Codon Usage Bias In 5’terminal Of Coding Sequences Reveales An Distinct Enrichment Of Gene Functions

Codon bias exists not only among species, but also within genome and in specific gene. It is closely related to genome GC content in bacteria species yet such association is not remained in eukaryotes. Codon bias plays important roles in different stages of translation regulation, including initiation, elongation, termination, co-translation folding of peptide and recognition of molecular chaperones. Previous studies showed that 5’terminal of coding sequence(CDS) prefers rare codons to regulate early translation and help co-translational regulations. Moreover, rare codons usage is different in diversity genes. Secretory protein genes, which make an important part of proteome, have a special signal sequence at very beginning of coding sequence, which leads to the targeting and export of protein to endoplasmic reticulum or bacteria cytoplasmic membrane. Generally, both signal sequences and the downstream regions have a higher incidence of rare codons. It is assumed that rare codons in secretory gene 5’terminal not only work as speed controller but also are involved in some other regulation progress. To our knowledge, researches about codon bias in secretory genes mostly focus on signal sequence but not the downstream region. Moreover, there are few studies about codon bias in secretory genes in specific species except for Escherichia coli and Saccharomyces cerevisiae.In this study, we analyzed codon bias of secretory genes in several eukaryotes. Secretory genes have a high incidence of rare codons in 5’terminal of CDS,and the bias is greater than the same region of non-secretory genes. There are two different regions where rare codons are highly enriched, the first 25 codons downstream start codon and the region from the 75 th to 100 th codons. GO analysis revealed that secretory genes which have clustered rare codons in different regions have distinct function. Another finding was that codon bias in hydrophobic region in two gene group are similar, thus the bias in secretory genes might be partly influenced by amino acid bias in hydrophobic region. Although rare codons cluster more frequently in specific regions, continuous rare codons are not favored. Similar to random sequences, rare codons tend to be interrupted by optimal codons. We propose that extremely continuous rare codons result in a raised probability of ribosome collision and drop-off. That is why continuous rare codon clusters are not highly enriched. Based on ribosome profiling data, we found that the average translation efficiencies of rare and optimal codons show no significant difference. All codons have a higher ribosomal densitity in the 5’terminal than the following region. Interestingly, secretory genes exhibit ribosome pausing at very beginning of CDS and the region of 20–30 codons downstream the start codon. Ribosome pausing in these two regions could be involved in different translation events.In conclusion, CDS 5’terminal of secretory genes tend to prefer rare codons and the rare codons cluster in different regions plays different roles in gene function. There is no significant differencein translation efficiencies between rare and optimal codons. Results in this study provided more information about codon bias in secretory genes, which may support the future researches about co-effect of codon bias, mRNA structure and tRNA abundance in translational regulations.