Identification and analysis of ribonuclease P and MRP RNA in a broad range of eukaryotes

RNases P and MRP are ribonucleoprotein complexes involved in tRNA and rRNA processing, respectively. The RNA subunits of these two enzymes are structurally related to each other and play an essential role in the enzymatic reaction. Both of the RNAs have a highly conserved helical region, P4, which is important in the catalytic reaction. We have used a bioinformatics approach based on conserved elements to computationally analyze available genomic sequences of eukaryotic organisms and have identified a large number of novel nuclear RNase P and MRP RNA genes. For MRP RNA for instance, this investigation increases the number of known sequences by a factor of three. We present secondary structure models of many of the predicted RNAs. Although all sequences are able to fold into the consensus secondary structure of P and MRP RNAs, a striking variation in size is observed, ranging from a Nosema locustae MRP RNA of 160 nt to much larger RNAs, e.g. a Plasmodium knowlesi P RNA of 696 nt. The P and MRP RNA genes appear in tandem in some protists, further emphasizing the close evolutionary relationship of these RNAs.

[1]  B. Dujon,et al.  Genome evolution in yeasts , 2004, Nature.

[2]  S. Altman,et al.  In search of RNase P RNA from microbial genomes. , 2004, RNA.

[3]  T. Pan,et al.  Design and isolation of ribozyme-substrate pairs using RNase P-based ribozymes containing altered substrate binding sites. , 1999, Nucleic acids research.

[4]  N. Pace,et al.  Phylogenetic analysis of the structure of RNase MRP RNA in yeasts. , 2002, RNA.

[5]  Sean R. Eddy,et al.  A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure , 2002, BMC Bioinformatics.

[6]  T. Pan,et al.  Domain structure of the ribozyme from eubacterial ribonuclease P. , 1996, RNA.

[7]  L. Lindahl,et al.  Identification of a functional core in the RNA component of RNase MRP of budding yeasts. , 2004, Nucleic acids research.

[8]  T. Pan,et al.  Modular construction for function of a ribonucleoprotein enzyme: the catalytic domain of Bacillus subtilis RNase P complexed with B. subtilis RNase P protein. , 2001, Nucleic acids research.

[9]  James W. Brown,et al.  Structural implications of novel diversity in eucaryal RNase P RNA. , 2005, RNA.

[10]  R. Durbin,et al.  RNA sequence analysis using covariance models. , 1994, Nucleic acids research.

[11]  M. Schmitt,et al.  RNase MRP Cleaves the CLB2 mRNA To Promote Cell Cycle Progression: Novel Method of mRNA Degradation , 2004, Molecular and Cellular Biology.

[12]  M. Ridanpää,et al.  Transplanting CY282 heterozygous livers is risky , 2003, Journal of medical genetics.

[13]  Yi Zhao,et al.  NONCODE: an integrated knowledge database of non-coding RNAs , 2004, Nucleic Acids Res..

[14]  N. Pace,et al.  Evolutionary perspective on the structure and function of ribonuclease P, a ribozyme , 1995, Journal of bacteriology.

[15]  N. Pace,et al.  Phylogenetic-comparative analysis of the eukaryal ribonuclease P RNA. , 2000, RNA.

[16]  A. S. Krasilnikov,et al.  Basis for Structural Diversity in Homologous RNAs , 2004, Science.

[17]  D. Engelke,et al.  An essential protein-binding domain of nuclear RNase P RNA. , 2001, RNA.

[18]  T. Pan,et al.  A thermodynamic framework and cooperativity in the tertiary folding of a Mg2+-dependent ribozyme. , 1999, Biochemistry.

[19]  M. A. Rosenblad,et al.  Prediction of signal recognition particle RNA genes. , 2002, Nucleic acids research.

[20]  N. Pace,et al.  Comparative photocross‐linking analysis of the tertiary structures of Escherichia coli and Bacillus subtilis RNase P RNAs , 1998, The EMBO journal.

[21]  J. Avis,et al.  A conserved element in the yeast RNase MRP RNA subunit can participate in a long-range base-pairing interaction. , 2004, Journal of molecular biology.

[22]  P. Stadler,et al.  Secondary structure prediction for aligned RNA sequences. , 2002, Journal of molecular biology.

[23]  Li Li,et al.  PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data , 2003, Nucleic Acids Res..

[24]  L. Lindahl,et al.  The RNA of RNase MRP is required for normal processing of ribosomal RNA. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[25]  A. S. Krasilnikov,et al.  Crystal structure of the specificity domain of ribonuclease P , 2003, Nature.

[26]  S. Altman,et al.  Similar cage-shaped structures for the RNA components of all ribonuclease P and ribonuclease MRP enzymes , 1990, Cell.

[27]  G. Crooks,et al.  WebLogo: a sequence logo generator. , 2004, Genome research.

[28]  D. Engelke,et al.  Eukaryotic ribonuclease P: a plurality of ribonucleoprotein enzymes. , 2002, Annual review of biochemistry.

[29]  D. Engelke,et al.  A conserved RNA motif involved in divalent cation utilization by nuclear RNase P. , 1996, RNA.

[30]  B. Séraphin,et al.  The POP1 gene encodes a protein component common to the RNase MRP and RNase P ribonucleoproteins. , 1994, Genes & development.

[31]  E Westhof,et al.  Derivation of the three-dimensional architecture of bacterial ribonuclease P RNAs from comparative sequence analysis. , 1998, Journal of molecular biology.

[32]  B. Séraphin,et al.  Accurate Processing of a Eukaryotic Precursor Ribosomal RNA by Ribonuclease MRP in Vitro , 1996, Science.

[33]  D A Clayton,et al.  Nuclear RNase MRP is required for correct processing of pre-5.8S rRNA in Saccharomyces cerevisiae , 1993, Molecular and cellular biology.

[34]  Sean R. Eddy,et al.  Rfam: annotating non-coding RNAs in complete genomes , 2004, Nucleic Acids Res..

[35]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[36]  N. Pace,et al.  The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme , 1983, Cell.

[37]  L. Lindahl,et al.  Functional equivalence of hairpins in the RNA subunits of RNase MRP and RNase P in Saccharomyces cerevisiae. , 2000, RNA.

[38]  M. Zuker.  On finding all suboptimal foldings of an RNA molecule. , 1989, Science.

[39]  Sean R. Eddy,et al.  Rfam: an RNA family database , 2003, Nucleic Acids Res..

[40]  W. Filipowicz,et al.  7‐2/MRP RNAs in plant and mammalian cells: association with higher order structures in the nucleolus. , 1992, The EMBO journal.

[41]  Rodrigo Lopez,et al.  Multiple sequence alignment with the Clustal series of programs , 2003, Nucleic Acids Res..

[42]  C. Zwieb,et al.  Identification and comparative analysis of components from the signal recognition particle in protozoa and fungi , 2004, BMC Genomics.

[43]  James W. Brown.  The ribonuclease P database , 1998, Nucleic Acids Res..

[44]  M. Schmitt,et al.  The Saccharomyces cerevisiae RNase mitochondrial RNA processing is critical for cell cycle progression at the end of mitosis. , 2002, Genetics.