Codon usage trend in genes associated with obesity
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ORIGINAL RESEARCH PAPER
Codon usage trend in genes associated with obesity Supriyo Chakraborty . Parvin A. Barbhuiya . Sunanda Paul . Arif Uddin . Yashmin Choudhury . Yeongseon Ahn . Yoon Shin Cho
Received: 29 February 2020 / Accepted: 29 May 2020 Springer Nature B.V. 2020
Abstract Obesity is not only a social menace but also an economic burden as it reduces productivity and increases health care cost. We used bioinformatic tools to analyze the CUB of obesity associated genes and compared with housekeeping genes (control) to explore the similarities and differences between two data sets as no work was reported yet. The mean effective number of codons (ENC) in genes associated with obesity and housekeeping gene was 50.45 and 52.03 respectively, indicating low CUB. The relative synonymous codon usage (RSCU) suggested that codons namely CTG and GTG were over-represented in both obesity and housekeeping genes while underrepresented codons were TCG, TTA, CTA, CCG, CAA, CGT, ATA, ACG, GTA and GCG in obesity genes and TCG, TTA, CCG, ATA, ACG, GTA, and
GCG in housekeeping genes. t test analysis suggested that 11 codons namely TTA (Leu), TTG (Leu), CCG (Pro), CAC (His), CAA (Gln), CAG (Gln), CGT (Arg), AGA (Arg), ATA (Ile), ATT (Ile) and GCG (Ala) were significantly differed (p \ 0.05 or p \ 0.01) between obesity and housekeeping genes. Highly significant correlation was observed between GC12 and GC3 in obesity and housekeeping genes i.e. r = 0.580** and r = 0.498** (p \ 0.01) respectively indicating the effect of directional mutation pressure present in all codon positions. Keywords Codon usage bias Obesity Directional mutation pressure GC richness
Introduction Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10529-020-02931-z) contains supplementary material, which is available to authorized users. S. Chakraborty (&) P. A. Barbhuiya S. Paul A. Uddin Y. Choudhury Department of Biotechnology, Assam University, Silchar, Assam 788011, India e-mail: [email protected] Y. Ahn Y. S. Cho (&) Department of Biomedical Science, Hallym University, Hallymdachak-gil, Chuncheon 24252, Gangwon-do, Korea e-mail: [email protected]
All amino acids (except methionine and tryptophan) are determined by 2–6 codons, known as synonymous codons, in standard genetic code. Several studies have reported that the usage of synonymous codons in mature mRNA molecules is not equal. This asymmetrical occurrence of synonymous codons for an amino acid leading to the preferential recurrence of specific codons in mRNA molecules is known as codon usage bias or CUB (Brown et al. 2009). CUB is generally believed to be the product of both mutational and selection pressures acting on genes or genomes (Grantham et al. 1980). Recent research has found that CUB affects the efficiency and accuracy of protein
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production (Akashi 1994), mRNA stability (Zhao et al. 2017) and protein folding (Fu et al. 2016). The pattern
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