Mikrobiol. Z. 2019; 81(1):106-123. Ukrainian.
doi: https://doi.org/10.15407/microbiolj81.01.106

Conserve Nucleotide Motifs and Secondary Structures within Tobamovirus Subgenomic Promoters

Kyrychenko A.N., Shcherbatenko I.S.

Zabolotny Institute of Microbiology and Virology, NAS of Ukraine
154 Akad. Zabolotny Str., Kyiv, 03143, Ukraine

Aim. Considering the restriction of experimental data and the inconsistency of opinions regarding the role of primary and secondary RNA structures in the activity of subgenomic (sg) promoters, the aim of the work was to search a conservative base motifs and stemloops in tobamoviral sg promoters and compare their properties. Methods. The complete genomic sequences of 17 TMV strains and 21 strains of other tobamovirus species were downloaded from the NCBI website (http://www.ncbi.nlm.nih.gov/). A computer search and comparative analysis of conservative promoter components was carried out using the consensus sequence of three-component nucleotide blocks (TNBs), linear sequences of unfolded stem-loops and a set of own tightly specialized computer programs. Results. A highly conserved TNBs were found in all of 76 tobamoviral sg promoters tested using the consensus sequence SSSSSnnnnnCYAAGCWWW-nnWWWWW, were SSSSS – GC-rich motif, nnnnn and nn – arbitrary (not-consensus) nucleotides, CYAAGCWWW – central motif, WWWWW – AU-rich motif, Y – nucleotide C or U. The identity of TNB motifs to consensus sequence consists 99.5% and 88.3%. for TMV strains and other tobamoviruses, respectively. The nucleotide coincidence of SL1, SL2 and SLcp stem-loops with the corresponding TMV-U1 loops is 74.4, 75.7 and 60.3%, respectively. All 75 of the 76 TNBs examined in this study in the sixth position of central motif contain a nucleotide C, which genomic positions correspond to the transcription start site (TSS) of sg RNAs. The TSSs of both genes of all tobamoviruses are localized upstream of the translation start codons, except the TSS of the Odontoglossum ringspot virus transport protein gene. The tobamoviruses studied are clearly divided into 4 groups according to the similarity of conservative motifs and nucleotide substitution in subgenomic promoters. Conclusions. The results of the studies contradict the assumption about more important role of secondary structures than primary nucleotide sequences in the functional activity of tobamovirus sg promoters. Localisation of AU-rich motifs downstream of the sg RNA TSS suggests the possibility of tobamovirus RNA synthesis on double-strand matrixes. The groups of tobamoviruses containing different strains and species with similar nucleotide substitutions supplement a limited demonstration of Vavilov’s homologous series at the molecular level, and are also consistent with our assumption about the molecular mechanism of homologous series – the possibility of fixing only those nucleotide substitutions that do not disturb of finely balanced functioning of several genetic codes in one cell.

Keywords: tobamoviruses, subgenomic promoters, conservative nucleotide motifs and secondary structures, homologous series of virus variability.

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