Finding the functions of orphan genes in microorganisms that naturally produce methane might accomplish several objectives at once----providing new insights into previously unknown enzymes, new methods for producing environmentally-friendly fuels, as well as new methods for conversion of harmful pollutants.

The Department of Energy (DOE) has funded an innovative three-year collaborative study involving three UMBI investigators: Dr. John Orban, Dr. Kevin Sowersand Dr. Zvi Kelman, as well as Dr. Basil Nikolau of the W.M. Keck Metabolomics laboratory at Iowa State University.

Virtually all of the chemical reactions of all living cells are mediated by proteins that function as enzymes. Each enzyme catalyzes a single step in chemical transformations that convert small molecules to other molecules, or that synthesize large molecules from smaller ones. The molecule on which a specific enzyme acts is called that enzyme's substrate.

Traditional approaches have relied on genetic mutants and biochemical analysis to determine all of the steps in these metabolic or biosynthetic pathways.

But sequencing the complete genomes of numerous organisms----which reveals all of the genes of each organism-- has revealed important gaps in our knowledge. Scientists have found that a substantial proportion of these genes----as many as 25-70%, depending on the organism, have unknown or poorly understood function. A significant proportion of these hypotheticals encode putative enzymes whose precise catalytic function, and substrate, are yet to be determined.

The collaborative study will address these questions----and will attempt to discover the precise functions and substrates of putative enzymes in an especially interesting microorganism that goes by the scientific name, Methanosarcina acetivorans. This microbe is a member of a relatively recently discovered kingdom of microbes known as Archaea, which are distinct from other kinds of microorganisms, and are related to the most ancient cells that have lived on planet Earth.

Many such Archaeal species live in extreme environments, such as boiling hot springs, and can convert a variety of different small molecules, including harmful wastes, into useful compounds, including methane gas, which is a potential energy source. The particular species being studied has an unusually large genome, and potentially contains many new and interesting enzymes.

In order to determine the functions and substrates of these enzymes, each of the investigators in this study brings his particular area of expertise to the collaboration. Dr. Orban is an expert in NMR (nuclear magnetic resonance spectroscopy), a physical technique that can be used to determine the structures of small molecules and larger proteins with which they interact. Dr. Orban has used this technique in the past to characterize orphan genes. Dr. Zvi Kelman is a biochemist with extensive experience in characterizing proteins from archaeal-cells. Dr. Kevin Sowers is an expert in the physiology and molecular biology of methane-producing Archaea. Dr. Basil Nikolau is an expert in the new field of metabolomics, which characterizes small molecule substrates of living cells.