Post-Genomics Blog

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A New Model Microbe for Extreme Biology

Extremophiles are organisms that are adapted to environments inhospitable for conventional life forms, e.g. extremes of salinity and temperature, oxygen-starved conditions, or exposure to toxic heavy metals and intense radiation. It turns out that one extremophile, Halobacterium sp. NRC-1, is resistant to all of the above extremes, and has become a favorite subject for in-depth post-genomic studies. This is because of our ability to easily culture it in the laboratory, knock out any of its non-essential genes, and simultaneously assay gene expression for all 2500 genes using DNA microarrays. The organism is a member of the Archaeal branch of the evolutionary tree, an evolutionary relic that displays some characteristics of higher organisms and exhibits novel features that make it ideal for applications in biotechnology.

Studies of extremophiles are usually limited by our inability to easily grow the organisms in the laboratory. This is because of the difficulty in mimicking the unusual ecological niches that they occupy and because of their adaptation to highly specialized growth conditions. Salt-loving halophilic microorganisms (nicknamed haloarchaea) are extremophiles that grow optimally under conditions of extremely high salinity, 5-10 times that of seawater. Unlike most extreme environments, hypersaline conditions required by haloarchaea are relatively easy to attain in the laboratory. One well-studied haloarchaeon, Halobacterium sp. NRC-1, is widely distributed in hypersaline environments and, in 2000, was among the first microorganisms to have its genome sequenced. Key post-genomic methods have been subsequently developed, including a facile gene knockout system and whole genome microarrays for transcriptome analysis.

Halobacterium sp. NRC-1, though growing best heterotrophically in a rich organic broth, is metabolically versatile. In addition to its aerobic metabolic capacity, it possesses facultative growth capabilities through anaerobic respiration, utilizing dimethyl sulfoxide (DMSO) and trimethylamine N-oxide (TMAO), and via arginine fermentation. It also has phototrophic capability through the light-driven proton pumping activity of the retinal protein, bacteriorhodopsin, in its purple membrane. Halobacterium sp. NRC-1 cells are highly motile, synthesizing gas vesicles, which are hollow protein structures, intracellularly, for buoyancy and flotation. Halobacterium sp. NRC-1 responds to many environmental effectors, including high and low temperatures and salinities, toxic heavy metals, and ultraviolet (UV) and ionizing radiation. As a result of its ability to cope with multiple extremes, this extremophile is an ideal model organism for studies of gene regulation.

Halobacterium sp. NRC-1 represents an excellent experimental model for extremophile biology, for fundamental aspects of archaeal and eukaryotic biology, and also for theoretical questions of evolutionary biology. For Halobacterium sp. NRC-1, the determination of the complete genome sequence and the development of many post-genomic experimental techniques, including gene knockout capability and DNA microarrays, as well as proteomics and in silico bioinformatics approaches, have elevated this organism to the status of a leading model system among extremophiles and Archaea. A particular advantage of post-genomic studies on Halobacterium sp. NRC-1 is that most are being conducted using well-characterized isogenic strains. Future research efforts on this model system are likely to contribute significantly to broadening our understanding of fundamental biological concepts and ultimately testing our predictive powers.

Further reading
DasSarma S, DasSarma P. 2006. Halophiles. In: Encyclopedia of Life Sciences. Wiley Press
DasSarma S. 2004. Genome sequence of an extremely halophilic archaeon. In: Microbial Genomes Edited by Fraser T, Read T, Nelson KE. Totowa, NJ: Humana Press, Inc.; pp. 383-399.
DasSarma, S. 2006. Extreme halophiles are models for astrobiology. Microbe 1:120-127.
DasSarma S, Berquist BR, Coker, JA, DasSarma P, Muller JA. 2006. Post-genomics of the model haloarchaeon Halobacterium sp. NRC-1. Saline Systems 1:3.

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