Non-Optimal Codon Usage Shapes Cell Cycle Regulators: Codon Optimization Studies on CDK1 and NUF2

Abstract

The expression and functions of genes are largely dependent on genome integrity and stability. Codon usage plays a significant role in maintaining stability and functions of genes. Perturbation in codon sequence can lead to functional and structural dysfunction of a gene. In our study, we performed the codon usage analyses of cell cycle-dependent genes. Various codon usage parameters analyzed using nucleotide compositions like RSCU, ENC, and GC analyses showed that cell cycle dependent genes follow non-optimal codon usage. Genes preferred AT-rich ending over GC-rich ending, thereby suggesting preference for non-optimal codons. Neutrality and parity plot showed that the codon preference is a result of mutation selection pressure. To study the codon usage implications, we optimized the codons of cell cycle dependent genes (CDK1 and NUF2) to study their effects on cell cycle and apoptosis in vitro. We observed that codon optimization alters the cell cycle length in cell cycle-dependent genes impacting cell fate and survival. Our studies revealed that codon usage preferences directly affect the stability of both mRNA and proteins. Specifically, genes and proteins with non-optimal codons exhibited reduced stability compared to their optimized counterparts, suggesting critical implications for cell cycle regulation and apoptosis.