Codon index to measure the effect of tRNA recycling
Yuta Nishino (1351083)
Codon is a triplet of nucleotides. Different types of codons do not appear in the genes with the same frequency.
The bias is called codon usage bias, and it is studied for decades. Many statistical indices are proposed to measure codon usage bias and its relationship with gene expression levels and other functions.
It was recently reported that codon usage bias is related not only to gene expression levels, but to biological regulations of important functions such as cell cycle progressions or DNA repair.
The regulation is correlated with another phenomenon that is called tRNA recycling.
The tRNA recycling is the phenomenon that tRNA molecules are relatively slow to diffuse away from ribosome than translation process so that the molecules are used many times for translation.
It is said that tRNA recycling is evolutionarily conserved because the phenomenon is positively correlated to translation efficiency.
tRNA Pairing Index (TPI) is the codon index that measures the tRNA recycling by calculating the degree that successive codons are the ones read by the same isoacceptor tRNA.
In this presentation, we propose a novel index Codon Pairing Index (CPI) that calculate the degree that how much the identical codons succeed.
Used together with TPI, CPI enables us to determine which phenomenon is conserved, successive identical codons or tRNA recycling.
The result shows successive identical codons are more strongly conserved than tRNA recycling.
In addition, CPI requires less information of target organism than TPI, thus it can be used instead of TPI.