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J Biomol Struct Dyn. 2008 Dec;26(3):321-8.

Nucleotide triplet based molecular phylogeny of class I and class II aminoacyl t-RNA synthetase in three domain of life process: bacteria, archaea, and eukarya.

Author information

  • 1Cheminformatics Bioinformatics Laboratory, Department of Chemistry, Raiganj College (University College), Raiganj-733134, Uttar Dinajpur, West Bengal, India.

Abstract

The aminoacyl-tRNA synthetases are one of the major protein components in the translation machinery. These essential proteins are found in all forms of life and are responsible for charging their cognate tRNAs with the correct amino acid. These important enzymes have been the subject of intense scientific inquiry for nearly half a century, but their complete evolutionary history has yet to emerge. Amino acids sequence based phylogeny has some limitation due to very low sequence similarity amongst the different tRNA synthetases and structure based phylogeny has also its limitation. In our study, tRNA nucleotide sequences of E. coli K12 (Bacteria), Saccharomyces cerevisiae (Eukarya), Thermococcus kodakaraensis KOD1, and Archaeoglobus fulgidus DSM 4304 (Archaea) were used for phylogenetic analysis. Our results complement the observation with the earlier studies based on multiple sequence alignment and structural alignment. We observed that relationship between archaeal tRNA synthetases are different that of bacteria and eucarya. Violation of Class rule of LysRS is observed here also. The uniqueness of this method is that it does not employ sequence alignment of complete nucleotide sequence of the corresponding gene.

PMID:
18808198
[PubMed - indexed for MEDLINE]

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