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| Author: Aaron Hall |
At the 95th meeting of the American Society of Microbiology held May 21-25 in Washington, D.C., Craig Venter [The Institute for Genomic Research (TIGR)] and Hamilton Smith (Johns Hopkins University) announced the complete sequencing of two bacterial genomes. With in-house TIGR support, the 1.9-Mb Haemophilus influenzae genome was finished and all gaps closed in less than a year; funding from the DOE microbial genome project, administered by Jay Grimes, allowed the 580-kb Mycoplasma genitalium genome to be completed in 3 months by Claire Fraser's team at TIGR.
"This is really an incredible moment in history," said Frederick Blattner (University of Wisconsin), who heads the NIH project to sequence the bacterium Escherichia coli. "It demonstrates the ability to take the whole sequence of an organism and work down from that to its genes, which is what geneticists have been dreaming of for a long time." Blattner noted that geneticists traditionally have studied genes by identifying functions that are impaired when a gene is mutated.
Whole-Genome Approach
The usual method of breaking DNA into overlapping segments (mapping), sequencing the pieces, and reassembling them is time-consuming. Smith (who won the Nobel prize for isolating restriction enzymes) and Venter developed a whole-genome shotgun sequencing approach that skipped the mapping stage. They employed ultrasonic waves to break the DNA into fragments, which were then sequenced and reordered with computer software developed at TIGR.
Free-Living Bacteria
H. influenzae and M. genitalium are free-living; that is, they contain all the genetic information needed for living independently. This contrasts with viruses, many already sequenced, which lack genes for independent living and replicate by using genetic information from the cells they infect.
M. genitalium, a eubacterium thought to be the simplest known self-replicating and free-living life form, has been used as a model for the minimum number of genes and protein products necessary for independent existence. As with other Mycoplasma species, it has been shown to have a very rapid rate of evolution.
Third Organism Under Way
Venter reported that his primary DOE project to sequence Methanococcus jannaschi is ahead of schedule and should be completed by September-less than a year after the award was made. M. jannaschi, an extreme thermophile belonging to the ancient Archaebacterial family, was isolated at the base of a Pacific Ocean thermal vent.
Sequence Analysis
Venter's group has started to analyze the full DNA sequence of H. influenzae, a common cause of ear infections in children. He said that although "it will take all of us months, if not years, to truly understand it," he already has predicted the biological role of most of the 1749 genes by comparing them with other genes of known function. After the paper is published in Science in late July, the entire H. influenzae sequence will be deposited in the Genome Sequence Data Base. Sequence data and a table of putative gene identifications and role categories will be available through the TIGR Home Page (http://www.tigr.org).
Venter predicted that TIGR could sequence ten or more microcrobial genomes each year with high efficiency. Further research on these and other bacterial genomes will enable researchers to identify bacterial genes, including those responsible for causing disease, and help search out comparable human genes that may be involved in disease processes. |
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