Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran.
Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran.
PLoS One. 2020 Aug 10;15(8):e0237334. doi: 10.1371/journal.pone.0237334. eCollection 2020.
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.
我们研究了同义密码子使用（SCU）与水稻干旱胁迫下基因表达水平的相关性。从水稻元分析数据中选择了 60 个与干旱胁迫相关的基因（高、中、低表达），并计算了有效密码子使用数（ENC）、密码子适应指数（CAI）和相对同义密码子使用（RSCU）等各种密码子使用指数。我们发现，在干旱胁迫下高表达的基因中：1）GC 含量较高；2）ENC 值较低；3）一些氨基酸的偏好密码子发生了变化；4）18 种氨基酸中 GC 端密码子相对于 AT 端密码子的 RSCU 比值显著增加。我们引入 ARSCU 作为每个基因中 GC 端密码子相对于 AT 端密码子的 RSCU 比值的平均值，该值可以将干旱胁迫下高表达基因与低表达基因显著区分开来。ARSCU 是使用我们小组开发的 ARSCU-Calculator 程序计算的，该程序有助于预测水稻基因在干旱下的表达水平。高于 ARSCU 阈值的指数预计表明研究中的基因可能属于“干旱下高表达基因”。这些信息可用于对水稻基因工程中的基因进行密码子优化。为了验证这些发现，我们进一步使用了 60 个其他基因（从 43233 个研究其对干旱胁迫反应的基因中随机选择的子集）。在 88.33%的情况下，ARSCU 值能够预测表达水平。在选择的第三组 60 个高表达且与干旱无关的基因中，只有 31.65%的基因的 ARSCU 值高于设定的阈值。这表明我们在本报告中描述的现象可能是与干旱相关基因所特有的。为了证明 CUB 与干旱下高表达基因之间的相关性，假设 tRNA 转录后修饰和 tRFs 的可能作用是潜在的生物学机制。
