Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
The Digital Health Center, I.M.Sechenov First Moscow State Medical University of the Russian Ministry of Health (Sechenov University), 119991 Moscow, Russia.
Int J Mol Sci. 2024 Nov 1;25(21):11758. doi: 10.3390/ijms252111758.
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 ; 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 and . We discuss possible reasons for the variability of the 5'-flanking regions of tRNA genes.
RNA 聚合酶 III（Pol III）使用 II 型启动子转录 tRNA 基因。内部控制区包含一个 Box A 和一个 Box B，它们被 TFIIIC 识别。tRNA 基因的 5'侧翼区显然在转录调控中起作用，但在一些植物和中只发现了其保守序列；尽管如此，TATA 结合蛋白（TBP）是所有真核生物中 TFIIIB 复合物的一个组成部分。古菌利用 TBP 的同源物。这项工作的目的是检测 Pol III 的基因内和基因外启动子的位置，这些启动子调节真核生物和古菌中 tRNA 基因的转录。为此，我们分析了 tRNA 基因 5'侧翼区以及具有 TBP 或其类似物（真核生物、古菌）和不具有 TBP 的生物体（细菌）中基因起始 30 个碱基和基因末端 60 个碱基的 DNA 的文本和一些结构、力学和物理化学特性。从 GtRNAdb 数据库中选取了 11 个生物体的代表性 tRNA 基因集。我们发现，来自所有三个领域的生物体的 A 框和 B 框的共识是相同的；尽管如此，它们在一些位置的保守性上有所不同。它们相对于 tRNA 基因末端的位置也是相同的。相比之下，tRNA 基因 5'侧翼区的 DNA 的结构和力学特性不仅在不同领域的生物体之间有所不同，而且在同一领域的生物体之间也有所不同。在和中只发现了表达良好的 TBP 结合位置。我们讨论了 tRNA 基因 5'侧翼区可变性的可能原因。
