Halobacterium 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
(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
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.
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.