Organisms Chosen for
DOE Microbial Genome Program
the MGP's first full year, DOE funded four microbial genome sequencing
projects focused on the bacterium Mycoplasma genitalium and three
other microbes. Now fully characterized, the tiny M. genitalium
genome—thought to have the smallest genome of any known free-living bacterium—provides
a model for a minimal set of genes necessary for life. Its genome contains
only 580,000 base pairs of DNA and yet encodes 470 genes. Future studies
on this and other minimal genomes will help increase our understanding
of more complex genomes.
Among the oldest life forms known, the Archaea make up one of three
phylogenetic or evolutionary domains into which all life is classified.
The other two are the Eukarya and the Bacteria. Archaea found thriving
in extreme environments of heat and cold, acidity, pressure, and salinity
are known as extremophiles ("extreme-loving" organisms). Understanding
the biological mechanisms underlying their hardiness may help researchers
develop new industrial, biomedical, and environmental applications.
Microbes may, for example, contain enzymes that are effective in driving
chemical reactions in extreme environments. Some may provide enzymes useful
in research; one such "extremozyme" derived from a bacterium living in
hot springs in Yellowstone National Park has become critical to current
protocols for sequencing any genome, including that of humans. Other microbes
have metabolic processes with potential for breaking down toxic waste or
even producing methane, an energy source.
Comparisons of the genomes of organisms from all three domains are helping
scientists better understand the evolution of all living things. Descriptions
of MGP-supported research on some other microbes follow.
- Methanococcus jannaschii was among the first archaea chosen
for sequencing. In 1996 its completed sequencing and analysis confirmed
that the "tree of life" has three domains,
a hypothesis first advanced nearly 20 years ago by Carl Woese (University
of Illinois) but not given much credence at the time. The single-celled
M. jannaschii was isolated from a sample collected beneath more
than 8000 feet of water at the base of a deep-sea thermal vent on the
floor of the Pacific Ocean. The microbe lives without the sunlight,
oxygen, and organic carbon important to most other forms of life and
uses carbon dioxide, nitrogen, and hydrogen expelled from the thermal
vent for its life functions. When the entire DNA sequence of M. jannaschii
was determined, scientists found that about 65% of its potential gene
sequences were not related to any gene previously discovered, representing
an exciting area for future investigation.
- The archaeon Archaeoglobus fulgidus and the bacterium Thermotoga
maritima have potential for practical applications in industry and
government-funded environmental remediation. Because they thrive in water
temperatures above the boiling point, these organisms may provide DOE,
the Department of Defense, and private companies with heat-stable enzymes
for use in industrial processes. These processes could include conversion
of wastes to useful chemicals. A. fulgidus has the added capability of
surviving at the high pressures associated with deep oil wells, and T.
maritima metabolizes simple and complex carbohydrates, including glucose,
sucrose, starch, xylan, and cellulose. Cellulose and xylan are the most
abundant biopolymers on Earth and, through their conversion to fuels such
as ethanol, have major potential as sources of renewable energy. Comparisons
of the genomic sequences of these two microbes will contribute to a greater
understanding of evolutionary relationships as well as high-temperature
- The archaeon Pyrobaculum aerophilum, first isolated from a boiling
marine vent, thrives at temperatures close to the maximum tolerated by
living systems (113oC). Unlike most hyperthermophiles, P.
aerophilum is able to withstand exposure to oxygen and can thus be
manipulated more easily in the laboratory. Also, the proteins encoded by
hyperthermophilic genomes are more stable than those of organisms living
in more temperate environments.
- The bacterium Shewanella putrefaciens, which can grow with or without
oxygen, is an excellent model system for manipulating organisms for remediation.
Whole-genome sequencing will elucidate metabolic pathways including those
involved in corrosion, consumption of toxic organic pollutants, and removal
of toxic metals and radiation waste by conversion to insoluble forms.
Other organisms that could be of great genetic and biochemical interest
are present in extreme surface environments but are almost impossible
to grow in the laboratory. The MGP funds a project to identify and determine
the abundance and activity of novel hard-to-cultivate organisms in two
extreme surface environments in the arid southwestern United States.
Preliminary samples indicate that most of these bacterial species contain
few similarities to the previously described cultivated bacteria. These
collections offer a rich resource for identifying and isolating novel
species with potentially unique sets of genes as well as proteins with
environmental, energy, biotechnological, and other applications.