Plasticity and diversity of tRNA anticodon determinants of substrate recognition by eukaryotic A37 isopentenyltransferases

RNA

Volumn 17, Issue 10, 2011, Pages 1846-1857

  Lamichhane, Tek N ^a   Blewett, Nathan H ^a,c   Maraia, Richard J ^a,b  

^a EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

^b U S PUBLIC HEALTH SERVICE   (United States)

^c UNIVERSITY OF MICHIGAN   (United States)

Author keywords

(isopentenyl)adenosine; Anticodon loop; Codon; i 6A; tRNA modification; tRNA trp; Wobble base

Indexed keywords

DIMETHYLALLYLTRANSFERASE; GENE PRODUCT; ISOPENTENYL DIPHOSPHATE; MOD5P PROTEIN; PROTEIN; TIT1P PROTEIN; TRANSFER RNA; TRIT1 PROTEIN; TUMOR SUPPRESSOR PROTEIN; UNCLASSIFIED DRUG;

AMINO ACID SUBSTITUTION; ANTICODON; ARTICLE; CAENORHABDITIS ELEGANS; CONTROLLED STUDY; CRYSTAL STRUCTURE; ESCHERICHIA COLI; EUKARYOTE; GENE MAPPING; IN VITRO STUDY; IN VIVO STUDY; LIFESPAN; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN MODIFICATION; PROTEIN MOTIF; PROTEIN RNA BINDING; RNA SEQUENCE; RNA STRUCTURE; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE;

ALKYL AND ARYL TRANSFERASES; ANTICODON; BASE SEQUENCE; HUMANS; MUTATION; NUCLEIC ACID CONFORMATION; RNA, TRANSFER; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SCHIZOSACCHAROMYCES; SUBSTRATE SPECIFICITY;

CAENORHABDITIS ELEGANS; ESCHERICHIA COLI; EUKARYOTA; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE;

EID: 80053194776     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2628611     Document Type: Article

References (40)

1. Agris PF. 2008. Bringing order to translation: the contributions of transfer RNA anticodon-domain modifications. EMBO Rep 9: 629-635.
2. Agris PF, Vendeix FA, Graham WD. 2007. tRNA's wobble decoding of the genome: 40 years of modification. J Mol Biol 366: 1-13.
3. Begley U, Dyavaiah M, Patil A, Rooney JP, DiRenzo D, Young CM, Conklin DS, Zitomer RS, Begley TJ. 2007. Trm9-catalyzed tRNA modifications link translation to the DNA damage response. Mol Cell 28: 860-870.
4. Benko AL, Vaduva G, Martin NC, Hopper AK. 2000. Competition between a sterol biosynthetic enzyme and tRNA modification in addition to changes in the protein synthesis machinery causes altered nonsense suppression. Proc Natl Acad Sci 97: 61-66.
5. Bjork GR. 1995. Biosynthesis and function of modified nucleosides. In tRNA: Structure, biosynthesis, and function (ed. D Soll, UL Rajbhandary), pp. 165-205. ASM Press, Washington, DC.
6. 6-isopentenyladenosine at the tRNA anticodon. Biochemistry 48: 5057-5065.
7. 6A modification of tRNAs. Nucleic Acids Res doi: 10.1093/nar/gkr178.
8. Dihanich ME, Najarian D, Clark R, Gillman EC, Martin NC, Hopper AK. 1987. Isolation and characterization of MOD5, a gene required for isopentenylation of cytoplasmic and mitochondrial tRNAs of Saccharomyces cerevisiae. Mol Cell Biol 7: 177-184.
9. Egel R, Kohli J, Thuriaux P, Wolf K. 1980. Genetics of the fission yeast Schizosaccharomyces pombe. Annu Rev Genet 14: 77-108.
10. El Yacoubi B, Lyons B, Cruz Y, Reddy R, Nordin B, Agnelli F, Williamson JR, Schimmel P, Swairjo MA, de Crecy-Lagard V. 2009. The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA. Nucleic Acids Res 37: 2894-2909.
11. El Yacoubi B, Hatin I, Deutsch C, Kahveci T, Rousset JP, Iwata-Reuyl D, Murzin AG, de Crecy-Lagard V. 2011. A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification. EMBO J 30: 882-893.
12. 6-(4-hydroxyisopentenyl)adenosine distinguish between bases 3′ of the codon. J Mol Biol 218: 509-516.
13. Ser contains an intervening sequence. Cell 18: 11-26.
14. 6N (γ,γ, dimethylallyl) adenosine in transfer RNA of Escherichia coli. Biochem Biophys Res Commun 36: 435-441.
15. 6-isopentenyladenosine modification of mitochondrial and cytoplasmic tRNA. Mol Cell Biol 11: 2382-2390.
16. Holness NJ, Atfield G. 1976. The nucleotide sequence of cysteine transfer ribonucleic acid from baker's yeast. Products of complete digestion with pancreatic ribonuclease and ribonuclease T1. Biochem J 153: 437-446.
17. Huang Y, Intine RV, Mozlin A, Hasson S, Maraia RJ. 2005. Mutations in the RNA polymerase III subunit Rpc11p that decrease RNA 3′cleavage activity increase 3′-terminal oligo(U) length and La-dependent tRNA processing. Mol Cell Biol 25: 621-636.
18. Huang Y, Bayfield MA, Intine RV, Maraia RJ. 2006. Separate RNA-binding surfaces on the multifunctional La protein mediate distinguishable activities in tRNA maturation. Nat Struct Mol Biol 13: 611-618.
19. Janner F, Vogeli G, Fluri R. 1980. The antisuppressor strain sin1 of Schizosaccharomyces pombe lacks the modification isopentenyladenosine in transfer RNA. J Mol Biol 139: 207-219.
20. Jenner LB, Demeshkina N, Yusupova G, Yusupov M. 2010. Structural aspects of messenger RNA reading frame maintenance by the ribosome. Nat Struct Mol Biol 17: 555-560.
21. Johansson MJ, Bystrom AS. 2005. Transfer RNA modifications and modifying enzymes in Saccharomyces cerevisiae. In Topics in current genetics: Fine-tuning of RNA functions by modification and editing (ed. H Grosjean), pp. 88-120. Springer-Verlag, Berlin, Heidelberg.
22. Jühling F, Mörl M, Hartmann RK, Sprinzl M, Stadler PF, Pütz J. 2009. tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res 37: D159-D162.
23. Keith G, Roy A, Ebel JP, Dirheimer G. 1971. The nucleotide sequences of two tryptophane-tRNAs from brewer's yeast. FEBS Lett 17: 306-308.
24. Kohli J, Kwong T, Altruda F, Soll D, Wahl G. 1979. Characterization of a UGA-suppressing serine tRNA from Schizosaccharomyces pombe with the help of a new in vitro assay system for eukaryotic suppressor tRNAs. J Biol Chem 254: 1546-1551.
25. Kohli J, Munz P, Soll D. 1989. Informational suppression, transfer RNA, and intergenic conversion. In Molecular biology of the fission yeast (ed. A Nasim et al.), pp. 75-96. Academic Press, San Diego.
26. Lemieux J, Lakowski B, Webb A, Meng Y, Ubach A, Bussiere F, Barnes T, Hekimi S. 2001. Regulation of physiological rates in Caenorhabditis elegans by a tRNA-modifying enzyme in the mitochondria. Genetics 159: 147-157.
27. Lowe TM. 2011. A genomic tRNA database. 〈http://gtrnadbucscedu/ 〉.
28. Madison JT, Kung HK. 1967. Large oligonucleotides isolated from yeast tyrosine transfer ribonucleic acid after partial digestion with ribonuclease T1. J Biol Chem 242: 1324-1330.
29. 2-isopentenyl transferase: Dependence on the anticodon arm structure. RNA 3: 721-733.
30. Persson BC, Esberg B, Olafsson O, Bjork GR. 1994. Synthesis and function of isopentenyl adenosine derivatives in tRNA. Biochimie 76: 1152-1160.
31. Rafalski A, Kohli J, Agris P, Soll D. 1979. The nucleotide sequence of a UGA suppressor serine tRNA from Schizosaccharomyces pombe. Nucleic Acids Res 6: 2683-2695.
32. Seif E, Hallberg BM. 2009. RNA-protein mutually induced fit: Structure of Escherichia coli isopentenyl-tRNA transferase in complex with tRNA(Phe). J Biol Chem 284: 6600-6604.
33. Soderberg T, Poulter CD. 2000. Escherichia coli dimethylallyl diphosphate: tRNA dimethylallyltransferase: Essential elements for recognition of tRNA substrates within the anticodon stem-loop. Biochemistry 39: 6546-6553.
34. Soderberg T, Poulter CD. 2001. Escherichia coli dimethylallyl diphosphate: tRNA dimethylallyltransferase: Site-directed mutagenesis of highly conserved residues. Biochemistry 40: 1734-1740.
35. Spinola M, Galvan A, Pignatiello C, Conti B, Pastorino U, Nicander B, Paroni R, Dragani TA. 2005. Identification and functional characterization of the candidate tumor suppressor gene TRIT1 in human lung cancer. Oncogene 24: 5502-5509.
36. 6A. EMBO J 30: 873-881.
37. Thuriaux P, Minet M, Hofer F, Leupold U. 1976. Genetic analysis of antisuppressor mutants in the fission yeast Schizosaccharomyces pombe. Mol Gen Genet 142: 251-261.
38. Vacher J, Grosjean H, Houssier C, Buckingham RH. 1984. The effect of point mutations affecting Escherichia coli tryptophan tRNA on anticodon-anticodon interactions and on UGA suppression. J Mol Biol 177: 329-342.
39. Zachau HG, Dutting D, Feldmann H. 1966. The structures of two serine transfer ribonucleic acids. Hoppe Seylers Z Physiol Chem 347: 212-235.
40. Zhou C, Huang RH. 2008. Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism. Proc Natl Acad Sci 105: 16142-16147.