Structure insight of ribonuclease J reveals the basis of RNA metabolism in Mycobacterium tuberculosis

RNA degradosome plays key roles in pre-rRNA maturation and mRNA decay, and mediates isoniazid tolerance in Mycobacterium tuberculosis (Mtb). Mtb ribonuclease J (Mtb-RNase J) is one core enzyme of the RNA degradosome, which comprises RNases, RNA helicases, and glycolytic enzymes. However, how Mtb-RNase J functions in RNA metabolism keeps unclear. Here, we solved the crystal structures of Mtb-RNase J and its complex with single-strand RNA (ssRNA). RNA binding induced the comformation change. Mtb-RNase J showed typical beta lactamase activity and exo/endoribonuclease activities. Mn2+ could dramatically enhanced the ribonuclease activity of Mtb-RNase J, which prefers to bind 8-9 nt ssRNA.We unveiled the novel mechanism of Mtb-RNase J to form the active ribonuclease homodimer. Knockout of RNase J dramatically changed the expression levels of 49 genes in the metabolic pathways and morphologies of Mycobacterium smegmatis. Thus, current study explored the structural basis and function of Mtb-RNase J in RNA metabolism.

RNA降解体（RNA degradosome）在核糖体RNA前体成熟与mRNA降解过程中发挥关键调控作用，并介导结核分枝杆菌（Mycobacterium tuberculosis，简称Mtb）的异烟肼耐受性。结核分枝杆菌核糖核酸酶J（Mtb-RNase J）是RNA降解体的核心酶组分之一，该降解体由核糖核酸酶、RNA解旋酶及糖酵解酶共同构成。然而，Mtb-RNase J在RNA代谢中的功能机制长期未被阐明。本研究解析了Mtb-RNase J及其与单链RNA（ssRNA）复合物的晶体结构。研究发现，RNA结合可诱导Mtb-RNase J发生构象改变。Mtb-RNase J具备典型的β-内酰胺酶活性，同时兼具外切核糖核酸酶与内切核糖核酸酶双重活性。二价锰离子（Mn²+）可显著提升Mtb-RNase J的核糖核酸酶活性，该酶偏好结合长度为8~9 nt的单链RNA。本研究揭示了Mtb-RNase J形成具有催化活性的核糖核酸酶同源二聚体的全新分子机制。对核糖核酸酶J进行基因敲除后，耻垢分枝杆菌代谢通路内49个基因的表达水平及菌体形态均出现显著变化。综上，本研究系统阐明了Mtb-RNase J在RNA代谢过程中的结构基础与生物学功能。