EURASIP Journal on Bioinformatics and Systems Biology
Volume 2006 (2006), Article ID 23613, 9 pages
doi:10.1155/BSB/2006/23613
Analysis of Free Energy Signals Arising from Nucleotide Hybridization Between rRNA and mRNA Sequences during Translation in Eubacteria
1Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC 27695, USA
2Department of Forestry, North Carolina State University, Raleigh, NC 27695, USA
3Department of Computer Science, North Carolina State University, Raleigh, NC 27695, USA
Received 14 April 2006; Revised 20 September 2006; Accepted 3 October 2006
Academic Editor: Yidong Chen
Copyright © 2006 Lalit Ponnala et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
A decoding algorithm is tested that mechanistically models the progressive alignments that arise as the mRNA moves past the rRNA tail during translation elongation. Each of these alignments provides an opportunity for hybridization between the single-stranded, 3′-terminal nucleotides of the 16S rRNA and the spatially accessible window of mRNA sequence, from which a free energy value can be calculated. Using this algorithm we show that a periodic, energetic pattern of frequency 1/3 is revealed. This periodic signal exists in the majority of coding regions of eubacterial genes, but not in the non-coding regions encoding the 16S and 23S rRNAs. Signal analysis reveals that the population of coding regions of each bacterial species has a mean phase that is correlated in a statistically significant way with species (G + C) content. These results suggest that the periodic signal could function as a synchronization signal for the maintenance of reading frame and that codon usage provides a mechanism for manipulation of signal phase.