RESUMEN
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.
RESUMEN
A comparative genomic analysis of three species of the soil bacterium Arthrobacter was undertaken with specific emphasis on genes involved in important and core energy metabolism pathways like glycolysis and amino acid metabolism. During the course of this study, it was revealed that codon bias of a particular species, namely Arthrobacter aurescens TC1, is significantly lower than that of the other two species A. chlorophenolicus A6 and Arthrobacter sp. FB24. The codon bias was also found to be negatively correlated with gene expression level which is determined by computing codon adaptation index of the genes. Uniformity in codon usage pattern among three species is evident in terms of genes which has high codon bias and multifunctional nature. Further, it was observed that this trend is present amongst the genes of important metabolic pathways, such as glycolysis and amino acid metabolism. The evolutionary divergence of the pathway gene sequences was calculated and was found to be equivalent in nature in the case of Arthrobacter sp. FB24 and Arthrobacter chlorophenolicus A6, but turned out to be dissimilar in the case of Arthrobacter aurescens TC1. A strong correlation between synonymous substitution rate and effective codon number or Nc was also observed. These observations clearly point out that the genes having low bias, in Arthrobacter aurescens TC1, and even of those that are part of highly conserved metabolic pathways like glycolysis and amino acid ensemble pathways have undergone a different type of evolution and might be subjected to positive selection pressure in comparison with Arthrobacter sp. FB24 and Arthrobacter chlorophenolicus A6.
RESUMEN
UNLABELLED: Bamboo, the "Green Gold", included in the non-timber forest products has both ecological and economic importance. Here is an attempt to describe a database named "Bambooinfoline" , which provides enumeration of the different species of bamboos found in North Bengal, with special emphasis on taxonomy, edible properties, chemical constituents, morphological features along with tissue culture specifications, which in turn benefits of scientific community. AVAILABILITY: The database is freely available at http://www.bamboodb.ind.in/
