Transfer RNA modifications and genes for modifying enzymes in Arabidopsis thaliana

BMC Plant Biology

Volumn 10, Issue , 2010, Pages

  Chen, Peng ^a,b   Jäger, Gunilla ^c   Zheng, Bo ^b  

^a QINGDAO INSTITUTE OF BIOENERGY AND BIOPROCESS TECHNOLOGY   (China)

^b SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^c UMEÅ UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS THALIANA; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; POPULUS; POPULUS TREMULA;

PLANT RNA; TRANSFER RNA;

AMINO ACID SEQUENCE; ARABIDOPSIS; ARTICLE; ASPEN; BIOLOGY; CONFORMATION; ENZYMOLOGY; GENE EXPRESSION REGULATION; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MOLECULAR GENETICS; PHYLOGENY; PLANT GENE; SEQUENCE ALIGNMENT;

AMINO ACID SEQUENCE; ARABIDOPSIS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; MOLECULAR SEQUENCE DATA; MUTAGENESIS, INSERTIONAL; NUCLEIC ACID CONFORMATION; PHYLOGENY; POPULUS; RNA, PLANT; RNA, TRANSFER; SEQUENCE ALIGNMENT;

EID: 77956458716     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-10-201     Document Type: Article

References (51)

1. Björk GR. Transfer RNA modification in different organisms. Chem Scripta 1986, 26:91-95.
2. Björk GR, Ericson JU, Gustafsson CE, Hagervall TG, Jonsson YH, Wikstrom PM. Transfer RNA modification. Annu Rev Biochem 1987, 56:263-287. 10.1146/annurev.bi.56.070187.001403, 3304135.
3. Montasser Kouhsari S, Keith G, Weil JH. Methylation of yeast tRNAPhe by enzymes from cytoplasm, chloroplasts and mitochondria of Phaseolus vulgaris. Biochim Biophys Acta 1978, 521(2):576-583.
4. Huang B, Lu J, Byström AS. A genome-wide screen identifies genes required for formation of the wobble nucleoside 5-methoxycarbonylmethyl-2-thiouridine in Saccharomyces cerevisiae. RNA 2008, 14(10):2183-2194. 10.1261/rna.1184108, 2553728, 18755837.
5. Persson BC, Gustafsson C, Berg DE, Björk GR. The gene for a tRNA modifying enzyme, m5U54-methyltransferase, is essential for viability in Escherichia coli. Proc Natl Acad Sci USA 1992, 89(9):3995-3998. 10.1073/pnas.89.9.3995, 525618, 1373891.
6. Anderson J, Phan L, Cuesta R, Carlson BA, Pak M, Asano K, Björk GR, Tamame M, Hinnebusch AG. The essential Gcd10p-Gcd14p nuclear complex is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA. Genes Dev 1998, 12(23):3650-3662. 10.1101/gad.12.23.3650, 317256, 9851972.
7. Gerber AP, Keller W. An adenosine deaminase that generates inosine at the wobble position of tRNAs. Science 1999, 286(5442):1146-1149. 10.1126/science.286.5442.1146, 10550050.
8. Gu W, Jackman JE, Lohan AJ, Gray MW, Phizicky EM. tRNAHis maturation: an essential yeast protein catalyzes addition of a guanine nucleotide to the 5' end of tRNAHis. Genes Dev 2003, 17(23):2889-2901. 10.1101/gad.1148603, 289149, 14633974.
9. Björk GR. Biosynthesis and function of modified nucleosides. tRNA: Structure, Biosynthesis, and Function 1995, 165-205. Washington, DC: American Society for Microbiology.
10. Kitchingman GR, Fournier MJ. Modification-deficient transfer ribonucleic acids from relaxed control Escherichia coli: structures of the major undermodified phenylalanine and leucine transfer RNAs produced during leucine starvation. Biochemistry 1977, 16(10):2213-2220. 10.1021/bi00629a027, 324516.
11. Vold BS, Sypherd PS. Modification in transfer RNA during the differentiation of wheat seedlings. Proc Natl Acad Sci USA 1968, 59(2):453-458. 10.1073/pnas.59.2.453, 224693, 5238976.
12. Shugart L. A possible age-related modification of phenylalanine transfer RNA from wheat tissue. Exp Gerontol 1972, 7(4):251-262. 10.1016/0531-5565(72)90015-0, 5073318.
13. Jones LH, Scott TK. Transfer Ribonucleic Acid Modification and Its Relationship to Tumorous and Nontumorous Plant Growth. Plant Physiol 1981, 67(3):535-538. 10.1104/pp.67.3.535, 425720, 16661709.
14. Maréchal-Drouard L, Weil JH, Guillemaut P. Import of several tRNAs from the cytoplasm into the mitochondria in bean Phaseolus vulgaris. Nucleic Acids Res 1988, 16(11):4777-4788. 10.1093/nar/16.11.4777, 336695, 3387208.
15. Szweykowska-Kulinska Z, Krajewski J, Wypijewski K. Mutations of Arabidopsis thaliana pre-tRNA(Tyr) affecting pseudouridylation of U35. Biochim Biophys Acta 1995, 1264(1):87-92.
16. Yu YT, Shu MD, Steitz JA. Modifications of U2 snRNA are required for snRNP assembly and pre-mRNA splicing. EMBO J 1998, 17(19):5783-5795. 10.1093/emboj/17.19.5783, 1170906, 9755178.
17. Huang ZP, Zhou H, Qu LH. Maintaining a conserved methylation in plant and insect U2 snRNA through compensatory mutation by nucleotide insertion. IUBMB Life 2005, 57(10):693-699. 10.1080/15216540500306983, 16223710.
18. Iida K, Jin H, Zhu JK. Bioinformatics analysis suggests base modifications of tRNAs and miRNAs in Arabidopsis thaliana. BMC Genomics 2009, 10:155. 10.1186/1471-2164-10-155, 2674459, 19358740.
19. Chen Z, Zhang H, Jablonowski D, Zhou X, Ren X, Hong X, Schaffrath R, Zhu JK, Gong Z. Mutations in ABO1/ELO2, a subunit of holo-Elongator, increase abscisic acid sensitivity and drought tolerance in Arabidopsis thaliana. Mol Cell Biol 2006, 26(18):6902-6912. 10.1128/MCB.00433-06, 1592858, 16943431.
20. Raviprakash KS, Cherayil JD. 2'-O-methyl-1-methyl adenosine: a new modified nucleoside in ragi (Eleusine coracana) tRNA. Biochem Biophys Res Commun 1984, 121(1):243-248. 10.1016/0006-291X(84)90713-7, 6547340.
21. Walden TL, Howes N, Farkas WR. Purification and properties of guanine, queuine-tRNA transglycosylase from wheat germ. J Biol Chem 1982, 257(22):13218-13222.
22. Miyawaki K, Tarkowski P, Matsumoto-Kitano M, Kato T, Sato S, Tarkowska D, Tabata S, Sandberg G, Kakimoto T. Roles of Arabidopsis ATP/ADP isopentenyltransferases and tRNA isopentenyltransferases in cytokinin biosynthesis. Proc Natl Acad Sci USA 2006, 103(44):16598-16603. 10.1073/pnas.0603522103, 1637627, 17062755.
23. Boland C, Hayes P, Santa-Maria I, Nishimura S, Kelly VP. Queuosine formation in eukaryotic tRNA occurs via a mitochondria-localized heteromeric transglycosylase. J Biol Chem 2009, 284(27):18218-18227. 10.1074/jbc.M109.002477, 2709355, 19414587.
24. Noma A, Kirino Y, Ikeuchi Y, Suzuki T. Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA. EMBO J 2006, 25(10):2142-2154. 10.1038/sj.emboj.7601105, 1462984, 16642040.
25. de Crecy-Lagard V. Identification of genes encoding tRNA modification enzymes by comparative genomics. Methods Enzymol 2007, 425:153-183. full_text, 17673083.
26. Xing F, Hiley SL, Hughes TR, Phizicky EM. The specificities of four yeast dihydrouridine synthases for cytoplasmic tRNAs. J Biol Chem 2004, 279(17):17850-17860. 10.1074/jbc.M401221200, 14970222.
27. Johansson MJ, Byström A. Transfer RNA modifications and modifying enzymes in Saccharomyces cerevisiae. Fine-Tuning of RNA Functions by Modification and Editing 2005, 12:87-120.
28. Jackman JE, Montange RK, Malik HS, Phizicky EM. Identification of the yeast gene encoding the tRNA m1G methyltransferase responsible for modification at position 9. RNA 2003, 9(5):574-585. 10.1261/rna.5070303, 1370423, 12702816.
29. Björk GR, Jacobsson K, Nilsson K, Johansson MJ, Byström AS, Persson OP. A primordial tRNA modification required for the evolution of life?. EMBO J 2001, 20(1-2):231-239. 10.1093/emboj/20.1.231, 140193, 11226173.
30. Purushothaman SK, Bujnicki JM, Grosjean H, Lapeyre B. Trm11p and Trm112p are both required for the formation of 2-methylguanosine at position 10 in yeast tRNA. Mol Cell Biol 2005, 25(11):4359-4370. 10.1128/MCB.25.11.4359-4370.2005, 1140639, 15899842.
31. Ellis SR, Morales MJ, Li JM, Hopper AK, Martin NC. Isolation and characterization of the TRM1 locus, a gene essential for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNA in Saccharomyces cerevisiae. J Biol Chem 1986, 261(21):9703-9709.
32. Alexandrov A, Martzen MR, Phizicky EM. Two proteins that form a complex are required for 7-methylguanosine modification of yeast tRNA. RNA 2002, 8(10):1253-1266. 10.1017/S1355838202024019, 1370335, 12403464.
33. Nordlund ME, Johansson JO, von Pawel-Rammingen U, Byström AS. Identification of the TRM2 gene encoding the tRNA(m5U54)methyltransferase of Saccharomyces cerevisiae. RNA 2000, 6(6):844-860. 10.1017/S1355838200992422, 1369962, 10864043.
34. Motorin Y, Grosjean H. Multisite-specific tRNA:m5C-methyltransferase (Trm4) in yeast Saccharomyces cerevisiae: identification of the gene and substrate specificity of the enzyme. RNA 1999, 5(8):1105-1118. 10.1017/S1355838299982201, 1369833, 10445884.
35. Gerber A, Grosjean H, Melcher T, Keller W. Tad1p, a yeast tRNA-specific adenosine deaminase, is related to the mammalian pre-mRNA editing enzymes ADAR1 and ADAR2. EMBO J 1998, 17(16):4780-4789. 10.1093/emboj/17.16.4780, 1170807, 9707437.
36. Wilkinson ML, Crary SM, Jackman JE, Grayhack EJ, Phizicky EM. The 2'-O-methyltransferase responsible for modification of yeast tRNA at position 4. RNA 2007, 13(3):404-413. 10.1261/rna.399607, 1800514, 17242307.
37. Pintard L, Lecointe F, Bujnicki JM, Bonnerot C, Grosjean H, Lapeyre B. Trm7p catalyses the formation of two 2'-O-methylriboses in yeast tRNA anticodon loop. EMBO J 2002, 21(7):1811-1820. 10.1093/emboj/21.7.1811, 125368, 11927565.
38. Kotelawala L, Grayhack EJ, Phizicky EM. Identification of yeast tRNA Um(44) 2'-O-methyltransferase (Trm44) and demonstration of a Trm44 role in sustaining levels of specific tRNA(Ser) species. RNA 2008, 14(1):158-169. 10.1261/rna.811008, 2151035, 18025252.
39. Cavaille J, Chetouani F, Bachellerie JP. The yeast Saccharomyces cerevisiae YDL112w ORF encodes the putative 2'-O-ribose methyltransferase catalyzing the formation of Gm18 in tRNAs. RNA 1999, 5(1):66-81. 10.1017/S1355838299981475, 1369740, 9917067.
40. Jablonowski D, Fichtner L, Stark MJ, Schaffrath R. The yeast elongator histone acetylase requires Sit4-dependent dephosphorylation for toxin-target capacity. Mol Biol Cell 2004, 15(3):1459-1469. 10.1091/mbc.E03-10-0750, 363168, 14718557.
41. Huang B, Johansson MJ, Byström AS. An early step in wobble uridine tRNA modification requires the Elongator complex. RNA 2005, 11(4):424-436. 10.1261/rna.7247705, 1370732, 15769872.
42. Johansson MJ, Byström AS. The Saccharomyces cerevisiae TAN1 gene is required for N4-acetylcytidine formation in tRNA. RNA 2004, 10(4):712-719. 10.1261/rna.5198204, 1370561, 15037780.
43. Esberg B, Leung HC, Tsui HC, Björk GR, Winkler ME. Identification of the miaB gene, involved in methylthiolation of isopentenylated A37 derivatives in the tRNA of Salmonella typhimurium and Escherichia coli. J Bacteriol 1999, 181(23):7256-7265. 103688, 10572129.
44. Dihanich ME, Najarian D, Clark R, Gillman EC, Martin NC, Hopper AK. Isolation and characterization of MOD5, a gene required for isopentenylation of cytoplasmic and mitochondrial tRNAs of Saccharomyces cerevisiae. Mol Cell Biol 1987, 7(1):177-184. 365054, 3031456.
45. Nelissen H, Clarke JH, De Block M, De Block S, Vanderhaeghen R, Zielinski RE, Dyer T, Lust S, Inzé D, Van Lijsebettens M. DRL1, a homolog of the yeast TOT4/KTI12 protein, has a function in meristem activity and organ growth in plants. Plant Cell 2003, 15(3):639-654. 10.1105/tpc.007062, 150019, 12615938.
46. Nelissen H, Fleury D, Bruno L, Robles P, De Veylder L, Traas J, Micol JL, Van Montagu M, Inze D, Van Lijsebettens M. The elongata mutants identify a functional Elongator complex in plants with a role in cell proliferation during organ growth. Proc Natl Acad Sci USA 2005, 102(21):7754-7759. 10.1073/pnas.0502600102, 1140448, 15894610.
47. Zhou X, Hua D, Chen Z, Zhou Z, Gong Z. Elongator mediates ABA responses, oxidative stress resistance and anthocyanin biosynthesis in Arabidopsis. Plant J 2009, 60(1):79-90. 10.1111/j.1365-313X.2009.03931.x, 19500300.
48. Barciszewska M, Dirheimer G, Keith G. The nucleotide sequence of methionine elongator tRNA from wheat germ. Biochem Biophys Res Commun 1983, 114(3):1161-1168. 10.1016/0006-291X(83)90684-8, 6615511.
49. Guillemaut P, Weil JH. The nucleotide sequence of the maize and spinach chloroplast isoleucine transfer RNA encoded in the 16 S to 23 S rDNA spacer. Nucleic Acids Res 1982, 10(5):1653-1659. 10.1093/nar/10.5.1653, 320556, 6917975.
50. Zurawski G, Bottomley W, Whitfeld PR. Junctions of the large single copy region and the inverted repeats in Spinacia oleracea and Nicotiana debneyi chloroplast DNA: sequence of the genes for tRNAHis and the ribosomal proteins S19 and L2. Nucleic Acids Res 1984, 12(16):6547-6558. 10.1093/nar/12.16.6547, 320095, 6089120.
51. Wakasugi T, Ohme M, Shinozaki K, Sugiura M. Structures of tobacco chloroplast genes for tRNAIle (CAU), tRNALeu (CAA), tRNACys (GCA), tRNASer (UGA) and tRNAThr (GGU): a compilation of tRNA genes from tobacco chloroplasts. Plant Molecular Biology 1986, 7(5):385-392.