A Crosstalk on Codon Usage in Genes Associated with Leukemia
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A Crosstalk on Codon Usage in Genes Associated with Leukemia Supriyo Chakraborty1 · Durbba Nath1 · Sunanda Paul1 · Yashmin Choudhury1 · Yeongseon Ahn2 · Yoon Shin Cho2 · Arif Uddin3 Received: 27 March 2020 / Accepted: 18 September 2020 © Springer Science+Business Media, LLC, part of Springer Nature 2020
Abstract Leukemia is the outcome of aggregation of damaged white blood cells. Several genes were reported to be associated with the pathogenesis of leukemia. These genes were computationally analyzed to decipher their codon usage bias (CUB) and to identify the prime factors influencing the codon usage profile as no work was reported yet. The mean values of synonymous codon usage order (SCUO) param‑ eter indicated low CUB of the genes. Significant positive association of SCUO with overall GC and positional GCs might signal the presence of mutational pressure. However, neutrality plot suggested the dominant role of natural selection across the genes. Along with natural selection, the role of mutation pressure was also promi‑ nent and that might be responsible for lower CUB (SCUO = 0.19) of genes. Low translational speed might permit accuracy in the process. A strong inverse relation‑ ship of translational rate was observed with CUB of genes and folding energy. Keywords Codon usage bias · Leukemia · Directional mutational pressure · Translational speed · Folding energy
Introduction In living cells, the intrinsic feature of redundant genetic code is not engaged impar‑ tially, so the counts of specific synonymous codons diverge from expected codon usage (Peng et al. 2018; Xiang et al. 2015). The phenomenon of codon usage bias (CUB) is a typical feature of the protein coding sequences and appears to be distinct * Supriyo Chakraborty [email protected] 1
Department of Biotechnology, Assam University, Silchar, Assam 788011, India
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Department of Biomedical Science, Hallym University, Hallymdachak‑gil, Chuncheon 24252, Gangwon‑do, Korea
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Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi, Assam 788150, India
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Biochemical Genetics
for each species. The CUB is the consequence of combinatorial action of mutation and natural selection. Since genetic code is not universal, therefore acclimatization of specific codons is a befitting choice to avoid divergent genetic code (Xiang et al. 2015). The nucleotide frameworks of mammalian genes are devised under muta‑ tional pressure (Sharp et al. 1993), although natural selection directed genetic com‑ position was even reported (Chamary and Hurst 2004; Duan and Antezana 2003; Smith and Eyre-Walker 2001). Errors in genome replications due to mutational pressure yield GC to AT changes that frame the entire base composition (Shack‑ elton et al. 2006). According to mutation selection drift balance model, selection pressure stringently opts for the frequent codons rather than uncommon codons to maintain the quality of protein production (Bulmer 1991). The rare/un-preferred codons appear in clusters in
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