Halobacterium 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. Prior to 1990 H. NRC-1 was classified as an archeabacterium under the prokaryote kingdom in the two-empire system which consisted of eukaryotes and prokaryotes. Since 1990 the prokaryotes were split into bacteria and archaea due to their different evolutionary paths and biochemical differences. Like all archaea H. NRC-1 has no nucleus or organelles within the cell, and like other archaea, have evolved many metabolic pathways to allow it to survive in extreme environments. ''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 its genome has been completely mapped. 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 scientists have used a combination of genetic, transcriptomic, proteomic and bioinformatic approaches to gain insights into both its extremophilic lifestyle as well as the fundamental cellular processes common to all life forms. In order to survive in its extreme environment H. NRC-1 has developed extensive capabilites to repair its own genome. In combination with its saline environment which provides some protection from UV radiation, its ability to repair its chromosomes after extensive damage is only exceeded by the extremely radiation resistant Deinococcus radiodurans.

While much of the published literature on this organism refers to these smaller genetic elements as replicons or megaplasmids,they don't really fit the definition of these terms. Replicons are considered to be exact copies of specific sequences of an original DNA or RNA genome, or even a whole copy of the original genome. Plasmids are referred to as being small extra chromosomal DNA elements that carry relatively few genes that code for genetic information that is not essential to an organism's biological processes. Considering that the genetic information carried on these replicons not only code for information that is essential to the organism's survival, but also contain nucleotide sequences that are not identical to that of it's larger chromosome, scientists are beginning to refer to them as "minichromosomes" rather than "megaplasmids".
 * 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 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).

Cell structure and metabolism
''Halobacterium sp. NRC-1'' is an obligate halophilic microorganism which has adapted to be able to grow in conditions of extremely high salinity, up to 10 times that of seawater. In order to survive under these conditions it maintains a very high concentration of salts internally in the form of KCl to enable it to remain isotonic to it's preferred environment. Halorhodopsin plays a very energy efficient role in helping to maintain the osmotic balance within the cell by acting as a light driven pump to transport chloride ions into the cell. This microorganism 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
''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. Their optimal temperature for reproduction is 42&deg;C. Often these highly saline bodies of water will be tinted red or purple. It is the red/purple color of the bacteriorhodopsins that give the red color you often see in these highly saline environments. Bacteriorhodopsin consists of a photosensitive protein pigment called retinal. This protein pigment is responsible for NRC-1's colorful properties. The more saline the environment the redder the color will be because halobacterium increase their production of bacteriorhodopsin in response to drops in oxygen which is less soluable in saline solutions. 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 of a few other organisms that can survive the high salt concentration, and they feed almost exclusively on the bacteria in their environment. Interestingly, the flamingo, whose pink color comes exclusively from its diet (it doesn't have the ability to make the carotinoids which give the pink color) feeds on the brine shrimp, so the carotinoids which give the flamingo its pink color actually come from the rhodopsins in the halobacterium that the shrimp eat and whatever carotinoids that the shrimp produce naturally.

Application to Biotechnology
Halobacterium NRC-1 can easily be analyzed just by placing it in a hypotonic solution. Due to the higher salt concentration within the microorganism in comparison to it's less salinic environment, water will flow into the cell following it's concentration gradient, causing the cell to swell and and undergo lysis. This explosion releases this microorganism's proteins, which then can be used by researchers for genetic analysis.''Halobacterium sp. NRC-1'' was one of the first Archaea to have its genome fully mapped and published. Since that time several more species have been successfully mapped and a few others partially mapped. This allows scientists to analyze the properties of halobacterium in silico to determine the activity of genes. Many transformation tools have also been developed to create loss-of-function mutants. These mutant strains are made to carry inoperative knockout genes which alters the organism's normal cellular processes. Scientists can then infer the function of the gene by comparing the physical and biochemical characteristics of the original organism with the new mutant's characteristics. The ability of this organism to be easily cultured along with these ingenious genetic research tools make ''Halobacterium sp. NRC-1'' an ideal model for testing the function of genes.

In addition, ''Halobacterium sp. NRC-1'' is an ideal study tool because it is an extremophile, it exists in environments that are very unfriendly toward life. This makes it very useful for studying many biological questions especially those involved with adaptation and survival in extreme environments. In fact, much research is being done to investigate whether or not halobacterium could be potential candidates for extraterrestrial life, such as on Mars or Europa. Recent research has shown that ''Halobacterium sp. NRC-1'' can not only survive at temperatures far below its optimal growth temperature, but continue to reproduce as well.

Survival and growth of Halobacterium sp. NRC-1 following incubation at -15&deg;C, freezing or freezedrying, and the protective effect of cations
The extremophillic properties and biological responses of Halobacteruim NRC-1 are currently being investigated to test the organism's survival potential in the harsh environmental conditions that exist on Mars. The recent discoveries that meterorites from Mars contain a mineral form of sodium chloride as well as the isolation of halophilic archaea from ancient rock salt has led scientists to believe that the existence of Halobacterium sp. NRC-1 in a Martian environment is quite possible. Halobacterium are known to be slightly thermophilic organisms, showing optimum growth at 40 degrees Celcius. In this experiment, cells of Halobacterium sp. NRC-1 were freeze dried and suspended in buffers containing specific cations, including Mg++,Ca++,or K+. Results showed that NRC-1 was still capable of growth at the extremely low temperature of -15 degrees Celcius, and the cations appeared to show protective characteristics. The conditions of the the Martian environment include very low temperatures and low water availabilty. Scientists will continue to research NRC-1's possibilty to survive in such inhospitable environments such as the one on Mars.

Functional Genomics of Thioredoxins in Halobacterium sp. NRC-1
This project addresses the functions of an ancient protein family in Archaea that occupy extreme environments. Some of these proteins may play roles similar to those of comparable proteins in other living organisms, and thus may tell us about functions that evolved in the last universal common ancestor of life. Others may have evolved as the Archaea began to occupy specialized and often extreme environments. This project also addresses the emergence of proto-metabolic networks that supplied the precursors for the RNA World.

A systems view of haloarchaeal strategies to withstand stress from transition metals
Given that transition metals are essential cofactors in central biological processes, misallocation of the wrong metal ion to a metalloprotein can have resounding and often detrimental effects on diverse aspects of cellular physiology. Therefore, in an attempt to characterize unique and shared responses to chemically similar metals, we have reconstructed physiological behaviors of Halobacterium NRC-1, an archaeal halophile, in sublethal levels of Mn(II), Fe(II), Co(II), Ni(II), Cu(II), and Zn(II).