are organized into a fairly large chromosome and 2 related minichromosomes-- pNRC100 (200 kb) and pNRC200 (365,425 bp). (1) These two plasmids are mostly responsible for the 91 insertion sequences. The Halobacterium sp. NRC-1 genome codes for about 2,630 proteins. (1) 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 NRC-1 uses two forms for motility. These include flagellar motility and the use of gas vesicles. Its movement consists of swimming in straight lines by the rotation of their flagella. Forward and backward movement can be done and they can reorient themselves by periodic tumbling. (7) The cells move towards chemicals they want by a process called chemotaxis. They also swim towards green light and away from strong damaging blue and UV light.

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. (4)

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. Ultraviolet radiation from sunlight can ultimately damage DNA by causing thymine-thymine dimers to be formed which will result in mutations in the DNA. Thus, Halobacterium NRC-1 has learned to adapt to these harsh environments they live in by constructing very active DNA repair systems. One such commonly used is called photoreactivation. An enzyme, photolyase is known to reverse the thymine-thymine dimers which use visible light to repair the DNA damage done by UV light. They also contain large quantities of red carotenoids which have been studied to be photoprotective. (7) Halobacterium sp. NRC-1 possesses nucleotide excision repair genes uvrA, uvrB and uvrC as well as multiple DNA repair pathways which probably explains its high UV resistance. (6) 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. (6)

Halobacterium NRC-1 can obtain energy by aerobic, anaerobic, or phototrophic use of the energy of light. This is done by using multiple pathways using organic molecules in their environment. Beause many haloarchaea can grow without the use of oxygen, they use instead dissimilatory nitrate reduction and denitrification, fermentation of different sugars, breakdown of arginine and the use of light energy mediated by retinal pigments. Haloarchaea, which includes Halobacterium NRC-1, have specialized regions that contain a two-dimensional crystalline lattice of bacteriorhodopsin which show as purple membranes. The membrane potential generated by bacteriorhodopsin can be used to drive ATP synthesis and maintain phototrophic growth. Halorhodopsin also contributes to phototrophic growth because of its inwardly-directed light-driven chloride pump. (7)

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. (2) GVs in their intracellular structures are purely protein, unlike standard membranes that also contain lipids. These gas vesicles are filled with air, thus helping them to float to the surface of masses of water. They also increase the availability of light and oxygen to the cells since they are closer to the surface and closer to sunlight. Cells appear pink and opaque and float to the top when gas vesicles are present. When these gas vesicles are absent, cells appear more red and translucent and sink to the bottom. (7) 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. (2) 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, studies 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 or strain ATCC 700922. (5) This raises questions and theories on the evolutionary factors of this genome.

Ecology

Artemia fransiscana, also known as Brine shrimp, are random filter feeders because such organisms consume Halobacterium that are available in the environment close to them, in addition to green algae and diatoms. (7)

Interestingly, the pink pigmentation in flamingo birds are produced through outside sources of food they consume. Flamingos are also random filter feeders and will turn their beaks upside down and take their meals from the water they survive in. Connectively, they consume Brine shrimps as well as Halobacteria when they have the chance, which helps with the beautiful colors people love to see at zoos. Without these external sources they may need, the feathers of these birds would be gray or white depending on the types of food they eat. (7)

Application to Biotechnology

Halobacterium NRC-1 takes part in many biotechnological applications. The production of recombinant gas vesicles are used for separation, antigen presentation and vaccine development. It is also used in genetically altering plants so that they are able to have high salt tolerance for dehydration and UV protection. The development of stable enzymes is made for catalysis and the use of proteases for oriental fish and soy sauces. The bacteriorhodopsin of the membrane develops a purple membrane film which is also used for holography in bio-computer chips. Also, the extraction of carotene is used as food supplements or food coloring, as well as the use of metabolic pathways for the recycling of polluted hypersaline brines. For everyday life, lipases in these bacteria are commonly used for detergents. (7)

Current Research

There are many recent studies of Halobacterium NRC-1 that are currently being conducted to analyze further genetic involvement as well as increasing development in biotechnological activities.

Experiments are being conducted where genes are being knocked out for analysis of gene function and gene regulation. A study currently in play is the arsenic resistance gene, which has led to the discovery of a new methylase gene involved in detoxification. (8)

Mapping of the functional replication origins for the large chromosome of Halobacterium NRC-1 and extrachromosomal pNRC replicons is being conducted. Genome sequence data will further help us understand the nature of this archaeon and the behavior of its growth. Also, the development of bioinformatics tools and databases for genome annotation, comparative genomics and gene regulation globally are being studied. (8)

For transcriptome studies, a development of a custom whole genome of the oligonucleotide microarray is being conducted for transcriptome analysis. After exposure to different environmental variables , the microarray was tested. This provides extra flexibility and minimum labor for current studies in its transcriptome investigations. (8)

References

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

2. 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.

3. 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 p. 9(3):219-27. Epub 2005 Apr 21.

4. 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 p. 187(5):1659-67.

5. 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.

6. 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.

7. The HaloEd Project http://halo.umbi.umd.edu/~haloed/Patents.htm/

8. DasSarma, Shiladitya http://www.umbi.umd.edu/~dassarma/



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

Edited KMG