SCIENCE & ENGINEERING NEWS
Rockville, MD. — The Institute for Genomic Research (TIGR) this week celebrated the completion of its 19th and 20th genome sequencing projects. The completion of the entire genome sequences of Chlorobium tepidum and Caulobacter crescentus mark a major milestone in TIGR’s history. The genome of Chlorobium tepidum is the first from a member of the green sulfur bacteria, a distinct lineage of bacteria that possess a unique mechanism of photosynthesis relative to other organisms. This species grows at moderately elevated temperatures (thermophily) and grows only in the absence of oxygen. The genome will help scientists understand global carbon cycles as well as the origins and mechanisms of photosynthesis and thermophily. Caulobacter are the most common bacteria in nutrient-poor fresh water streams and are being modified for use as a bioremediation agent – meaning they will be used in environmental cleanup of contaminated wastewater. The U.S. Department of Energy (DOE) provided funding for both projects.
“The completion of the 20th genome sequencing project at TIGR represents a landmark achievement for our organization and is one in which we collectively take great pride,” said Claire M. Fraser, Ph.D., President of TIGR. “The follow-on use of microbial genome sequence information has already begun to have a major impact on the development of new anti-microbial compounds and new vaccines and the identification of novel enzymes and metabolic pathways of environmental relevance.”
In 1995, TIGR scientists revolutionized the field of genome sequencing with the publication of the first complete genome sequence from a free-living organism, Haemophilus influenzae, using the whole-genome shotgun strategy. Since that time, TIGR has sequenced 61% of the genomes and chromosomes in the public domain, and TIGR scientists have authored 14 papers on the sequence and analysis of these genomes. These genomes and chromosomes total nearly 60 million base pairs (Mbp) of sequence information and nearly 50,000 genes have been identified.
Other recent accomplishments by TIGR scientists include the completion and annotation of the genomes of a recent clinical isolate of Mycobacterium tuberculosis, the organism which is the leading cause of death due to infection world-wide; Neisseria meningitidis, which causes life-threatening invasive bacterial infections, especially in infants; and Vibrio cholerae, which causes epidemics of cholera, which is continuing to affect Asia, Africa and South America. TIGR is also leading the way in plant genomics and has recently published the sequence of chromosome 2 of Arabidopsis thaliana, a small flowering plant used extensively as a model organism in many plant laboratories. TIGR has sequenced nearly 92,000 Expressed Sequence Tags (EST) from tomato for a project funded by the National Science Foundation Plant Genome Initiative. These ESTs reflect genes that are being expressed throughout tomato growth and development as well as in response to various environmental stresses. In addition, TIGR has sequenced 4,300 ESTs from potato, part of a 55,000 potato EST project that focuses on potato functional genomics with an emphasis on late blight disease.
As part of the International Rice Genome Sequencing Project, TIGR is sequencing parts of chromosome 10 and chromosome 3 of Oryza sativa spp japonica. Data on the rice genome is released daily via TIGR’s database to ensure it is accessible to scientists and researchers worldwide. “Plant genomics at TIGR is aimed at understanding the genes or blueprints of specific plants so that we can then make healthier, more nutritious plants which will enable us to feed the growing populations of the world,” said Robin Buell, PhD., principal investigator of the rice genome project.
Genomics at TIGR is more than sequencing. TIGR’s microarray facility is performing a variety of array projects on a number of microbial organisms including major human pathogens and organisms of evolutionary and environmental interest, including Deinococcus radiodurans, Methanococcus jannaschi, funded by DOE, and other microarray studies of gene expression in rat and human cancers funded in part by the National Institutes of Health (NIH). Microarray expression analysis is a recently developed method of genome analysis that allows the expression levels of thousands, or tens of thousands of genes to be assayed in a single experiment. Microarray analysis requires advanced instrumentation, including high precision robotics, confocal laser scanners, and sophisticated computer software to generate, record, and analyze the data. This technique can provide information on how large numbers of genes interact with each other and can lead to an understanding of the gene networks that underlie cellular metabolism.
An innovator in many areas of science and technology, TIGR scientists and bioinformatics engineers recently developed the Comprehensive Microbial Resource (CMR), a database and web interface that allows access to data from all of the completed bacterial genomes through a single web source. Funded in part by DOE, the CMR represents sequence and annotation of each of the completed genomes as well as associated information about the organisms, the structure and composition of their DNA molecules and many attributes of the protein sequences predicted from the DNA sequence. For genomes not originating from TIGR, annotation from the sequencing center that sequenced the genome, as well as automated annotation from TIGR, are included for complete uniform display and attribution of bacterial information. Further information is available on TIGR’s web site at http://www.tigr.org .