On the possible role of trna base modifications in the evolution of codon usage: Queuosine and Drosophila

Journal of Molecular Evolution

Volumn 70, Issue 4, 2010, Pages 339-345

  Chiari, Ylenia ^a,b   Dion, Kirstin ^a   Colborn, James ^a,c,d   Parmakelis, Aristeidis ^a,e   Powel, Jeffrey R ^a  

^a YALE UNIVERSITY   (United States)

^b INSTITUT DES SCIENCES DE L EVOLUTION   (France)

^c CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

^d Idaho Department of Health and Welfare   (United States)

^e UNIVERSITY OF ATHENS   (Greece)

Author keywords

Codon usage bias; Development; Drosophila willistoni; Evolution; qRT PCR; Queuosine; RpL32

Indexed keywords

DROSOPHILA PROTEIN; GUANINE; QUEUOSINE; RIBOSOME PROTEIN; RPL32 PROTEIN, DROSOPHILA; TRANSFER RNA;

ANALYSIS OF VARIANCE; ANIMAL; ARTICLE; CODON; DROSOPHILA; FEMALE; GENETICS; MALE; METABOLISM; MOLECULAR EVOLUTION; PHYSIOLOGY;

ANALYSIS OF VARIANCE; ANIMALS; CODON; DROSOPHILA; DROSOPHILA PROTEINS; EVOLUTION, MOLECULAR; FEMALE; GUANINE; MALE; NUCLEOSIDE Q; RIBOSOMAL PROTEINS; RNA, TRANSFER;

DROSOPHILA MELANOGASTER; DROSOPHILA PSEUDOOBSCURA; DROSOPHILA WILLISTONI;

EID: 77954458981     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-010-9329-z     Document Type: Article

References (33)

1. Alexondrov A, Chernyokov I, Gu W, Hiley SL, Hughes TR, Grayhack EJ, Phizicky EM (2006) Rapid tRNA decay can result from lack of nonessential modifications. Mol Cell 21:87-96
2. Anderson C, Carew EA, Powell JR (1993) Evolution of the Adh locus in the Drosophila willistoni group: the loss of an intron, and shift in codon usage. Mol Biol Evol 10:605-618
3. Bathia P, Taylor WR, Greenberg AH, Wright JA (1994) Comparison of glyceraldehydes-3-phosphate dehydrogenase and 28S-ribo-somal RNA gene expression as RNA loading controls for Northern Blot analysis of cell lines of varying malignant potential. Anal Biochem 216:223-226
4. Borek E, Baliga BS, Gehrke CW, Kuo CW, Belman S, Troll W, Waalkes TP (1977) High turnover rate of transfer RNA in tumor tissue. Cancer Res 37:3362-3366
5. Bustin SA, Nolan T (2004) Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction. J Biomol Tech 15:155-166
6. De Leeuw WJF, Slagboom PE, Vijg J (1989) Quantitative comparison of mRNA levels in mammalian tissues: 28S ribosomal RNA level as an accurate internal control. Nucleic Acids Res 17:10137-10138
7. Drosophila 12 Genomes Consortium (2007) Evolution of genes and genomes in the context of the Drosophila phylogeny. Nature 450:203-218
8. Engelke DR, Hopper AK (2006) Modified view of tRNA: stability amid sequence diversity. Mol Cell 21:144-145
9. Harada E, Nishimura S (1972) Possible anticodon sequences of tRNAHis, tRNAAsn, and tRNAAsp from Escherichia coli B. Universial presence of nulceoside Q in the first position of the anticodon of three transfer ribonulceic acids. Biochemistry 11:301-308
10. Higgs PF, Ran W (2008) Coevolution of codon usage and tRNA leads to alternative stable states of biased codon usage. Mol Biol Evol 25:2279-2291
11. Hosbach HA, Kubli E (1979) Transfer RNA in Aging Drosophila: II. Isoaccptor patterns. Mech Ageing Develop 10:141-149 (Pubitemid 9129390)
12. Huggett J, Dheda K, Bustin S, Zumla A (2005) Real-time RT-PCR normalization; strategies and considerations. Genes Immun 6:279-284
13. Ikemura T (1981) Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in the protein genes: a proposal for a synonymous codon choice that is optimal for E. coli translational system. J Mol Biol 151:389-409
14. Ikemura T (1982) Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes: differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs. J Mol Biol 158:573-597
15. Ikemura T (1992) Correlation between codon usage and tRNA content in microorganisms. In: Hatfield DL, Lee BJ, Pirtle RM (eds) Transfer RNA in protein synthesis. CRC Press, Boca Raton, pp 87-111
16. Karnahl U, Wasternack C (1992) Half-fife of cytoplasmic rRNA and tRNA of plastid rRNA of uridine nucleotides in heterotrophically and photoorganotrophically grown cells of Euglena gracilis and its apoplastic mutant W3Bul. Int J Biochem 24:493-497
17. Kim B-R, Nam H-Y, Kim S-U, Chang Y-J (2003) Normalization of reverse transcription quantitative-PCR with housekeeping genes in rice. Biotechnol Lett 25:1869-1872
18. Klemen F, Klambt D (1974) Half-life of sRNA from primary roots of Zea mays. A contribution to the cytokinin production. Physiol Plant 31:186-188
19. Meier F, Suter B, Grosjean H, Keith G, Kubli E (1985) Queuosine modification of the wobble base in tRNAHis influences in vivo decoding properties. EMBO J 4:823-836
20. Moriyama EN, Powell JR (1997) Codon usage bias and tRNA abundance in Drosophila. J Mol Evol 45:514-523
21. Morris RC, Elliott MS (2001) Queuosine modification of tRNA: a case for convergent evolution. Mol Genet Metabolism 74:147-159
22. Okada N, Noguchi S, Dasai H, Shindo-Okada N, Ohgi T, Goto T, Nishimura S (1979) Novel mechanism of posttranscriptional modification of tRNA. Insertion of bases of Q precursors into tRNA by a specific tRNA transglycosylase reaction. J Biol Chem 254:3067-3073
23. Owenby RK, Stulberg MP, Jacobson KB (1979) Alteration of the Q family of transfer RNAs in adult Drosophila melanogaster as a function of age, nutrition, and genotype. Mech Ageing Dev 11:91-103
24. Powell JR, Moriyama EN (1997) Evolution of codon usage bias in Drosophila. Proc Natl Acad Sci USA 94:7784-7790
25. Powell JR, Sezzi E, Moriyama EN, Gleason JM, Caccone A (2003) Analysis of a shift in codon usage in Drosophila. J Mol Evol 57:S214-S225
26. Shields DC, Sharp PM, Higgins DG, Wright F (1988) "Silent'' sites in Drosophila are not neutral: evidence of selection among synonymous codons. Mol Biol Evol 5:704-716
27. Siard TJ, Jacobson KB, Farkas WR (1991) Queuine metabolism and cadmium toxicity in Drosophila melanogaster. Biofactor 3:41-47
28. The R Development Core Team (2008) R: A Language and Environment for Statistical Computing. Version 2.7.
29. Urbonavicius J, Qian Q, Durand JMB, Hagervall RG, Björk GR (2001) Improvement of reading frame maintenance is a common function for several tRNA modifications. EMBO J 20:4863-4873
30. Vandesompele J, de Preter K, Pattyn F, Poppe B, van Roy N, de Paepe, Speleman F (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3:34
31. Vicario S, Moriyama EN, Powell JR (2007) Codon usage in twelve species of Drosophila. BMC Evol Biol 7:226
32. Vicario S, Mason CE, White KP, Powell JR (2008) Developmental stage and level of codon usage bias in Drososophila. Mol Biol Evol 25:2269-2277
33. White BN, Tener GN, Holden J, Suzuki DT (1973) Analysis of tRNAs during the development of Drosophila. Develop Biol 33:185-195