Bioinformatics
Professor Wackett, in collaboration with Bioinformatics Professor Lynda Ellis , have constructed World Wide Web databases focused on microbial biocatalytic and biodegradative reactions (UMBBD) (Ellis, et al, 2006) and for biofuels (UM-BFD). This effort presages a time when anyone can sit at a desktop computer and theoretically design efficient biochemical pathways for purposes of biosynthesis or biodegradation and find out rapidly if the genes and organisms are available to carry out the plan. In this context, there is ongoing effort in collaboration with Kathrin Fenner of the EAWAG for developing methodologies for the biodegradation pathway predictions system Predict-BT.
Biodegradation
The Wackett laboratory investigates bacterial degradation of the herbicide atrazine and related compounds, see for example the UM-BBD atrazine pathway elucidated by our group. Bacteria initiate metabolism of atrazine via the enzyme atrazine chlorohydrolase (deSouza, et al, 1998; Shapir, et al, 2006), which renders the herbicide non-toxic. The enzyme is being studied as a model to better understand dechlorination biocatalysts and for its applicability to treat soil and water contaminated with atrazine; we carried out an environmental cleanup of 1000 pounds of atrazine spilled into a soil in South Dakota (Strong, et al, 2000). This is part of a program for good environmental stewardship for herbicides , working with Syngenta Crop Protection. This research is conducted in collaboration with Professor Michael Sadowsky .
Genomics and Biocatalysis
It is the overall objective of this research to explore the breadth of Earth's biochemical diversity and help uncover the function of unknown genes in the widespread microbial genome sequencing projects. We have sequenced and annotated the complete genome of Arthrobacter aurescens TC1 and related microorganisms.
The enormous taxonomic and genomic diversity of microbes provides a corresponding metabolic diversity, of which only a narrow slice has been discovered, for a basic understanding of microbial metabolism. Novel metabolism can be exploited for biocatalytic production of commercial chemicals. Example discoveries are new metabolism directed toward thioamide, boronic acids and organobismuth compounds.
Catabolic Enzyme Evolution
The Wackett laboratory studies protein ancestry and modulation via evolutionary processes. Research has shown that microbes and their enzymes and pathways are extremely plastic. For example, in conjunction with Professor Michael Sadowsky, we have shown that virtually identical atrazine-catabolism genes have spread globally with the aid of catabolic plasmids and transposons. Other research is identifying enzymes catalyzing different reactions but having nearly identical sequences, thus allowing the opportunity to emulate natural evolutionary transition of catalytic function in the laboratory (Seffernick, et al, 2001). Natural diversity within the amidohydrolase superfamily is also being studied in collaboration with Professor Patricia Babbitt and the University of California, San Francisco.
TrzN, the atrazine chlorohydrolase from Arthrobacter aurescens TC1
Bacterial Production of Petroleum Fuels
Petroleum is a major source of fuels for society. There is increasing interest in bio-based fuels, but petroleum is still most desirable because of its high energy density and compatibility with existing infrastructure. The most desirable components of petroleum consist of clean-burning hydrocarbons. We are investigating the microbial biosynthesis of hydrocarbons. This research is currently funded by the Institute for Renewable Energy and the Environment (IREE) and a Discovery Grant for Biofuels from the University of Minnesota. As part of our efforts, we have developed the University of Minnesota BioFuels Database, to help inform and foster biofuels research throughout the world.
The BioFuels Database, go to: http://www.biofuelsdatabase.org/
