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Circular code motifs in transfer RNAs

Paper ID Volume ID Publish Year Pages File Format Full-Text
15129 1380 2013 13 PDF Available
Title
Circular code motifs in transfer RNAs
Abstract

•Identification of circular code motifs in the 5′ and/or 3′ regions of tRNAs.•Identification of a gene circular code property in the 3′ regions of tRNAs.•Search algorithm of circular code motifs.

In 1996, a trinucleotide circular code X is identified in genes of prokaryotes and eukaryotes ( Arquès and Michel, 1996). In 2012, X motifs are identified in the transfer RNA (tRNA) Phe and 16S ribosomal RNA ( Michel, 2012). A statistical analysis of X motifs in all available tRNAs of prokaryotes and eukaryotes in the genomic tRNA database (September 2012, http://lowelab.ucsc.edu/GtRNAdb/, Lowe and Eddy, 1997) is carried out here. For this purpose, a search algorithm of X motifs in a DNA sequence is developed. Two definitions allow to determine the occurrence probabilities of X motifs and the circular codes X  , X1=P(X) and X2=P2(X) (P being a circular permutation map applied on X) in a population of tRNAs. This approach identifies X motifs in the 5′ and/or 3′ regions of 16 isoaccepting tRNAs (except for the tRNAs Arg, His, Ser and Trp). The statistical analyses are performed on different and large tRNA populations according to the taxonomy (prokaryotes and eukaryotes), tRNA length and tRNA score. Finally, a circular code property observed in genes of prokaryotes and eukaryotes is identified in the 3′ regions of 19 isoaccepting tRNAs of prokaryotes and eukaryotes (except for the tRNA Leu). The identification of X motifs and a gene circular code property in tRNAs strengthens the concept proposed in Michel (2012) of a possible translation (framing) code based on a circular code.

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Keywords
Circular code motif; Search algorithm; Statistical distribution; Transfer RNA; 5′ and 3′ regions of transfer RNA
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 45, August 2013, Pages 17–29
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us