One clear fact emerging in this post genomic age is that there are many genes, so called hypothetical genes, in the organisms on earth for which we have no idea as to their function. Nowhere is this more acute than in the prokaryotes. To begin to address this problem this project will address the unknown genes involved in the biosynthesis of the coenzymes (vitamins) in the hyperthermophilic euryarchaeon Methanocaldococcus jannaschii, one of the billions of different types of prokaryotes. The research will allow the annotation of function to some of these hypothetical genes and define new biochemical reactions. Discovery of these new biochemical reactions will extend the general understanding of the breadth of specific reactions that could have been involved in the production of coenzymes, compounds critical in the origin of life. The broader impact of this project is that it will help sustain ongoing undergraduate and graduate training of young scientists. Students will be exposed to many different scientific disciplines and methods, including but not limited to molecular biology, organic synthesis, different forms of spectroscopy, enzymology, bioinformatics, analytical biochemistry, prebiotic chemistry, and anaerobic microbiology, all in one setting. Undergraduate students will participate in this work through undergraduate research in the lab. Students are expected to produce one original reviewed published scientific work during their time in the lab, which further prepares them for a future career in the sciences. The training of post-docs to work in this area of research is also critical.
Microorganisms function based on the gene products encoded in their genomes. Defining the biochemical function these gene products, termed functional genomics, is an important endeavor in this post genomics age. Only after the functions of these many unknown gene products are identified can the true metabolic diversity present in our planet's organisms be assessed. Our NSF funded work was concerned with discovering the genes involved with biosynthetic reactions in organisms that produce methane. The result of this work has established the biochemical function of the enzymes that operate in pathways involved in coenzyme biosynthesis in methane producing microorganisms. The applications of this knowledge can range from reducing greenhouse methane emissions to more efficiently producing methane as a source of energy from anthropogenic waste. Worldwide, these microorganisms produce more than 400 million tons of the greenhouse gas methane each year as part of the global carbon cycle. Another reason we have studied the metabolism of these organisms is to uncover the nature of the chemical reactions that were occurring in the earth’s oceans after the early earth’s surface cooled enough to have hot liquid oceans where life could evolve. These reactions, which we have described as "protobiochemistry", represent the chemical reactions that would have been specifically used by the last universal common ancestor (LUCA). LUCA is likely closely related to present day methane producing microorganisms, that we are studying. Protobiochemistry reveal "metabolic fossils," or remnants of primitive metabolism that may still be functioning in present day methane producing organisms. We have found several such reactions, but the discovery of an enzyme that uses formaldehyde to make sugars is perhaps the most significant. Broader Impacts Science itself is the most effective tool for motivating students to become the next generation of scientists. Through the research described above, students in my lab have been exposed to many different scientific disciplines and methods, including but not limited to enzymology, molecular biology, organic synthesis, varying forms of spectroscopy, bioinformatics, protein chemistry, analytical biochemistry, prebiotic chemistry, and anaerobic microbiology all in one setting. Undergraduate students participated in this experience through undergraduate research in the lab. Over the last 10 years, 1-2 undergraduate students have worked on a continual basis in the White laboratory. Students were expected to publish one original reviewed scientific work during their time in the lab, further preparing them for a future career in the sciences. The discovery of new biochemical pathways and the associated genes and enzymes has a far-reaching impact both within the scientific community and also to society at large. The work outlined here will not only further our understanding of coenzyme biosynthesis in methane producing organisms, but may also provide a glimpse into some of the chemistry used by the earliest forms of life. In this post-genomics era every newly characterized enzyme aids in the annotation of many genes and provides insight into the metabolic potential of diverse organisms, both benign and pathogenic. Every gene function identified adds to the toolbox for metabolic engineering.
