Statistical analysis of pentose phosphate pathway genes from eubacteria and eukarya reveals translational selection as a major force in shaping codon usage pattern



Ayon Pal1, Subhasis Mukhopadhyay2 & Asim Kumar Bothra3*



1Department of Botany, Raiganj College (University College) P.O.- Raiganj, Dist.- Uttar Dinajpur, PIN-733134, West Bengal, India; 2Bioinformatics Centre, Department of Biophysics, Molecular Biology and Bioinformatics University of Calcutta, 92 APC Road, Kolkata-700009, West Bengal, India; 3Cheminformatics Bioinformatics Lab, Department of Chemistry, Raiganj College (University College) P.O.- Raiganj, Dist.- Uttar Dinajpur, PIN-733134, West Bengal, India


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Received March 26, 2013; Accepted March 27, 2013; Published April 13, 2013



Comparative analysis of metabolic pathways among widely diverse species provides an excellent opportunity to extract information about the functional relation of organisms and pentose phosphate pathway exemplifies one such pathway. A comparative codon usage analysis of the pentose phosphate pathway genes of a diverse group of organisms representing different niches and the related factors affecting codon usage with special reference to the major forces influencing codon usage patterns was carried out. It was observed that organism specific codon usage bias percolates into vital metabolic pathway genes irrespective of their near universality. A clear distinction in the codon usage pattern of gram positive and gram negative bacteria, which is a major classification criterion for bacteria, in terms of pentose phosphate pathway was an important observation of this study. The codon utilization scheme in all the organisms indicates the presence of translation selection as a major force in shaping codon usage. Another key observation was the segregation of the H. sapiens genes as a separate cluster by correspondence analysis, which is primarily attributed to the different codon usage pattern in this genus along with its longer gene lengths. We have also analyzed the amino acid distribution comparison of transketolase protein primary structures among all the organisms and found that there is a certain degree of predictability in the composition profile except in A. fumigatus and H. sapiens, where few exceptions are prominent. In A. fumigatus, a human pathogen responsible for invasive aspergillosis, a significantly different codon usage pattern, which finally translated into its amino acid composition model portraying a unique profile in a key pentose phosphate pathway enzyme transketolase was observed.



Metabolic pathway, codon usage, pentose phosphate pathway, Nc, CAI, transketolase.



Pal et al. Bioinformation 9(7): 349-356 (2013)


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P Kangueane






Biomedical Informatics



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