Mikrobiol. Z. 2019; 81(3):53-67. Ukrainian.
doi: https://doi.org/10.15407/microbiolj81.03.053

Conserve Nucleotide Motifs within Tobamovirus Genomic Promoters

Kyrychenko A.N., Shcherbatenko I.S.

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

Aim. Replication of tobamoviruses, like that of other single-stranded positive sense RNA viruses involves the production of both genomic minus-strand and plus‑strand RNAs as well as the transcription of two subgenomic positive‑strand RNAs. The sequence elements and secondary structures required for promotion of the subgenomic RNAs have been characterized for many viruses, but only little is known about the promoter elements essential for genomic RNAs synthesis. Taking into consideration the insufficiency of experimental data and contradictoriness of notions regarding the promotion of viral genomic RNA replication, a comparative computational analysis of a conservative components in tobamovirus replycative promoters was the goal of our study. Methods. Complete genomic sequences of 38 tobamoviruses 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 by means of a set of own tightly specialized computer programs using consensus sequence of the ICR2 motif of tRNA genes and the unfolded sequence of D1L3S3 stem-loop of ВТМ-L strain. Results. We show that the 3’-end regions of genomic RNA of all 38 tobamovirus tested contain a highly conserved ICR2- and D1L3S3-like nucleotide motifs. In replicative promoters of the genomic minusstrand RNA this motifs are localized upstream and hereabouts of the start positions of (-)RNA synthesis, contain the common palindromic consensus sequence – TTCGAA, surrounding by 2–4 pairs of complementary nucleotides, and have only compensatory nucleotide exchange, which do not disruption of the complementary base pairing. On the contrary, no ICR2-, D1L3S3-like or others highly conserved nucleotide motifs were found hereabouts of the start point of (+)RNA synthesis localized at the 3’-end of genomic (-)RNA. By analyses of a possible cause of this appearance we propose the hypothetic models for subgenomic and genomic RNA synthesis on double-stranded and circular templates. Conclusions. The hypothetic models suggested are well consistent with our results and literature data, in particular: i) presence a similar conservative motifs in different promoter types – subgenomic, genomic, viral and eukaryotic; ii) ability of virus RNA polymerases for using of double stranded and circular templates; iii) possibility to initiate synthesis of opposite RNA strands by one palindromic signaling motif; iv) localization of viral ATreach sequence regions downstream of replication and transcription start points of virus RNA, and localization of GC-reach sequences upstream of such points; v) enhancing of virus replication through promoting linkage between 5’- and 3’-untranslated regions.

Keywords: Tobamoviruses, conserved motifs in genomic promoters, primary and secondary structures of conserved motifs, hypothetic models for subgenomic and genomic RNA synthesis.

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