http://192.168.1.40:8080/xmlui/handle/123456789/1070 Sun, 31 May 2026 14:24:32 GMT 2026-05-31T14:24:32Z http://192.168.1.40:80/xmlui/bitstream/id/937a3364-ee6c-41d5-a623-610722def1fb/tapashda.jpg http://192.168.1.40:8080/xmlui/handle/123456789/1070 http://192.168.1.40:8080/xmlui/handle/123456789/3531 Studies On The Relative Contribution Of Different Factors That Influence Codon Usage Patterns In Different Organisms Victor, Manish Prakash Codon usage bias (CUB) and mRNA structural stability are important intrinsic features of mRNA that correlate positively with mRNA expression level. However, it remains unclear whether the mRNA expression level can be regulated by adjusting these two parameters, influencing the mRNAs’ structure. Here we explored the influence of CUB and mRNA structural stability on mRNA expression levels in Saccharomyces cerevisiae, using both wild type and computationally mutated mRNAs. Although in wild type, both CUB and mRNA stability positively regulate the mRNA expression level, any deviation from natural situation breaks such equilibrium. The naturally occurring codon composition is responsible for optimizing the mRNA expression, and under such composition, the mRNA structure having highest stability is selected by nature. Codon choice which we see in the organisms have shown to evolve from its close ancestors. These changes that happen can be either synonymous or non-synonymous in nature. It has been seen that chaperones act as buffers and help in having these changes. As chaperones facilitate protein folding in the mutated proteins they enable evolution to be sustained. But, in our study we found that chaperone clients evolved slowly as compared to non-client proteins. The study was done in Escherichia coli, Saccharomyces cerevisiae, Drosophila melanogaster, Homo sapiens and Thermus aquaticus. We included T.aquaticus (extremophile) to look for any natural overexpression of chaperones that may have helped in the evolution of genes but, they too showed slower evolutionary rates. Slower evolutionary rates, tends to provide codon usage restriction which has seen to result in a smoother, rapid and accurate translations. Looking from an evolutionary perspective it seems codon usage bias may result due to accuracy requirements in translation but, also a cell can’t survive without the appropriate abundance in transcripts and proteins. We did a study in codons and anti-codons present in Saccharomyces cerevisiae. It was found that tRNA pool is affecting the synonymous codon usage choices which in turn is affecting the mRNA abundance and its stability. These stable mRNAs positively affects ribosomal density that finally takes care of the protein abundance. The work elaborately presents the influence of all these factors. Tue, 01 Jan 2019 00:00:00 GMT http://192.168.1.40:8080/xmlui/handle/123456789/3531 2019-01-01T00:00:00Z http://192.168.1.40:8080/xmlui/handle/123456789/2459 Synonymous Codon Usage in Lactococcus lactis: Mutational Bias Versus Translational Selection Gupta, S. K.; Bhattacharyya, T. K.; Ghosh, Tapash Chandra In this study codon usage bias of all experimentally known genes of Lactococcus lactis has been analyzed. Since Lactococcus lactis is an AT rich organism, it is expected to occur A and/or T at the third position of codons and detailed analysis of overall codon usage data indicates that A and/or T ending codons are predominant in this organism. However, multivariate statistical analyses based both on codon count and on relative synonymous codon usage (RSCU) detect a large number of genes, which are supposed to be highly expressed are clustered at one end of the first major axis, while majority of the putatively lowly expressed genes are clustered at the other end of the first major axis. It was observed that in the highly expressed genes C and T ending codons are significantly higher than the lowly expressed genes and also it was observed that C ending codons are predominant in the duets of highly expressed genes, whereas the T endings codons are abundant in the quartets. Abundance of C and T ending codons in the highly expressed genes suggest that, besides, compositional biases, translational selection are also operating in shaping the codon usage variation among the genes in this organism as observed in other compositionally skewed organisms. The second major axis generated by correspondence analysis on simple codon counts differentiates the genes into two distinct groups according to their hydrophobicity values, but the same analysis computed with relative synonymous codon usage values could not discriminate the genes according to the hydropathy values. This suggests that amino acid composition exerts constraints on codon usage in this organism. On the other hand the second major axis produced by correspondence analysis on RSCU values differentiates the genes into two groups according to the synonymous codon usage for cysteine residues (rarest amino acids in this organism), which is nothing but a artifactual effect induced by the RSCU values. Other factors such as length of the genes and the positions of the genes in the leading and lagging strand of replication have practically no influence in the codon usage variation among the genes in this organism. Sun, 01 Feb 2004 00:00:00 GMT http://192.168.1.40:8080/xmlui/handle/123456789/2459 2004-02-01T00:00:00Z http://192.168.1.40:8080/xmlui/handle/123456789/2429 Correlations between genomic GC levels and optimal growth temperatures: some comments Basak, S.; Mandal, S.; Ghosh, Tapash Chandra Regarding the existence of any specific correlation between optimal growth temperature and genomic GC levels, Musto et al. [FEBS Lett. 573 (2004) 73] have recently performed analysis on 20 prokaryotic families and showed that in most of the families there exists a positive correlation between these two parameters. On the basis of these results they claimed that optimal growth temperature is one of the factors that influence genomic GC composition in prokaryotes. In a subsequent article, Marashi and Ghalanbor [Biochem. Biophys. Res. Commun. 325 (2004) 381] have demonstrated that the correlation values change substantially when very few points in some of the families were excluded from the data set of Musto et al. [FEBS Lett. 573 (2004) 73]. But Marashi and Ghalanbor have not provided any reason behind this. The points excluded by Marashi and Ghalanbor are actually the outliers in the data set, which strongly affect the correlation coefficients. But the presence of outliers in large data set hardly had any effect on the correlation values. Marashi and Ghalanbor have excluded points from only those families that have small sample sizes and observed a substantial change in correlation coefficient values. Therefore, we argue that any conclusion drawn for a small sample size having outliers is always questionable. Although Music's approach is a novel one, but to make any generalization one needs to be careful about the flawlessness in the data set. DOI: 10.1016/j.bbrc.2004.12.100 Fri, 25 Feb 2005 00:00:00 GMT http://192.168.1.40:8080/xmlui/handle/123456789/2429 2005-02-25T00:00:00Z http://192.168.1.40:8080/xmlui/handle/123456789/2427 The compositional transition of vertebrate genomes: an analysis of the secondary structure of the proteins encoded by human genes D'Onofrio, G.; Ghosh, Tapash Chandra Fluctuations and increments of both C-3 and G(3) levels along the human coding sequences were investigated comparing two sets of Xenopus/human orthologous genes. The first set of genes shows minor differences of the GC(3) levels, the second shows considerable increments of the GC(3) levels in the human genes. In both data sets, the fluctuations of C-3 and G(3) levels along the coding sequences correlated with the secondary structures of the encoded proteins. The human genes that underwent the compositional transition showed a different increment of the C-3 and G(3) levels within and among the structural units of the proteins. The relative synonymous codon usage (RSCU) of several amino acids were also affected during the compositional transition, showing that there exists a correlation between RSCU and protein secondary structures in human genes. The importance of natural selection for the formation of isochore organization of the human genome has been discussed on the basis of these results. DOI: 10.1016/j.gene.2004.11.037 Mon, 17 Jan 2005 00:00:00 GMT http://192.168.1.40:8080/xmlui/handle/123456789/2427 2005-01-17T00:00:00Z