Ekaterina A. Savina1, Anastasia A. Anashkina1, Irina A. Il’icheva1, Yuriy L. Orlov2*
1 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
2 Sechenov First Moscow State Medical University of the Russian Ministry of Health (Sechenov University), Moscow, Russia
orlov [at] d-health.institute
Abstract
RNA polymerase III (Pol III) transcribes tRNA genes using type 2 promoters, namely intragenic boxes A and B. In addition, 5’-flanking regions of tRNA genes of plants and S. pombe contain octanucleotides similar to the well-known TATA-box in the promoters of mRNA genes. The TATA box has not been found in other eukaryotes, although TBP is the component of the transcription factor TFIIIB. Archaea use the orthologue. The goal of this work was to determine the position of possible TBP binding while tRNA genes transcription in various eukaryotes as well as the comparison of structural properties of nucleotide sequences of tRNA genes and their up-stream regions in eukaryotes, archaea and bacteria. We have analyzed representative sets of tRNA gene sequences from 11 organisms from the Genomic tRNA Database (GtRNAdb) (http://gtrnadb.ucsc.edu). The nature of the upstream DNA sequences has been discussed earlier. It was proposed to consider these areas as a fine-tuning control of the transcriptional activity and starting specificity of a given tRNA gene. The results of experimental work already existing by that time led to the conclusion that transcription initiation of eucaryotic tRNA genes thus appears to depend critically on DNA conformation, both within and around the genes. The characteristics of textual and spatial structure in the vicinity of the start of tRNA genes were detected. Textual characteristics of 60 bp sequences aligned to the ends of the genes were also analyzed and the position of B-box was defined. It was found that belonging to different domains has little effect on the consensuses of A and B boxes. They differ only at the degree of conservatism of some positions. The mechanical properties of the upstream regions of all eukaryotes allow TBP to bind not in one, but in several positions, but with different affinities. These properties are less pronounced in archaea, and absent in bacteria.
Keywords: tRNA transcription, TBP (TATA-binding protein), text complexity, archaea, bacteria, eukaryotes, DNA spatial structure