Gaining Insights into the Codon Usage Patterns of TP53 Gene across Eight Mammalian Species

Mazumder, Tarikul Huda; Chakraborty, Supriyo

Previously, several studies were conducted on synonymous codon usage bias in a wide variety of organisms including prokaryotes and eukaryotes [10] [11] [12] [13] [14] [15] [16] , and till date in many organisms the codon usage patterns have been interpreted for diverse reasons. Many genomic factors such as gene length, GC-content, recombination rate, gene expression level, or modulation in the genetic code are associated with CUB in different organisms [17] [18] [19] [20] [21] . In general, compositional constraints under natural selection or mutation pressure are considered as major factors in the codon usage variation among different organisms [8, [22] [23] [24] [25] . Moreover, studies revealed that mutation pressure, natural or translational selection, secondary protein structure, replication and selective transcription, hydrophobicity and hydrophilicity of the protein and the external environment play a major role in the codon usage pattern of organisms [26] . In unicellular and multicellular organisms it was observed that, preferred synonymous codons/optimal codons with abundant tRNA gene copy number rise with gene expression level within the genome that supports selection on high codon bias confirmed by positive correlation between optimal codons and tRNA abundance [18, 22, 27] . Urrutia and Hurst (2003) reported weak correlation between gene expression level and codon usage bias within human genome though not related with tRNA abundance [19] . However, Comeron (2004) observed that in human genome, highly expressed genes have preference towards codon bias favoring codons with most abundant tRNA gene copy number compared to less highly expressed genes [28] .