Halobacterium sp.


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Systems Biology's Research with Halobacteria

The Halobacterium sp. is an ideal model organism for systems biology research--that is, while it is only one-celled, with one chromosome and two mini-chromosomes, it is a complete biological system in and of itself, and thus serves as a microcosm of several basic processes in more complex systems, such as in the human being. The halobacteria are totally non-pathogenic, making them a useful and appropriate organism for high-school educational studies as well as scientific research.                      

(Right: The main chromosome is circular.
Halobacteria also has two other chromosomes,
as dipicted in the upper right hand corner.)
HB chromosomes

Halobacterium ColoniesHalobacterium sp. has evolved with sophisticated systems for adapting to the environment, including fluctuations in sunlight, oxygen, temperature, nutrients, and salinity. The genetic and biochemical regulatory networks within the Halobacterium sp. easily lend themselves to systems biology observation and analyses.    

(Halobacterium colonies growing on a petri dish)

Scientists at the Institute of Systems Biology (ISB)  are working with a strain of halobacteria known as Halobacterium NRC-1. With its remarkable physiology and array of molecular biology and functional genomic tools, the organism provides a relatively simple yet resilient model for observing complex cellular adjustments to environmental changes. ISB scientists compare lab-engineered mutant strains of Halobacterium sp. with one another and with the non-mutant version to gain an understanding of the complex physiological processes that occur at a systems level.


For example, the phototrophic growth stage of Halobacterium sp. is associated with the expression of a group of genes that encode the synthesis of the protein bacterioopsin and retinal, a molecule that absorbs light. Bacterioopsin and retinal bind together to form a protein complex or "molecular machine" called bacteriorhodopsin in the cell membrane, which mediates the conversion of light energy to ATP energy. Numerous bacteriorhodopsin complexes join to form a two-dimensional crystalline lattice in the cell membrane that is purple in color and therefore, easily visible for scientific observation.

Using microarray and ICAT-based technologies, ISB scientists recently discovered that the regulatory mechanism for synthesizing the bacteriorhodopsin and converting light to ATP energy stage works in exact inverse proportion to another process that ferments the amino acid arginine, also needed for ATP production. Both of these processes take place during the phototrophic stage when the organism is in an anaerobic environment. Scientists speculate that when the first process increases, the second decreases, maintaining steady state levels of ATP. This discovery could only have taken place by studying all the genes of the organism at a systems level rather than at a single gene or protein level.


Numerous discrete databases regarding the halobacteria, including protein-protein interactions, functional links between genes, chromosome maps, metabolic pathways, and protein expression patterns have been integrated into a large visual display tool developed at the ISB. Known as Cytoscape this tool is used to rapidly explore vast amounts of genome and proteomic data, thus facilitating discovery science.

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