Structural Biology Unit, CIC bioGUNE, CIBERehd, 48160 Derio, Spain.
Nucleic Acids Res. 2012 Oct;40(19):9941-52. doi: 10.1093/nar/gks692. Epub 2012 Jul 30.
Multi-subunit RNA polymerases (RNAPs) in all three domains of life share a common ancestry. The composition of the archaeal RNAP (aRNAP) is not identical between phyla and species, with subunits Rpo8 and Rpo13 found in restricted subsets of archaea. While Rpo8 has an ortholog, Rpb8, in the nuclear eukaryal RNAPs, Rpo13 lacks clear eukaryal orthologs. Here, we report crystal structures of the DNA-bound and free form of the aRNAP from Sulfolobus shibatae. Together with biochemical and biophysical analyses, these data show that Rpo13 C-terminus binds non-specifically to double-stranded DNA. These interactions map on our RNAP-DNA binary complex on the downstream DNA at the far end of the DNA entry channel. Our findings thus support Rpo13 as a RNAP-DNA stabilization factor, a role reminiscent of eukaryotic general transcriptional factors. The data further yield insight into the mechanisms and evolution of RNAP-DNA interaction.
多亚基 RNA 聚合酶（RNAP）在所有三个生命领域都具有共同的起源。古菌的 RNAP（aRNAP）的组成在门和物种之间并不相同，亚基 Rpo8 和 Rpo13 仅在少数古菌中发现。虽然 Rpo8 在核真核 RNAP 中有直系同源物 Rpb8，但 Rpo13 缺乏明确的真核直系同源物。在这里，我们报告了来自 Sulfolobus shibatae 的 aRNAP 的 DNA 结合形式和游离形式的晶体结构。这些数据与生化和生物物理分析一起表明，Rpo13 C 末端非特异性地结合双链 DNA。这些相互作用映射在我们的 RNAP-DNA 二元复合物上，位于 DNA 进入通道远端的下游 DNA 上。因此，我们的发现支持 Rpo13 作为 RNAP-DNA 稳定因子的作用，这与真核一般转录因子的作用相似。这些数据进一步深入了解了 RNAP-DNA 相互作用的机制和进化。
