Predicting Characteristics of the Potentially Binding Sites for miRNA in the mRNA of the TCP Transcription Factor Genes of Plants

Abstract

The expression of the TCP transcription factor family genes depends on miRNA, whose effect on the translation of their mRNA is poorly studied. Interactions between miRNA and mRNA were studied with the MirTarget program, which allows estimating of quantitative characteristics of binding of the whole nucleotide sequence of miRNA to mRNA. The analysis of binding of 125 miRNAs to mRNAs of 28 genes of the TCP family of Triticum aestivum L. revealed eight target genes for miR319-3p, miR444a-3p, miR5086-5p, miR9666a-3p, and miR9780-3p. miRNA binding sites in mRNA of the TCP family genes of T. aestivum were located in the CDS only. Only 12 of 22 mRNAs of the ТСР family genes of Oryza sativa L. bounded to the miR1437b-5p, miR1846a-5p, miR1848-5p, miR1858a-5p, miR1858b-5p, miR1861d-5p, miR1861h-5p, miR2102-3p, miR2102-5p, miR2919, miR2925-5p, miR319a-3, miR408-3p, miR5075-3p, and miR5819-5p out of 738 miRNAs in total. miRNA binding sites were located in the 5'UTR and CDS regions of mRNAs of the TCP family genes of O. sativa. Only 10 of 46 TCP family genes of Zea mays L. were shown to be targets for the miR164g-3p, miR164h-5p, miR166a-5p, miR168a-5p, miR171d-5p, miR399d-3p, and miR408a-3p out of 325 miRNAs of Z. mays. The zma-miR166a-5p was bound to mRNAs of the genes GRMZM2G031905_P01, GRMZM2G055024_P01, GRMZM2G062711_P01, and GRMZM2G170232_P01. Two miRNAs were shown to bind to mRNAs of the genes AC213524.3_FGP003, AC233950.1_FGP002, and GRMZM2G034638_P01. Only one miRNA was bound to mRNAs of the genes GRMZM2G035944_P01, AC190734.2_FGP003, and AC205574.3_FGP006. miRNA binding sites were located in the 5'UTR and CDS regions of mRNAs of the TCP family genes of Z. mays. Ten of 27 TCP family genes of Arabidopsis thaliana (L.) Heynh. were shown to be targets for the miR319-3р, miR4228-5p, miR4228-3p, miR5021-5p, miR5658-5p, and miR8181-5p out of 429 miRNAs of A. thaliana. mRNAs of the AT1G53230 and AT2G31070 genes had binding sites for the miR319c-3p, miR5021-5p, and miR5658-5p, while mRNA of the AT3G15030 gene had binding site for the miR319a-3p and miR4228-3p. Two miRNAs bounded to mRNAs of the genes AT1G69690, AT3G02150, and AT3G47620. One miRNA bounded to mRNAs of the genes AT1G30210, AT4G18390, and AT5G08330. miRNA binding sites were located in the 5'UTR, CDS and 3'UTR regions of mRNA of the TCP gene family of A. thaliana. mRNAs of six groups of the TCP family genes had binding sites for the miR319-3p, miR444a-3p, miR5021-5p, miR5658-5p, and miR2102-5p, which encode the oligopeptides QRGPLQS, STSETS, SSSSSS, HHHHHH, GGGGGG, and AAAAAA conservative in the TCP family proteins of different plant species. Quantitative characteristics of miRNA binding to mRNAs of plant transcription factors of the TCP family, which participate in regulation of growth and development of plants, have been predicted.