CODON CONTEXT ANALYSIS OF METHANOCALDOCOCCUS JANNASCHII

Verma D.K.1, Gokhale M.S.2
1Department of Biotechnology and Bioinformatics, Padmashree Dr. D Y Patil University, Navi Mumbai, 400614, India
2Department of Biotechnology and Bioinformatics, Padmashree Dr. D Y Patil University, Navi Mumbai, 400614, India

Received : -     Accepted : -     Published : 21-12-2009
Volume : 1     Issue : 2       Pages : 65 - 69
Int J Bioinformatics Res 1.2 (2009):65-69
DOI : http://dx.doi.org/10.9735/0975-3087.1.2.65-69

Keywords : Codon Context, Evolution, tRNA, mRNA, Methanocaldococcus jannaschii, amino acids
Conflict of Interest : None declared

Cite - MLA : Verma D.K. and Gokhale M.S. "CODON CONTEXT ANALYSIS OF METHANOCALDOCOCCUS JANNASCHII." International Journal of Bioinformatics Research 1.2 (2009):65-69. http://dx.doi.org/10.9735/0975-3087.1.2.65-69

Cite - APA : Verma D.K., Gokhale M.S. (2009). CODON CONTEXT ANALYSIS OF METHANOCALDOCOCCUS JANNASCHII. International Journal of Bioinformatics Research, 1 (2), 65-69. http://dx.doi.org/10.9735/0975-3087.1.2.65-69

Cite - Chicago : Verma D.K. and Gokhale M.S. "CODON CONTEXT ANALYSIS OF METHANOCALDOCOCCUS JANNASCHII." International Journal of Bioinformatics Research 1, no. 2 (2009):65-69. http://dx.doi.org/10.9735/0975-3087.1.2.65-69

Copyright : © 2009, Verma D.K. and Gokhale M.S., Published by Bioinfo Publications. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution and reproduction in any medium, provided the original author and source are credited.

Abstract

Evolution has caused major changes as well as minor changes in the mRNA sequences. Changes in the nucleotides can be result of some selectional pressure leading changes in the codon or due to influences of neighboring codon on selected possible synonymous codon. This research generally analyze the concept of evolutionary constraints on the biased selection of a particular codonpair present in mRNA to be influenced by the 5’-3’ tRNA anti-codon and its neighboring triplet explaining reason for the lesser amount of tRNA in a particular genome as compared to that of the standard genetic code available. The occurrence of one codon next to another has co-evolved with the structure of tRNA and lead to accommodate maximum amount of genetic code to be translated by limited number of tRNA.

References

[1] Irwin B., Heck J.D., Hatfield G.W. (1995) J. Biol.Chem., 270, 22801–22806  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[2] Berg O.G., Silva P.J. (1997) Nucleic Acids 25(7), 1397-1404  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[3] Fedorov A., Saxonov S., Gilbert W. (2002) Nucleic Acids 30(5), 1192-1197  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[4] Boycheva S., Chkodrov G., Ivanov I. ( 2003) Bioinformatics 19(8), 987-998  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[5] Moura G., Pinheiro M., Silva R., Miranda I., Afreixo V., Dias G., Freitas A.,Oliveira J.L., Santos M.A. (2005) Genome Biol 6(3), R28  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[6] Moura G., Pinheiro M., Arrais J., Gomes A.C., Carreto L., Freitas A.,Oliveira J.L., Santos M.A. (2007) PLoS ONE 2(9), 847  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[7] Murgola E.J., Pagel F.T., Hijazi K.A. (1984) J Mol Biol, 175(1), 19-27.  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[8] Bossi L., Ruth J.R. (1980) Nature, 286(5769), 123-127  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[9] Miller J.H., Albertini A.M. (1983) J Mol Biol, 164(1), 59-71  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[10] Kopelowitz J., Hampe C., Goldman R., Reches M., Engelberg-Kulka (1992) J Mol Biol, 225(2), 261-269  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[11] Stormo G.D., Schneider T.D., Gold L. (1986) Nucleic Acids Res, 14(16), 6661- 6679  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[12] Curran J.F., Poole E.S., Tate W.P., Gross B.L. (1995) Nucleic Acids Res, 23(20), 4104-4108  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[13] Shah A.A., Giddings M.C., Gesteland R.F., Atkins J.F., Ivanov I.P. (2002) Bioinformatics 18, 1046–1053  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[14] Murgola E.J., Pagel F.T., Hijazi K.A. (1984) J Mol Biol 175, 19–27  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[15] Tork S., Hatin I., Rousset J.P., Fabret C. (2004) Nucleic Acids Res 32, 415–421  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[16] Rheinberger H.J., Sternbach H., Nierhaus K.H. (1981) Proc Natl Acad Sci U S A. 1981 Sep; 78(9), 5310-5314  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[17] Yi Lu and Stephen Freeland (2006) Genome Biology 7, 102  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[18] Margaret E. Saks and John S. Conery. (2007) RNA 13, 651-660  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus