Halobacterium NRC-1

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Halobacterium sp. NRC-1
Scientific classification
Kingdom: Archaea Phylum: Euryarchaeota Class: Halobacteria Order: Halobacteriales Family: Halobacteriaceae Genus: Halobacterium Species: Halobacterium sp. NRC-1
Binomial name
Halobacterium sp. NRC-1

Description and significance

Halobacterium sp. NRC-1 is a halophilic archaea which thrives all over the world in high salt environments, including salt production facilities, brine inclusions in salt crystals, natural lakes and ponds, and salt marshes. Halobacterium sp. NRC-1 is motile using both flagella and gas vesicles, and respond to their environment by moving towards chemicals using a process called chemotaxis and toward or away from light using phototaxis using its sensory rhodopsins. They reproduce via binary fission and grow best in a 42 degree Celsius aerobic high salt environment.

Halobacterium sp. NRC-1 is very easy to culture in the lab, and is genetically tractable. It's genome has been completely mapped and whole-genome DNA microarrays are available to investigate gene expression. This makes it an excellent model microorganism for research into the basic cellular process and gene expression as well as for teaching.

Genome structure

The genome of Halobacterium sp. NRC-1 was published in 2000. Since that time, a combination of genetic, transcriptomic, proteomic and bioinformatic approaches have provided insights into both its extremophilic lifestyle as well as fundamental cellular processes common to all life forms.

Halobacterium sp. NRC-1 contains the smallest genome to date among the halophiles. It is 2,571,010 bp in size, and is composed of a large GC-rich chromosome (2,014,239 bp, 68 % G+C), and two smaller extrachromosomal replicons, pNRC100 (191,346 bp) and pNRC200 (365,425 bp), with 58–59 % G+C composition. The two smaller replicons contain 145,428 bp of identical DNA and 33–39 kb inverted repeats catalyzing inversion isomers, and the majority of the 91 IS elements, representing 12 families, found in the genome. As a result of the large number of repeated sequences, genome assembly required extensive genomic mapping and an ordered clone library of pNRC100. Of the 2,630 likely protein-coding genes in the genome, 2,532 are unique. Halobacterium predicted proteins were found to be highly acidic [27] and a substantial number had bacterial homologs as their closest relatives, suggesting that they might have been acquired through lateral gene transfer. In addition, 52 RNA genes were also identified; however, the 16S rRNA sequence and other unique characteristics did not allow placement within a validly described Halobacterium species, and this point has been the subject of some controversy. Interestingly, about 40 genes in pNRC100 and pNRC200 code for functions likely to be essential or important for cell viability (e.g. thioredoxin and thioredoxin reductase, a cytochrome oxidase, a DNA polymerase, multiple TATA-binding proteins (TBP) and transcription factor B (TFB) transcription factors, and the only arginyl-tRNA synthetase in the genome). As a result, these replicons were suggested to be essential "minichromosomes" rather than megaplasmids.

Cell structure and metabolism

Halobacterium species are obligately halophilic microorganisms that have adapted to optimal growth under conditions of extremely high salinity—10 times that of sea water. They contain a correspondingly high concentration of salts internally and exhibit a variety of unusual and unique molecular characteristics. This high salt concentration enables this microorganism to remain isotonic to it's preferred environment. It has been extensively studied and shown to contain some of the classic features found in halophilic archaea, for example, an S-layer glycoprotein, ether-linked lipids, and purple membrane. The purple membrane consists of the light-driven ion transporters bacteriorhodopsin and halorhodopsin, and the phototaxis receptors, sensory rhodopsins I and II. In order to survive in low oxygen environments, Halobacterium sp. NRC-1 synthesizes Bacteriorhodopsin, which is a unique protein that can use light as an energy source, much like chlorophyll can in cyanobacteria and phototrophic eukaryotes. When the retinal in in Bacteriorhodopsin absorbs light, it results in a series of conformational changes that translocates the proton into the periplasmic space. This light driven proton pumping generates a pH gradient which is then used to power the synthesis of ATP by chemiosmosis. This phototrophic capability is particularly useful to Halobacterium sp. NRC-1 as oxygen is not very soluble in concentrated salt solutions. In addition to its phototrophic respiration capabilities, is also capable of anaerobic respiration using dimethyl sulfoxide (DMSO) and trimethylamine-N-oxide (TMAO).

Halobacterium NRC-1 is an aerobic chemoorganotroph, growing on the degradation products of less halophilic organisms as the salinity reaches near saturation. In the laboratory, cells are cultured best in a complex medium. A minimal medium described for Halobacterium includes all but 5 of the 20 amino acids for growth. Several amino acids may be used as a source of energy, including arginine and aspartate, which are passed to the citric acid cycle via 2-oxoglutarate and oxaloacetate, respectively. Under aerobic conditions, arginine is presumably converted to glutamate via the arginine deiminase pathway, and this amino acid then enters the cycle via glutamate dehydrogenase. The arginine deiminase pathway is coded by the arcRACB genes, which are found on pNRC200.

Ecology

Image ISS007-E-13002 from the ISS of the Great Salt Lake showing purple tint due to halobacterium presence and increased bacteriorhodopsin production due to high salt concentration. Image courtesy of the Image Science & Analysis Laboratory, NASA Johnson Space Center.

Halobacterium sp. NRC-1 is one of many strains of halobacterium which thrive in extremely high salinity environments such as salt lakes, salt marshes and salt drying ponds. There are not many other organisms that can survive in these high salt environments, in fact one of its primary sources of food is the amino acids of other organisms which have lysed due to the high salt concentration in this environment. Brine shrimp are one few other organism that can survive the high salt concentration, and they feed almost exclusively on the bacteria in their environment.