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Research Articles

Favored and less favored codon–anticodon duplexes arising from the GC codon family box encoding for alanine: some computational perspectives

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Pages 1029-1049 | Received 10 Dec 2016, Accepted 12 Mar 2017, Published online: 10 Apr 2017

References

  • Aduri, R., Psciuk, B. T., Saro, P., Taniga, H., Schlegel, H. B., & SantaLucia, Jr., J. (2007). AMBER force field parameters for the naturally occurring modified nucleosides in RNA. Journal of Chemical Theory and Computation, 3, 1464–1475.10.1021/ct600329w
  • Agris, P. F. (1991). Wobble position modified nucleosides evolved to select transfer RNA codon recognition: A modified-wobble hypothesis. Biochimie, 73, 1345–1349.10.1016/0300-9084(91)90163-U
  • Andachi, Y., Yamao, F., Muto, A., & Osawa, S. (1989). Codon recognition patterns as deduced from sequences of the complete set of transfer RNA species in Mycoplasma capricolum. Journal of Molecular Biology, 209, 37–54.10.1016/0022-2836(89)90168-X
  • Arnott, S. (1970). The geometry of nucleic acids. Progress in Biophysics and Molecular Biology, 21, 265–319.10.1016/0079-6107(70)90027-1
  • Arnott, S., Hukins, D. W. L., & Dover, S. D. (1972). Optimised parameters for RNA double-helices. Biochemical and Biophysical Research Communications, 48, 1392–1399.10.1016/0006-291X(72)90867-4
  • Bjork, G. R., Ericson, J. U., Gustafsson, C. E. D., Hagervall, T. G., Jonsson, Y. H., & Wikstrom, P. M. (1987). Transfer RNA modification. Annual Review of Biochemistry, 56, 263–285.10.1146/annurev.bi.56.070187.001403
  • Bunn, C. C., & Mathews, B. M. (1987). Two human tRNA(Ala) families are recognized by autoantibodies in polymyositis sera. Molecular Biology and Medicine, 4, 21–36.
  • Case, D. A., Darden, T. A., Cheatham, T. E., III, Simmerling, C. L., Wang, J., Duke, R. E., … Kollman, P. A. (2008). AMBER 10. San Francisco, CA: University of California.
  • Chithambaram, S., Prabhakaran, R., & Xia, X. (2014a). The effect of mutation and selection on codon adaptation in Escherichia coli bacteriophage. Genetics, 197, 301–315.10.1534/genetics.114.162842
  • Chithambaram, S., Prabhakaran, R., & Xia, X. (2014b). Differential codon adaptation between dsDNA and ssDNA phages in Escherichia coli. Molecular Biology and Evolution, 31, 1606–1617.10.1093/molbev/msu087
  • Claesson, C., Lustig, F., Borén, T., Simonsson, C., Barciszewska, M., & Lagerkvist, U. (1995). Glycine codon discrimination and the nucleotide in position 32 of the anticodon loop. Journal of Molecular Biology, 247, 191–196.10.1006/jmbi.1994.0132
  • Corfield, P. W. R., Hunter, W. N., Brown, T., Robinson, P., & Kennard, O. (1987). Inosine.adenine base pairs in a B-DNA duplex. Nucleic Acids Research, 15, 7935–7949.10.1093/nar/15.19.7935
  • Crick, F. H. C. (1966). Codon—anticodon pairing: The wobble hypothesis. Journal of Molecular Biology, 19, 548–555.10.1016/S0022-2836(66)80022-0
  • Das, G., & Lyngdoh, R. H. D. (2014). Configuration of wobble base pairs having pyrimidines as anticodon wobble bases: significance for codon degeneracy. Journal of Biomolecular Structure and Dynamics, 32, 1500–1520.10.1080/07391102.2013.824822
  • Das, G., & Lyngdoh, R. H. D. (2008). Can configuration of solitary wobble base pairs determine the specificity and degeneracy of the genetic code? Clues from molecular orbital modelling studies. Journal of Molecular Structure: THEOCHEM, 851, 319–334.10.1016/j.theochem.2007.11.027
  • Das, G., & Lyngdoh, R. H. D. (2012). Role of wobble base pair geometry for codon degeneracy: purine-type bases at the anticodon wobble position. Journal of Molecular Modeling, 18, 3805–3820.10.1007/s00894-012-1385-4
  • Daviter, T., Gromadski, K. B., & Rodnina, M. V. (2006). The ribosome’s response to codon–anticodon mismatches. Biochimie, 88, 1001–1011.10.1016/j.biochi.2006.04.013
  • Dickerson, R. E. (1989). Definitions and nomenclature of nucleic acid structure components. Nucleic Acids Research, 17, 1797–1803.10.1093/nar/17.5.1797
  • Grosjean, H., & Westhof, E. (2016). An integrated, structure- and energy-based view of the genetic code. Nucleic Acids Research, 44, 8020–8040.10.1093/nar/gkw608
  • Gu, X.-R., Nicoghosian, K., Cedergren, R. J., & Wong, J. T.-F. (1983). Sequences of halobacterial tRNAs and the paucity of U in the first position of their anticodons. Nucleic Acids Research, 11, 5433–5442.10.1093/nar/11.16.5433
  • Gupta, R. (1984). Halobacterium volcanii tRNAs identification of 41 tRNAs covering all amino acids, and the sequences of 33 class I tRNAs. Journal of Biological Chemistry, 259, 9461–9471.
  • Hani, J., & Feldmann, H. (1998). tRNA genes and retroelements in the yeast genome. Nucleic Acids Research, 26, 689–696.10.1093/nar/26.3.689
  • Heckman, J. E., Sarnoff, J., Alzner-DeWeerd, B., Yin, S., & RajBhandary, U. L. (1980). Novel features in the genetic code and codon reading patterns in Neurospora crassa mitochondria based on sequences of six mitochondrial tRNAs. Proceedings of the National Academy of Sciences, 77, 3159–3163.10.1073/pnas.77.6.3159
  • Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., & Simmerling, C. (2006). Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins: Structure, Function, and Bioinformatics, 65, 712–725.10.1002/prot.v65:3
  • Johansson, M. J. O., Esberg, A., Huang, B., Bjork, G. R., & Bystrom, A. S. (2008). Eukaryotic wobble uridine modifications promote a functionally redundant decoding system. Molecular and Cellular Biology, 28, 3301–3312.10.1128/MCB.01542-07
  • Kothe, U., & Rodnina, M. V. (2007). Codon reading by tRNAAla with modified uridine in the wobble position. Molecular Cell, 25, 167–174.10.1016/j.molcel.2006.11.014
  • Lavery, R., & Sklenar, H. (1988). The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. Journal of Biomolecular Structure and Dynamics, 6, 63–91.10.1080/07391102.1988.10506483
  • Ledoux, S., Olejniczak, M., & Uhlenbeck, O. C. (2009). A sequence element that tunes Escherichia coli tRNAAlaGGC to ensure accurate decoding. Nature Structural & Molecular Biology, 16, 359–364.10.1038/nsmb.1581
  • Leonard, G. A., Booth, E. D., Hunter, W. N., & Brown, T. (1992). The conformational variability of an adenosine-inosine base-pair in a synthetic DNA dodecamer. Nucleic Acids Research, 20, 4753–4759.10.1093/nar/20.18.4753
  • Lund, E. & Dahlberg, J. E. (1977). Spacer transfer RNAs in ribosomal RNA transcripts of E. coli: Processing of 30S ribosomal RNA in vitro. Cell, 11, 247–262.10.1016/0092-8674(77)90042-3
  • Mangang, S. U., & Lyngdoh, R. H. D. (2001). Wobble base pairing in codon-anticodon interactions: A theoretical modelling studies. Indian Journal of Biochemistry and Biophysics, 38, 115–119.
  • Mims, B. H., Prather, N. E., & Murgola, E. J. (1985). Isolation and nucleotide sequence analysis of tRNAGGC from Escherichia coli K-12. Journal of Bacteriology, 162, 837–839.
  • Morales, J. L., & Nocedal, J. (2000). Automatic preconditioning by limited memory quasi-newton updating. SIAM Journal on Optimization, 10, 1079–1096.10.1137/S1052623497327854
  • Murao, K., Saneyoshi, M., Harada, F., & Nishimura, S. (1970). Uridin-5-oxy acetic acid: A new minor constituent from E. coli valine transfer RNA I. Biochemical and Biophysical Research Communications, 38, 657–662.10.1016/0006-291X(70)90631-5
  • Murao, K., Hasegawa, T., & Ishikura, H. (1976). 5-Methoxyuridine a new minor constituent located in the first position of the anticodon of tRNAAla, tRNAThr, and tRNAVal from Bacillus subtilis. Nucleic Acids Research, 3, 2851–2860.10.1093/nar/3.10.2851
  • Murphy, F. V. I. V., & Ramakrishnan, V. (2004). Structure of a purine-purine wobble base-pair in the decoding center of the ribosome. Nature Structural & Molecular Biology, 11, 1251–1252.10.1038/nsmb866
  • Nasvall, S. J., Chen, P., & Bjork, G. R. (2007). The wobble hypothesis revisited: Uridine-5-oxyacetic acid is critical for reading of G-ending codons. RNA, 13, 2151–2164.10.1261/rna.731007
  • Ogle, J. M., Murphy, F. V. I. V., Tarry, M., & Ramakrishnan, V. (2002). Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell, 111, 721–732.10.1016/S0092-8674(02)01086-3
  • Ogle, J. M., & Ramakrishnan, V. (2005). Structural insights into translational fidelity. Annual Review of Biochemistry, 74, 129–177.10.1146/annurev.biochem.74.061903.155440
  • Penswick, J. R., Martin, R., & Dirheimer, G. (1975). Evidence supporting a revised sequence for yeast alanine tRNA. FEBS Letters, 50, 28–31.10.1016/0014-5793(75)81033-7
  • Percudani, R., Pavesi, A., & Ottonello, S. (1997). Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae. Journal of Molecular Biology, 268, 322–330.10.1006/jmbi.1997.0942
  • Phelps, S. S., Malkiewicz, A., Agris, P. F., & Joseph, S. (2004). Modified nucleotides in tRNALys and tRNAVal are important for translocation. Journal of Molecular Biology, 338, 439–444.10.1016/j.jmb.2004.02.070
  • Prabhakaran, R., Chithambaram, S., & Xia, X. (2015). Escherichia coli and Staphylococcus phages: effect of translation initiation efficiency on differential codon adaptation mediated by virulent and temperate lifestyles. Journal of General Virology, 96, 1169–1179.10.1099/vir.0.000050
  • Rozov, A., Demeshkina, N., Khusainov, I., Westhof, E., Yusupov, M., & Yusupova, G. (2016). Novel base- pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code. Nature Communications, 7, 10457–10466.10.1038/ncomms10457
  • Rozov, A., Demeshkina, N., Westhof, E., Yusupov, M., & Yusupova, G. (2015). Structural insights into the translational infidelity mechanism. Nature Communications, 6, 7251–7259.10.1038/ncomms8251
  • Rozov, A., Westhof, E., Yusupov, M., & Yusupova, G. (2016). The ribosome prohibits the G•U wobble geometry at the first position of the codon-anticodon helix. Nucleic Acids Research, 44, 6434–6441.
  • Sadlej-Sosnowska, N. (2009). Quantum chemical considerations on degeneracy of the genetic code: Anticodon-codon wobble base pairing. Journal of Molecular Structure: THEOCHEM, 913, 270–276.10.1016/j.theochem.2009.08.006
  • Saenger, W. (1984). Principles of nucleic acid structure. New York, NY: Springer-Verlag. doi:10.1007/978-1-4612-5190-3
  • Sakai, Y., Miyauchi, K., Kimura, S., & Suzuki, T. (2016). Biogenesis and growth phase-dependent alteration of 5-methoxycarbonylmethoxyuridine in tRNA anticodons. Nucleic Acids Research, 44, 509–523.10.1093/nar/gkv1470
  • Sakore, T. D., & Sobell, H. M. (1969). Crystal and molecular structure of a hydrogen-bonded complex containing adenine and hypoxanthine derivatives: 9-Ethyl-8-bromoadenine-9-ethyl-8-bromohypoxanthine. Journal of Molecular Biology, 43, 77–87.10.1016/0022-2836(69)90080-1
  • Samuelsson, T., Guindy, Y. S., Lustig, F., Boren, T., & Lagerkvist, U. (1987). Apparent lack of discrimination in the reading of certain codons in Mycoplasma mycoides. Proceedings of the National Academy of Sciences, 84, 3166–3170.10.1073/pnas.84.10.3166
  • Sprague, K. U., Hagenbüchie, O., & Zuniga, M. C. (1977). The nucleotide sequence of two silk gland alanine tRNAs: Implications for fibroin synthesis and for initiator tRNA structure. Cell, 11, 561–570.10.1016/0092-8674(77)90074-5
  • Takemura, S., & Ogawa, K. (1973). The primary structure of alanine transfer ribonucleic Acid 1 from Torulopsis utilis II. Partial digestion with ribonuclease T and derivation of the complete sequence. Journal of Biochemistry, 74, 323–333.
  • Tsui, V., & Case, D. A. (2000). Molecular dynamics simulations of nucleic acids with a generalized born solvation model. Journal of the American Chemical Society, 122, 2489–2498.10.1021/ja9939385
  • Wei, Y., & Xia, X. (2017). The role of +4u as an extended translation termination signal in bacteria. Genetics, 205, 539–549.10.1534/genetics.116.193961
  • Wei, Y., Wang, J., & Xia, X. (2016). Coevolution between stop codon usage and release factors in bacterial species. Molecular Biology and Evolution, 33, 2357–2367.10.1093/molbev/msw107
  • Williams, R. J., Nagel, W., Roe, B., & Dudock, B. (1974). Primary structure of E. coli alanine transfer RNA: Relation to the yeast phenylalanyl tRNA synthetase recognition site. Biochemical and Biophysical Research Communications, 60, 1215–1221.10.1016/0006-291X(74)90328-3
  • Xia, X. (2008). The cost of wobble translation in fungal mitochondrial genomes: integration of two traditional hypotheses. BMC Evolutionary Biology, 8, 211–221.10.1186/1471-2148-8-211
  • Yarus, M. (1982). Translational efficiency of transfer RNA’s: uses of an extended anticodon. Science, 218, 646–652.10.1126/science.6753149
  • Yarus, M., & Smith, D. (1995). tRNA on the ribosome: A waggle theory. In D. Soll & U. L. RajBhandary (Eds.), tRNA (pp. 443–469). Washington, DC: American Society of Microbiology.10.1128/9781555818333
  • Yokoyama, S., Watanabe, T., Murao, K., Ishikura, H., Yamaizumi, Z., Nishimura, S., & Miyazawa, T. (1985). Molecular mechanism of codon recognition by tRNA species with modified uridine in the first position of the anticodon. Proceedings of the National Academy of Sciences, 82, 4905–4909.10.1073/pnas.82.15.4905

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