Sequence Analysis and Comparative Study of the Protein Subunits of Archaeal RNase P.
RNase P, a ribozyme-based ribonucleoprotein (RNP) complex that catalyzes tRNA 5'-maturation, is ubiquitous in all domains of life, but the evolution of its protein components (RNase P proteins, RPPs) is not well understood. Archaeal RPPs may provide clues on how the complex evolved from an ancient ribozyme to an RNP with multiple archaeal and eukaryotic (homologous) RPPs, which are unrelated to the single bacterial RPP. Here, we analyzed the sequence and structure of archaeal RPPs from over 600 available genomes. All five RPPs are found in eight archaeal phyla, suggesting that these RPPs arose early in archaeal evolutionary history. The putative ancestral genomic loci of archaeal RPPs include genes encoding several members of ribosome, exosome, and proteasome complexes, which may indicate coevolution/coordinate regulation of RNase P with other core cellular machineries. Despite being ancient, RPPs generally lack sequence conservation compared to other universal proteins. By analyzing the relative frequency of residues at every position in the context of the high-resolution structures of each of the RPPs (either alone or as functional binary complexes), we suggest residues for mutational analysis that may help uncover structure-function relationships in RPPs.
Systemix Institute, Redmond, WA 98053, USA. samanta@homolog.us.
Manoj P
MP
Samanta
Department of Chemistry &amp; Biochemistry, The Ohio State University, Columbus, OH 43210, USA. lai.231@osu.edu.|Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA. lai.231@osu.edu.
Stella M
SM
Lai
Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA. daniels.7@osu.edu.|Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA. daniels.7@osu.edu.
Charles J
CJ
Daniels
Department of Chemistry &amp; Biochemistry, The Ohio State University, Columbus, OH 43210, USA. gopalan.5@osu.edu.|Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA. gopalan.5@osu.edu.
Venkat
V
Gopalan
D001105:Archaea / Q000378:metabolism*; D019843:Archaeal Proteins / Q000737:chemistry / Q000378:metabolism*; D000072417:Protein Domains; D054730:Protein Interaction Domains and Motifs; D021122:Protein Subunits / Q000737:chemistry / Q000378:metabolism; D043262:Ribonuclease P / Q000737:chemistry / Q000378:metabolism*
D019843:Archaeal Proteins; D021122:Protein Subunits; D043262:Ribonuclease P
RNP evolution; RNase P; archaea; sequence analysis; tRNA processing