Construction of anti-codon table of the plant kingdom and evolution of tRNA selenocysteine (tRNA Sec )
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RESEARCH ARTICLE
Open Access
Construction of anti-codon table of the plant kingdom and evolution of tRNA selenocysteine (tRNASec) Tapan Kumar Mohanta1*† , Awdhesh Kumar Mishra2†, Abeer Hashem3,4 , Elsayed Fathi Abd_Allah5 , Abdul Latif Khan1 and Ahmed Al-Harrasi1*
Abstract Background: 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. Results: 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 tRNAMet has highest (5.039%) whereas GCG anti-codon of tRNAArg has lowest (0.004%) abundance. However, when we compared the anti-codon frequencies according to the tRNA isotypes, we found tRNALeu (7.808%) has highest abundance followed by tRNASer (7.668%) and tRNAGly (7.523%). Similarly, suppressor tRNA (0.036%) has lowest abundance followed by tRNASec (0.066%) and tRNAHis (2.109). The genome of Ipomoea nil, Papaver somniferum, and Zea mays encoded the highest number of anticodons (isoacceptor) at 59 each whereas the genome of Ostreococcus tauri was found to encode only 18 isoacceptors. The tRNASec genes undergone losses more frequently than duplication and we found that tRNASec showed anti-codon switch during the course of evolution. Conclusion: 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. Keywords: tRNA, Evolution, Anti-codon, tRNASec, Protein translation, Wobble
* Correspondence: [email protected]; [email protected]; [email protected] † Tapan Kumar Mohanta and Awdhesh Kumar Mishra contributed equally to this work. 1 Natural and Medical Sciences Research Center, University of Nizwa, 616 Nizwa, Oman Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/license
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