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| Azotobacter vinelandii. |
Tuesday, 02 July 2002
Susan McGinley
Scientists at the University of Arizona in Tucson and the United States Department of Energy (DOE) recently completed mapping the genetic sequence of a microbe used in research laboratories worldwide. The bacterium, Azotobacter vinelandii, commonly found in soil, is important in understanding a range of scientific problems from agriculture and medicine, to energy and industrial uses.
Working together, scientists from the UA and the DOE Joint Genome Institute in Walnut Creek, Calif., sequenced the entire genome of A. vinelandii in a joint project. Next week (July 8-13), scientists from nine institutions in five countries will convene at the UA to annotate the genome using computer software developed for the project. UA undergraduate researchers are included in the project.
The DOE and the Arizona Research Laboratory at the UA are sponsoring the project as part of the Microbial Genome Program, a DOE spinoff of the Human Genome Project. The goal is to completely sequence the genomes of microbes that have properties important to current scientific investigations and make them available in public databases.
This is the first whole genome annotation to be held at the UA. Christina Kennedy, a microbiologist in the UA plant pathology department, and Nirav Merchant, head of the UA Biotechnology Computing Facility, which developed the software to be used in the annotation, are the principal investigators on the project.
Academic and industrial scientists will use this data to make comparisons they were not able to do before among genes and with the genomes of other organisms. The results could help in solving problems pertaining to agriculture, medicine, industrial processes, and energy production and use.
"By having the sequence of every gene in A. vinelandii, we will know the sequence of every protein," Kennedy said. "We will then recognize the appearance of new genes we hadn't known before, with new functions related to nitrogen, carbon and energy metabolism."
Found in soils worldwide, A. vinelandii has been studied for its unique characteristics by scientists for more than 90 years. It can utilize nitrogen gas from the atmosphere and convert it to a form that serves as a nutrient for plant growth and development. Unlike other nitrogen-fixing bacteria, it can perform this process in the presence of oxygen. This attribute makes it more flexible in adapting to a wider range of environmental conditions.
In addition, A. vinelandii has the unusual ability to carry out nitrogen fixation by using any one of three different enzymes with different metal content–molybdenum, vanadium, or iron–all of which are encoded by different genes, according to Kennedy. It has a very high respiratory rate, and can grow on a wide variety of organic acids, alcohols and carbohydrates, making it useful for applications in a wide variety of scientific studies.
"We still do not understand all of the genes in this organism. We already know the sequence of 250 because they were individually discovered and analyzed over the last 20 years," Kennedy says. "The total number of genes in Azotobacter vinelandii is 5,000, so there are 4,800 in this recently sequenced genome that we have not seen before." (The human genome contains approximately 10 times the number of genes in A. vinelandii.)
The week-long annotation process will be overseen by bioinformatics expert Paul Rudnick, a UA graduate now working at Scientific Applications International Corporation, National Cancer Institute in Frederick, Md. Scientists from the United States, Germany, Norway, Canada and Mexico will be assisted by computer scientists, by DNA sequencers from the DOE, and also by five undergraduate students from the UA who have studied microbial genetics and have learned the process of gene annotation.
The team will refine the computer annotation process by examining each gene in the database individually to correct errors. After the week-long workshop, they will return to their home institutions where they will continue to annotate the remaining genes and communicate their findings for inclusion in the public database.
- Updated: July 02, 2002
