JWB
James W. Brown

Associate Professor & Undergraduate Coordinator
Department of Microbiology, NC State University

Abstract# 84, RNA 2009 (RNA Society), May 26-31, 2009, Madison, WI

Discovery of the Elusive Pyrobaculum RNase P: The Smallest Active P RNA

Todd Lowe1, Lien Lai2, Patricia Chan1, Aaron Cozen1, David Bernick1, James Brown3, Venkat Gopalan2

1University of California, Santa Cruz, CA, USA, 2The Ohio State University, Columbus, OH, USA, 3North Carolina State University, Raleigh, NC, USA

RNase P RNA is an ancient, universal feature of life with the exception of a few unique cases. As part of the ribonucleoprotein RNase P complex, the RNA component catalyzes essential removal of 5' leaders in precursor tRNAs. In 2004, Li and Altman identified the RNase P RNA gene in all but three sequenced hyperthermophilic microbes: Nanoarchaeum equitans, Pyrobaculum aerophilum, and Aquifex aeolicus. A recent study established that N. equitans does not have or require RNase P activity due to the lack of 5' tRNA leaders. The "missing" RNase P RNAs in the other two species is perplexing given evidence or predictions that tRNAs are trimmed in both, prompting speculation that they may have developed novel solutions to pre-tRNA processing. Using comparative genomics and improved computational methods, we have now identified a radically minimized, active form of the RNase P RNA in five Pyrobaculum species and the related crenarchaeon Caldivirga maquilingensis. We confirmed tRNA processing activity in Pyrobaculum by high-throughput RNA sequencing and in vitro biochemical assays. The Pyrobaculum RNase P RNA is the smallest naturally occurring form (~210 nucleotides) yet discovered to function as a ribozyme, retaining a conventional catalytic domain, but lacking a recognizable specificity domain. Loss of the specificity domain in the RNA may suggest altered substrate specificity, and could be a model for finding other potential roles for RNase P in Archaea. This collaborative study illustrates an effective combination of next-generation RNA sequencing, computational genomics, and biochemistry to identify a divergent, formerly undetectable variant of an essential non-coding RNA gene.

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