Discovery of a minimal form of RNase P in Pyrobaculum.
RNase P RNA is an ancient, nearly universal feature of life. As part of the ribonucleoprotein RNase P complex, the RNA component catalyzes essential removal of 5' leaders in pre-tRNAs. In 2004, Li and Altman computationally identified the RNase P RNA gene in all but three sequenced microbes: Nanoarchaeum equitans, Pyrobaculum aerophilum, and Aquifex aeolicus (all hyperthermophiles) [Li Y, Altman S (2004) RNA 10:1533-1540]. A recent study concluded that N. equitans does not have or require RNase P activity because it lacks 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 alternatives to 5' pre-tRNA processing. Using comparative genomics and improved computational methods, we have now identified a radically minimized form of the RNase P RNA in five Pyrobaculum species and the related crenarchaea Caldivirga maquilingensis and Vulcanisaeta distributa, all retaining a conventional catalytic domain, but lacking a recognizable specificity domain. We confirmed 5' tRNA processing activity by high-throughput RNA sequencing and in vitro biochemical assays. The Pyrobaculum and Caldivirga RNase P RNAs are the smallest naturally occurring form yet discovered to function as trans-acting precursor tRNA-processing ribozymes. Loss of the specificity domain in these RNAs suggests altered substrate specificity and could be a useful model for finding other potential roles of RNase P. This study illustrates an effective combination of next-generation RNA sequencing, computational genomics, and biochemistry to identify a divergent, formerly undetectable variant of an essential noncoding RNA gene.
Department of Biochemistry and Center for RNA Biology, Ohio State University, 484 West Twelfth Avenue, Columbus, OH 43210, USA.
Lien B
LB
Lai
Patricia P
PP
Chan
Aaron E
AE
Cozen
David L
DL
Bernick
James W
JW
Brown
Venkat
V
Gopalan
Todd M
TM
Lowe
D019843:Archaeal Proteins / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D001483:Base Sequence; D055162:Biocatalysis; D019295:Computational Biology / Q000379:methods; D004591:Electrophoresis, Polyacrylamide Gel; D020745:Genome, Archaeal / Q000235:genetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D041543:Pyrobaculum / Q000145:classification / Q000201:enzymology / Q000235:genetics*; D012322:RNA Precursors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D019642:RNA, Archaeal / Q000235:genetics* / Q000378:metabolism; D016337:RNA, Catalytic / Q000235:genetics / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D043262:Ribonuclease P / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D013379:Substrate Specificity
D019843:Archaeal Proteins; D012322:RNA Precursors; D019642:RNA, Archaeal; D016337:RNA, Catalytic; D012343:RNA, Transfer; D043262:Ribonuclease P