Structural Features of DNA in tRNA Genes and Their Upstream Sequences

RNA polymerase III (Pol III) transcribes tRNA genes using type II promoters. The internal control regions contain a Box A and a Box B, which are recognized by TFIIIC. The 5′-flanking regions of tRNA genes clearly play a role in the regulation of transcription, but consensus sequences in it have been found only in some plants and S. pombe; although, the TATA binding protein (TBP) is a component of the TFIIIB complex in all eukaryotes. Archaea utilize an ortholog of the TBP. The goal of this work is the detection of the positions of intragenic and extragenic promoters of Pol III, which regulate the transcription of tRNA genes in eukaryotes and archaea. For this purpose, we analyzed textual and some structural, mechanical, and physicochemical properties of the DNA in the 5′-flanking regions of tRNA genes, as well as in 30 bp at the beginning of genes and 60 bp at the end of genes in organisms possessing the TBP or its analog (eukaryotes, archaea) and organisms not possessing the TBP (bacteria). Representative tRNA gene sets of 11 organisms were taken from the GtRNAdb database. We found that the consensuses of A- and B-boxes in organisms from all three domains are identical; although, they differ in the conservativism of some positions. Their location relative to the ends of tRNA genes is also identical. In contrast, the structural and mechanical properties of DNA in the 5′-flanking regions of tRNA genes differ not only between organisms from different domains, but also between organisms from the same domain. Well-expressed TBP binding positions are found only in S. pombe and A. thaliana. We discuss possible reasons for the variability of the 5′-flanking regions of tRNA genes.

Авторы
Савина Е.А. , Шумилина Т.Г. , Пороло В.А. , Лебедев Г.С. , Орлов Ю.Л. 1 , Анашкина А.А. , Ильичева И.А.
Издательство
MDPI AG
Номер выпуска
21
Язык
Английский
Страницы
11758
Статус
Опубликовано
Подразделение
Аграрно-технологический Институт РУДН
Том
25
Год
2024
Организации
  • 1 Российский университет дружбы народов
  • 2 Институт молекулярной биологии им.Энгельгардта РАН
  • 3 Первый МГМУ им.Сеченова Минздрава России (Сеченовский Университет)
Ключевые слова
tRNA transcription; RNA polymerase III; TBP; regulatory regions; archaea; bacteria; eukaryotes; DNA local spatial structure; ultrasonic cleavage; DNase I cleavage; DNA–protein interactions
Дата создания
29.11.2024
Дата изменения
29.11.2024
Постоянная ссылка
https://repository.rudn.ru/ru/records/article/record/157752/
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