Identification and Sequence Analysis of Metazoan tRNA 3′-End Processing Enzymes tRNase Zs

PLoS ONE

Volumn 7, Issue 9, 2012, Pages

  Wang, Zhikang ^a   Zheng, Jia ^a   Zhang, Xiaojie ^a   Peng, Jingjing ^a,b   Liu, Jinyu ^a   Huang, Ying ^a  

^a NANJING NORMAL UNIVERSITY   (China)

^b TAISHAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO TERMINAL TELOPEPTIDE; CARBOXY TERMINAL TELOPEPTIDE; RIBONUCLEASE; TRANSFER RIBONUCLEASE Z; TRANSFER RNA; UNCLASSIFIED DRUG;

ANIMAL TISSUE; ARTICLE; DEUTEROSTOMIA; ECDYSOZOA; ENZYME ACTIVITY; GENE; GENETIC COMPLEMENTATION; GENETIC CONSERVATION; HUMAN; HUMAN TISSUE; HYDROGEN BOND; LOPHOTROCHOZOA; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN MOTIF; RAT; RNA ANALYSIS; RNA PROCESSING; RNA SEQUENCE; RNA SPLICING; RNA TRANSLATION; SEQUENCE ANALYSIS; SPECIES DIFFERENTIATION; START CODON; TRNASE Z GENE;

ALTERNATIVE SPLICING; AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ANIMALS; CELL NUCLEUS; ENDORIBONUCLEASES; HUMANS; ISOENZYMES; MITOCHONDRIA; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; RNA 3' END PROCESSING; RNA PRECURSORS; RNA, TRANSFER; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

DEUTEROSTOMIA; ECDYSOZOA; LOPHOTROCHOZOA; METAZOA;

EID: 84866014716     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0044264     Document Type: Article

References (59)

1. Ceballos M, Vioque A, (2007) tRNase Z. Protein Pept Lett. 14: 137-145.
2. Hartmann RK, Gossringer M, Spath B, Fischer S, Marchfelder A, (2009) Chapter 8 The Making of tRNAs and More- RNase P and tRNase Z. Prog Nucleic Acid Res Mol Biol. 85C: 319-368.
3. Redko Y, Li de Lasierra-Gallay I, Condon C, (2007) When all's zed and done: the structure and function of RNase Z in prokaryotes. Nat Rev Microbiol 5: 278-286.
4. Spath B, Canino G, Marchfelder A, (2007) tRNase Z: the end is not in sight. Cell Mol Life Sci 64: 2404-2412.
5. Fan L, Wang Z, Liu J, Guo W, Yan J, et al. (2011) A survey of green plant tRNA 3′-end processing enzyme tRNase Zs, homologs of the candidate prostate cancer susceptibility protein ELAC2. BMC Evol Biol 11: 219.
6. Tavtigian SV, Simard J, Teng DH, Abtin V, Baumgard M, et al. (2001) A candidate prostate cancer susceptibility gene at chromosome 17p. Nat Genet 27: 172-180.
7. Zhao W, Yu H, Li S, Huang Y, (2010) Identification and analysis of candidate fungal tRNA 3′-end processing endonucleases tRNase Zs, homologs of the putative prostate cancer susceptibility protein ELAC2. BMC Evol Biol 10: 272.
8. Canino G, Bocian E, Barbezier N, Echeverria M, Forner J, et al. (2009) Arabidopsis encodes four tRNase Z enzymes. Plant Physiol.
9. Brzezniak LK, Bijata M, Szczesny RJ, Stepien PP (2011) Involvement of human ELAC2 gene product in 3′ end processing of mitochondrial tRNAs. RNA Biol 8.
10. Rossmanith W (2011) Of P and Z: Mitochondrial tRNA processing enzymes. Biochim Biophys Acta.
11. Takahashi M, Takaku H, Nashimoto M, (2008) Regulation of the human tRNase ZS gene expression. FEBS Lett 582: 2532-2536.
12. Aravind L, (1999) An evolutionary classification of the metallo-beta-lactamase fold proteins. In Silico Biol 1: 69-91.
13. Daiyasu H, Osaka K, Ishino Y, Toh H, (2001) Expansion of the zinc metallo-hydrolase family of the beta-lactamase fold. FEBS Lett 503: 1-6.
14. Dominski Z, (2007) Nucleases of the metallo-beta-lactamase family and their role in DNA and RNA metabolism. Crit Rev Biochem Mol Biol 42: 67-93.
15. Schiffer S, Rosch S, Marchfelder A, (2002) Assigning a function to a conserved group of proteins: the tRNA 3'-processing enzymes. EMBO J 21: 2769-2777.
16. Minagawa A, Ishii R, Takaku H, Yokoyama S, Nashimoto M, (2008) The flexible arm of tRNase Z is not essential for pre-tRNA binding but affects cleavage site selection. J Mol Biol 381: 289-299.
17. Zareen N, Hopkinson A, Levinger L, (2006) Residues in two homology blocks on the amino side of the tRNase Z His domain contribute unexpectedly to pre-tRNA 3' end processing. RNA 12: 1104-1115.
18. de la Sierra-Gallay IL, Pellegrini O, Condon C, (2005) Structural basis for substrate binding, cleavage and allostery in the tRNA maturase RNase Z. Nature. 433: 657-661.
19. Karkashon S, Hopkinson A, Levinger L, (2007) tRNase Z catalysis and conserved residues on the carboxy side of the His cluster. Biochemistry 46: 9380-9387.
20. Minagawa A, Takaku H, Ishii R, Takagi M, Yokoyama S, et al. (2006) Identification by Mn2+ rescue of two residues essential for the proton transfer of tRNase Z catalysis. Nucleic Acids Res 34: 3811-3818.
21. Ishii R, Minagawa A, Takaku H, Takagi M, Nashimoto M, et al. (2007) The structure of the flexible arm of Thermotoga maritima tRNase Z differs from those of homologous enzymes. Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 637-641.
22. Ishii R, Minagawa A, Takaku H, Takagi M, Nashimoto M, et al. (2005) Crystal structure of the tRNA 3' processing endoribonuclease tRNase Z from Thermotoga maritima. J Biol Chem 280: 14138-14144.
23. Kostelecky B, Pohl E, Vogel A, Schilling O, Meyer-Klaucke W, (2006) The crystal structure of the zinc phosphodiesterase from Escherichia coli provides insight into function and cooperativity of tRNase Z-family proteins. J Bacteriol 188: 1607-1614.
24. Li de la Sierra-Gallay I, Mathy N, Pellegrini O, Condon C, (2006) Structure of the ubiquitous 3' processing enzyme RNase Z bound to transfer RNA. Nat Struct Mol Biol 13: 376-377.
25. Hopkinson A, Levinger L (2008) Effects of conserved D/T loop substitutions in the pre-tRNA substrate on tRNase Z catalysis. RNA Biol 5.
26. Schilling O, Spath B, Kostelecky B, Marchfelder A, Meyer-Klaucke W, et al. (2005) Exosite modules guide substrate recognition in the ZiPD/ElaC protein family. J Biol Chem 280: 17857-17862.
27. Dubrovsky EB, Dubrovskaya VA, Levinger L, Schiffer S, Marchfelder A, (2004) Drosophila RNase Z processes mitochondrial and nuclear pre-tRNA 3' ends in vivo. Nucleic Acids Res 32: 255-262.
28. Xie X, Dubrovskaya VA, Dubrovsky EB (2010) RNAi knockdown of dRNaseZ, the Drosophila homolog of ELAC2, impairs growth of mitotic and endoreplicating tissues. Insect Biochem Mol Biol.
29. Smith MM, Levitan DJ, (2004) The Caenorhabditis elegans homolog of the putative prostate cancer susceptibility gene ELAC2, hoe-1, plays a role in germline proliferation. Dev Biol 266: 151-160.
30. Roy SW, Gilbert W, (2005) Complex early genes. Proc Natl Acad Sci U S A 102: 1986-1991.
31. Chothia C, Gough J, Vogel C, Teichmann SA, (2003) Evolution of the protein repertoire. Science 300: 1701-1703.
32. Rogozin IB, Sverdlov AV, Babenko VN, Koonin EV, (2005) Analysis of evolution of exon-intron structure of eukaryotic genes. Brief Bioinform 6: 118-134.
33. Dumont M, Frank D, Moisan AM, Tranchant M, Soucy P, et al. (2004) Structure of primate and rodent orthologs of the prostate cancer susceptibility gene ELAC2. Biochim Biophys Acta 1679: 230-247.
34. Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, et al. (2008) Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452: 745-749.
35. Lopez Sanchez MI, Mercer TR, Davies SM, Shearwood AM, Nygard KK, et al. (2011) RNA processing in human mitochondria. Cell Cycle 10.
36. Rossmanith W, (2011) Localization of human RNase Z isoforms: dual nuclear/mitochondrial targeting of the ELAC2 gene product by alternative translation initiation. PLoS One 6: e19152.
37. Zhao Z, Su W, Yuan S, Huang Y, (2009) Functional conservation of tRNase ZL among Saccharomyces cerevisiae, Schizosaccharomyces pombe and humans. Biochem J 422: 483-492.
38. Kortschak RD, Samuel G, Saint R, Miller DJ, (2003) EST analysis of the cnidarian Acropora millepora reveals extensive gene loss and rapid sequence divergence in the model invertebrates. Curr Biol 13: 2190-2195.
39. Kusserow A, Pang K, Sturm C, Hrouda M, Lentfer J, et al. (2005) Unexpected complexity of the Wnt gene family in a sea anemone. Nature 433: 156-160.
40. Yan H, Zareen N, Levinger L, (2006) Naturally occurring mutations in human mitochondrial pre-tRNASer(UCN) can affect the transfer ribonuclease Z cleavage site, processing kinetics, and substrate secondary structure. J Biol Chem 281: 3926-3935.
41. Dubrovsky EB, Dubrovskaya VA, Bilderback AL, Berger EM, (2000) The isolation of two juvenile hormone-inducible genes in Drosophila melanogaster. Dev Biol 224: 486-495.
42. Wilusz JE, Freier SM, Spector DL, (2008) 3' end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell 135: 919-932.
43. Haussecker D, Huang Y, Lau A, Parameswaran P, Fire AZ, et al. (2010) Human tRNA-derived small RNAs in the global regulation of RNA silencing. RNA 16: 673-695.
44. Lee YS, Shibata Y, Malhotra A, Dutta A, (2009) A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes Dev 23: 2639-2649.
45. Bogerd HP, Karnowski HW, Cai X, Shin J, Pohlers M, et al. (2010) A mammalian herpesvirus uses noncanonical expression and processing mechanisms to generate viral MicroRNAs. Mol Cell 37: 135-142.
46. Diebel KW, Smith AL, van Dyk LF, (2010) Mature and functional viral miRNAs transcribed from novel RNA polymerase III promoters. Rna 16: 170-185.
47. Yanaihara N, Kohno T, Takakura S, Takei K, Otsuka A, et al. (2001) Physical and transcriptional map of a 311-kb segment of chromosome 18q21, a candidate lung tumor suppressor locus. Genomics 72: 169-179.
48. Cavener DR, (1987) Comparison of the consensus sequence flanking translational start sites in Drosophila and vertebrates. Nucleic Acids Res 15: 1353-1361.
49. Kozak M, (2002) Pushing the limits of the scanning mechanism for initiation of translation. Gene 299: 1-34.
50. Smith CW, Patton JG, Nadal-Ginard B, (1989) Alternative splicing in the control of gene expression. Annu Rev Genet 23: 527-577.
51. Kozak M, (1995) Adherence to the first-AUG rule when a second AUG codon follows closely upon the first. Proc Natl Acad Sci U S A 92: 2662-2666.
52. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
53. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol doi: 10.1093/molbev/msr121.
54. Abascal F, Zardoya R, Posada D, (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21: 2104-2105.
55. Ronquist F, Huelsenbeck JP, (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
56. Ho SN, Hunt HD, Horton RM, Pullen JK, Pease LR, (1989) Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77: 51-59.
57. Gan X, Yang J, Li J, Yu H, Dai H, et al. (2011) The fission yeast Schizosaccharomyces pombe has two distinct tRNase ZLs encoded by two different genes and differentially targeted to the nucleus and mitochondria. Biochem J.
58. Levinger L, Hopkinson A, Desetty R, Wilson C, (2009) Effect of changes in the flexible arm on tRNase Z processing kinetics. J Biol Chem 284: 15685-15691.
59. Guex N, Peitsch MC, (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18: 2714-2723.