Construction of anti-codon table of the plant kingdom and evolution of tRNA selenocysteine (tRNASec)

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 anti-codons (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.

Anticodon Table of the Chloroplast Genome and Identification of Putative Quadruplet Anticodons in Chloroplast tRNAs

“…A similar level of abundance has been found for tRNA Leu (7.80%), for the nuclear encoded tRNA genes, reflecting a similarity in the anticodon abundance in the nuclear and chloroplast genomes [10]. However, an abundance of the nuclear-encoded anticodons tRNA Leu is followed by tRNA Ser (7.66%), tRNA Gly (7.52%), and tRNA Arg (7.28%) [10]. Although, tRNA Leu is the highest encoding isotype/isodecoder in nuclear-(7.80%) and chloroplast (10.27%)-encoded genomes, there is a great difference in their percentage.…”

“…However, at the isotype/isodecoder level, tRNA Leu (10.27%) has been found to contain the highest percentage of anticodons followed by tRNA Ile (9.93%) and tRNA Arg (7.96%) (Supplementary File 1). A similar level of abundance has been found for tRNA Leu (7.80%), for the nuclear encoded tRNA genes, reflecting a similarity in the anticodon abundance in the nuclear and chloroplast genomes [10]. However, an abundance of the nuclear-encoded anticodons tRNA Leu is followed by tRNA Ser (7.66%), tRNA Gly (7.52%), and tRNA Arg (7.28%) [10].…”

“…However, the CAU anticodon encoding tRNA Met has been seen to have the highest percentage (5.47%) in the chloroplast genome (Supplementary File 1). The CAU anticodon of tRNA Met , of the nuclear encoded genome has also been found in the highest (5.03%) abundance [10], thus corroborating CAU, as the most abundant anticodon in the nuclear and chloroplast genomes. The anticodons CAU (tRNA Met ), GUU (tRNA Asn ), UGC (tRNA Ala ), and ACG (tRNA Arg ) have been found to encode more than 5% each of the total anticodons, suggesting the role of positive selection pressure in these anticodons (Supplementary File 1).…”

Comparative Analysis of Genomic and Transcriptome Sequences Reveals Divergent Patterns of Codon Bias in Wheat and Its Ancestor Species

“…In many cases, codon usage correlates with the cognate tRNA abundance with highly used codons generally having higher intracellular tRNA concentrations than low-use codons ( Zalucki et al, 2009 ). This fact indicates that tRNA abundance may be the main selection pressure for synonymous codon usage ( Mohanta et al, 2020 ). In the present study of Triticum , more codon-anticodon interaction occurred in amino acids with two synonymous codons in T. aestivum and T. urartu and in amino acids with four or six synonymous codons in T. turgidum and Ae.…”

“…Wobble rules say that tRNAs with a GCU anticodon can pair with AGU, which explains the apparent discrepancy in the ability to translate AGU codons to Ser with extremely few tRNAs with ACU anticodons ( Supplementary Table 5 ). In a recent research of 128 species of the plants ( Mohanta et al, 2020 ), high and low frequencies of wobble base-pairing were occurred at the G:U base pairing to meet translational demand.…”