SGER: Embedded Crop Genes Expressed From Coupled AUG Codons

Oregon State University, Corvallis OR

Investigators

Abstract

PI: Theo W. Dreher (Oregon State University) The expectation from past knowledge is that eukaryotic messenger RNAs encode a single protein. This expectation guides the way we currently interpret the coding properties of plant genomes and predict the set of expressed proteins. Recent research from this laboratory has uncovered a mechanism that allows the robust expression of two proteins from one messenger RNA if the two initiation sites are particularly closely spaced. This project will use a bioinformatics approach to explore whether the newly discovered phenomenon results in the production of a previously unrecognized set of proteins in plants, including key crop plants such as rice and corn. Attention will focus on "embedded genes," in which the potential information lies within the coding regions for proteins that have already been identified. Current genome interpretations typically miss such potentially embedded genes, hundreds of which would exist in a plant genome. This in silico study will analyze patterns that would allow prediction of those embedded genes that are likely to be expressed. Broader impact: With additional genome sequences of several major crop plants expected over the next few years, correct interpretation is important in fully utilizing the value of the new information. If proven as a true entity, the discovery of embedded genes has the potential to advance the understanding of protein translation mechanism and contribute significantly to plant proteome. This may include genes that are important for crop improvement. The study, which will bring together scientists trained in computer programming, mathematics, molecular biology and genetics, is expected to produce synergies that will advance the field of plant research.