Mohanta Tapan Kumar, Mishra Awdhesh Kumar, Hashem Abeer, Abd Allah Elsayed Fathi, Khan Abdul Latif, Al-Harrasi Ahmed
Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman.
Department of Biotechnology, Yeungnam University, 38541, Gyeongsan, South Korea.
BMC Genomics. 2020 Nov 19;21(1):804. doi: 10.1186/s12864-020-07216-3.
The tRNAs act as a bridge between the coding mRNA and incoming amino acids during protein translation. The anti-codon of tRNA recognizes the codon of the mRNA and deliver the amino acid into the protein translation chain. However, we did not know about the exact abundance of anti-codons in the genome and whether the frequency of abundance remains same across the plant lineage or not.
Therefore, we analysed the tRNAnome of 128 plant species and reported an anti-codon table of the plant kingdom. We found that CAU anti-codon of tRNA has highest (5.039%) whereas GCG anti-codon of tRNA has lowest (0.004%) abundance. However, when we compared the anti-codon frequencies according to the tRNA isotypes, we found tRNA (7.808%) has highest abundance followed by tRNA (7.668%) and tRNA (7.523%). Similarly, suppressor tRNA (0.036%) has lowest abundance followed by tRNA (0.066%) and tRNA (2.109). The genome of Ipomoea nil, Papaver somniferum, and Zea mays encoded the highest number of anti-codons (isoacceptor) at 59 each whereas the genome of Ostreococcus tauri was found to encode only 18 isoacceptors. The tRNA genes undergone losses more frequently than duplication and we found that tRNA showed anti-codon switch during the course of evolution.
The anti-codon table of the plant tRNA will enable us to understand the synonymous codon usage of the plant kingdom and can be very helpful to understand which codon is preferred over other during the translation.
在蛋白质翻译过程中，转运RNA（tRNA）充当编码信使核糖核酸（mRNA）与进入的氨基酸之间的桥梁。tRNA的反密码子识别mRNA的密码子，并将氨基酸传递到蛋白质翻译链中。然而，我们并不清楚基因组中反密码子的确切丰度，以及这种丰度频率在整个植物谱系中是否保持不变。
因此，我们分析了128种植物的tRNA基因组，并报告了植物界的反密码子表。我们发现，tRNA的CAU反密码子丰度最高（5.039%），而GCG反密码子丰度最低（0.004%）。然而，当我们根据tRNA同型异构体比较反密码子频率时，我们发现tRNA（7.808%）丰度最高，其次是tRNA（7.668%）和tRNA（7.523%）。同样，抑制性tRNA（0.036%）丰度最低，其次是tRNA（0.066%）和tRNA（2.109%）。圆叶牵牛、罂粟和玉米的基因组编码的反密码子（同功受体）数量最多，各有59个，而莱茵衣藻的基因组仅编码18个同功受体。tRNA基因发生丢失的频率比复制更频繁，并且我们发现tRNA在进化过程中发生了反密码子转换。
植物tRNA的反密码子表将使我们能够了解植物界同义密码子的使用情况，并且对于理解在翻译过程中哪种密码子比其他密码子更受青睐非常有帮助。
