New Approach to Understand Microbial Gene Function


Understanding the functions of the thousands of genes found in a microbial genome is a difficult but important challenge. Derek Lovley and his team at the University of Massachusetts, Amherst, have used a new approach that combines several experiment-based predictions of gene function (called “annotations”) to understand the biology of Geobacter sulfurreducens, a microbe with important roles in bioremediation of contaminant metals. The team integrated data on messenger RNA transcription, RNA translation into proteins, and biochemical data obtained under a variety of conditions to achieve a more precise and comprehensive annotation of Geobacter. Their approach resulted in the identification of previously undetected genes and other features in the Geobacter, genome such as “antisense” transcripts, that could be tentatively linked to functions and Geobacter’s regulatory complexity. This new, experimental-based approach to predicting gene function reveals a much greater richness in gene expression phenomena than approaches based solely on DNA sequence or comparisons with other sequenced microbes.


Qiu Y, Cho BK, Park YS, Lovley D, Palsson B&oslash, Zengler K. “Structural and operational complexity of the Geobacter sulfurreducens genome,” Genome Res. 2010 (Sept.); 20, 1304-11.