Abstracts

Genetic Bases of Biodiversity

In eukaryotes the tRNA gene promoters are composed of two distinct elements known as the boxes A and B. The 11-12 bp box A occupies the region of the DNA sequence that corresponds to the 5'-end part of the D-arm region of the tRNA structure. The 11 bp box B is in the DNA region corresponding to the tRNA T-loop with dinucleotides of the tRNA T-stem flanking it at both ends. We carried out a structural-functional analysis of aligned nucleotide sequences from regions where the A and B boxes are located. The samples were drawn from the tRNA genes of three eukaryotic (Protozoa, Plant, Metazoa) and two prokaryotic (Archae, Eubacteria) kingdoms. The novel pol III SCAN method was used. This method allows to estimate not only nucleotide distribution at each position of a box, but also the interaction set between different positions within a box and between the boxes A and B. We subdivided the boxes A and B into modules on the basis of the intermittent pattern of positions with highly conserved nucleotides and positions with relatively variable nucleotides. We showed that each module of the boxes A and B is represented by a limited number of structural variants. Combinations of the structural variants of the different modules are characteristic features of a particular tRNA gene type and these combinations conserved in distant species within two kingdoms (Metazoa, Plant) of multicellular organisms. The particular combinations of the structural variants of the different modules correlate, as a rule, with the features of the secondary DNA structures at their junction sites. We established an association between the structural features of the tRNA promoter and the amino acids specificity of the acceptor ability of the tRNA molecule. The combinations of the structural variants of the DNA found for the modules in the same tRNA gene types were different in Protozoa and multicellular organisms. The nucleotide sequences from tRNA genes corresponding to the D-arm of the tRNA molecule, where the A box is located in eukaryotes, are characterized by extreme variability in nucleotide composition, especially in the 3'- end of this stretch in prokaryotes. In the prokaryotes, only adenine at position 7 of this undeca- dodecaoligonucleotide is conserved, while there are several such conserved positions (1, 3, 7 and 11,12) in the 12 bp box A or 1, 3, 7, 10 and 11 in the 11 bp box A in the tRNA genes of the eukaryotes. No interactions between positions were found for this stretch of the nucleotide sequence in prokaryotes. Furthermore DNA structure of this region may considerably vary in the same tRNA gene type in different species of prokaryotes. The number of revealed conserved positions was greater in the nucleotide sequences where eukaryotic B box are located from the tRNA genes in prokaryotes. However, this region is structurally more variable in the prokaryotic than the eukaryotic tRNA genes. Therefore, DNA structure in the location sites of the A and B boxes become more conserved in the eukaryotic relative to the prokaryotic tRNA genes. Accepting that the translational tRNA molecule function remained unaltered during evolution, these structural changes in the tRNA gene may be explained by the emergence of an interagenic promoter. Comparative structural analysis of DNA in the intragenic promoters of the eukaryotic tRNA genes demonstrates that their module organization can provide both unique and group structural features for each tRNA gene type. This is very consequential for their expression and the formation of the tRNA composition of a particular pool in the cell.

Note. Abstracts are published in author's edition

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