VBI Scientists Sequence Genome of Soil-Living Bacterium
A collaboration of researchers, which includes scientists at the Virginia Bioinformatics Institute and Virginia Tech, recently completed the genome sequence of Azotobacter vinelandii, uncovering important genetic information that will contribute to a more complete understanding of the biology of this versatile, soil-living bacterium.
The work will help advance research on A. vinelandii’s role as a model study organism for investigation of nitrogen fixation and other biochemical processes. It will also pave the way for new applications in biotechnology, including the possible use of A. vinelandii as a “factory†for the production of other proteins, in particular those that may be damaged by the presence of oxygen.
A. vinelandii lives in soil and has the ability to convert nitrogen from the atmosphere into ammonia via bacterial enzymes called nitrogenases. Nitrogen fixation is essential for life since different nitrogen-containing molecules are used to produce DNA and the amino acids that are the building blocks of proteins. For most bacteria, the nitrogenase enzymes involved in nitrogen fixation are very susceptible to destruction by oxygen. A. vinelandii is one of the few bacteria that can fix nitrogen in the presence of oxygen, using three distinct nitrogenase systems.
The work of the Azotobacter vinelandii genome project team, which will be featured on the cover of the Journal of Bacteriology*, identifies unique features of the A. vinelandii genome that explain how the bacteria is involved in oxygen-sensitive reactions such as nitrogen fixation, while maintaining strictly aerobic metabolism.
A. vinelandii has one of the highest respiratory rates of any known bacterium and has the capacity to maintain low levels of cytoplasmic oxygen through a process called respiratory protection. The sequence of the bacteria’s genome allowed the team of researchers to identify the genes involved in respiration, including those responsible for respiratory protection.
Genome analysis helped pinpoint the chromosomal location of the three known oxygen-sensitive nitrogenases, as well as the genes that code for other oxygen-sensitive enzymes such as carbon-monoxide dehydrogenase and a formate dehydrogenase. The sequence also provided important information on the genes that code for alginate, a polymer that further protects the organism from excess oxygen by forming a physical barrier around the bacterium.
The work will also provide more information about the unique biosynthetic pathways involved in the bacteria’s ability to adapt its metabolism to diverse sources of nutrients. For example, if no carbon source is present, A. vinelandii will undergo a differentiation process, forming cysts that are resistant to desiccation and other chemical and physical challenges.
A. vinelandii belongs to the Pseudomonadaceae family. The completion of the A. vinelandii genome will serve as an essential phylogenetic anchor point for comparative genomics work with other systems. This research has also helped the Azotobacter vinelandii genome project expand its existing undergraduate training platform in genomics technology. Undergraduate researchers from around the world worked on many aspects of the project, including the finishing, annotation, bioinformatics, and analytical phases. This work provided critical training for these new scientists in the fields of genomics and bioinformatics.
“The key to the success of this project was an extremely effective multinational collaboration between Azotobacter biologists and our core genomics team,†explained Derek Wood, associate professor in Seattle Pacific University’s Department of Biology and the University of Washington’s Department of Microbiology. “Numerous undergraduate researchers both in the classroom and in the laboratory worked closely with the team on annotation and analyses. This multilevel interdisciplinary collaboration led to an excellent annotation and informed analysis of this model bacterial system and provided an excellent training platform for our undergraduate partners.â€
According to Dennis Dean, biochemistry professor in Virginia Tech’s College of Agriculture and Life Sciences and director of the Fralin Life Science Institute, “Given the long history of Virginia Tech’s research involving nitrogen fixation studies, including work from J.S. Chen, Bill Newton and others, it is particularly satisfying that the university has contributed to this important endeavor.â€
