Correlation between gene expression levels under drought stress and synonymous codon usage in rice plant by in-silico study

Abstract

We studied the correlation of synonymous codon usage (SCU) on gene expression levels under drought stress in rice. Sixty genes related to drought stress (with high, intermediate and low expression) were selected from rice meta-analysis data and various codon usage indices such as the effective number of codon usage (ENC), codon adaptation index (CAI) and relative synonymous codon usage (RSCU) were calculated. We found that in genes highly expressing under drought 1) GC content was higher, 2) ENC value was lower, 3) the preferred codons of some amino acids changed and 4) the RSCU ratio of GC-end codons relative to AT-end codons for 18 amino acids increased significantly compared with those in other genes. We introduce ARSCU as the Average ratio of RSCUs of GC-end codons to AT-end codons in each gene that could significantly separate high-expression genes under drought from low-expression genes. ARSCU is calculated using the program ARSCU-Calculator developed by our group to help predicting expression level of rice genes under drought. An index above ARSCU threshold is expected to indicate that the gene under study may belong to the "high expression group under drought". This information may be applied for codon optimization of genes for rice genetic engineering. To validate these findings, we further used 60 other genes (randomly selected subset of 43233 genes studied for their response to drought stress). ARSCU value was able to predict the level of expression at 88.33% of the cases. Using third set of 60 genes selected amongst high expressing genes not related to drought, only 31.65% of the genes showed ARSCU value of higher than the set threshold. This indicates that the phenomenon we described in this report may be unique for drought related genes. To justify the observed correlation between CUB and high expressing genes under drought, possible role of tRNA post transcriptional modification and tRFs was hypothesized as possible underlying biological mechanism.

Codon usage bias

“…Codon usage may reflect degree of gene expression, though gene expression is determined mainly by transcriptional and post-transcriptional regulations. Codon usage reflects the pool of tRNAs available when a gene is expressed, which in turn depends on the physiological state of the cell [51]. Highly expressed genes have a much stronger codon usage bias and are encoded by optimal codons corresponding to abundant tRNAs, for more rapid and efficient translation.…”

“…In Arabidopsis, codon bias was related to the composition of 3′ flanking region, in both strongly and weakly expressed genes [56]. A measure termed as ARSCU (Average ratio of Relative Synonymous Codon Usage of GC-end codons to AT-end codons in each gene) was devised to separate high-expression from low-expression genes, where genes with ARSCU values above threshold value 13 were classified highly expressed under drought [51]. The codon usage bias of highly expressed genes and comparison with lowly expressed genes in few plants are presented in Table 5 [51,53,57,58].…”

“…An RSCU value of 1 shows no codon bias and greater than 1 means that a codon is used more often than expected, while values less than 1 indicate its relative rarity [9]. RSCU values can be 2, 3, 4 and 6 when a single codon is used to encode aminoacids having 2,3,4 and 6 synonymous codons respectively [51].…”

Comparative Expression Analysis of Stress-Inducible Candidate Genes in Response to Cold and Drought in Tea Plant [Camellia sinensis (L.) Kuntze]

“…However, we continue to lack a complex picture of the interactions between the core network and their downstream-regulated target proteins. Additionally, comparison of molecular profiles of an organism under different stresses would make it possible to identify the conserved stress mechanisms (Amrine et al, 2015 ; Muthuramalingam et al, 2017 ; Chamani Mohasses et al, 2020 ). Thus, we have to continue searching for new evolutionarily conserved and species-specific genes related to the stress response.…”

Table_1.XLSX

“…However, we continue to lack a complex picture of the interactions between the core network and their downstreamregulated target proteins. Additionally, comparison of molecular profiles of an organism under different stresses would make it possible to identify the conserved stress mechanisms (Amrine et al, 2015;Muthuramalingam et al, 2017;Chamani Mohasses et al, 2020). Thus, we have to continue searching for new evolutionarily conserved and species-specific genes related to the stress response.…”