Critical domain interactions for type A RNase P RNA catalysis with and without the specificity domain

Mao, Guanzhong; Srivastava, Abhishek; Wu, Shiying; Kosek, David; Lindell, Magnus; Kirsebom, Leif A.

doi:10.1371/journal.pone.0192873

Cited by 11 publications

(17 citation statements)

References 54 publications

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“…The modular architecture of large ribozymes, such as bacterial RNase P ribozymes and group I ribozymes, is an important feature in ribozyme biochemis-the S-domain retained residual catalytic activity. [27,28] To address the ribozyme activity of the B-type C-domain RNA, an in vitro evolution experiment was also performed, [29] in which RNA sequences were successfully identified to serve as artificial substrates for the C-domain RNA from B. subtilis RNase P.…”

Section: Modular Organization Of Bacterial Rnase P Ribozymesmentioning

confidence: 99%

Modular Architecture of Bacterial RNase P Ribozymes as a Structural Platform for RNA Nanostructure Design

Nozawa

Hagihara

Matsumura

et al. 2018

Chimia

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Ribonuclease P (RNase P) is a class of enzymes involved in the processing of precursor tRNAs to remove their 5'-leader sequences. Ribonuclease P enzymes are classified into two completely distinct classes, i.e. an RNA-based enzyme and a protein-only enzyme. The RNA-based enzyme functions as a ribozyme in which the catalytic machinery is supported by its RNA component consisting of a single RNA molecule. Bacterial RNase P RNAs are a classical class of ribozymes and their structures and catalytic mechanisms have been studied extensively. The bacterial RNase P ribozyme has a modular tertiary structure consisting of two large domains, each of which can self-fold without the partner domain. Such modular architecture, identification of which provided important insight into the function of this ribozyme, is attractive as a structural platform to design functional RNA nanostructures. The first section of this article briefly summarizes the diversity of RNase P mainly focusing on RNA-based enzymes. The second section describes the structures of bacterial RNase P ribozymes from the viewpoint of their application as modular tools in RNA nanostructure design. The last section summarizes the current state and next steps in modular engineering of RNase P RNAs, including possible design of RNase P ribozyme-based nanostructures.

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Section: Modular Organization Of Bacterial Rnase P Ribozymesmentioning

confidence: 99%

Modular Architecture of Bacterial RNase P Ribozymes as a Structural Platform for RNA Nanostructure Design

Nozawa

Hagihara

Matsumura

et al. 2018

Chimia

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“…Structural information of both bacterial A-type and B-type RPRs reveals that RPR consists of two independently folded domains, the catalytic domain (C-domain) and the specificity domain (S-domain), which play key roles in substrate cleavage and substrate binding, respectively 6–11 . It has been found that bacterial RPR even the C domain alone possesses catalytic activity under high ionic strength condition or in the presence of spermidine in vitro 12,13 . But the sole protein subunit RPP is essential for enhancing the efficiency and fidelity of substrate recognition and cleavage under physiological conditions 14–19 .…”

Section: Introductionmentioning

confidence: 99%

Cryo-electron microscopy structure of an archaeal ribonuclease P holoenzyme

et al. 2019

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Ribonuclease P (RNase P) is an essential ribozyme responsible for tRNA 5′ maturation. Here we report the cryo-EM structures of Methanocaldococcus jannaschii ( Mja ) RNase P holoenzyme alone and in complex with a tRNA substrate at resolutions of 4.6 Å and 4.3 Å, respectively. The structures reveal that the subunits of Mja RNase P are strung together to organize the holoenzyme in a dimeric conformation required for efficient catalysis. The structures also show that archaeal RNase P is a functional chimera of bacterial and eukaryal RNase Ps that possesses bacterial-like two RNA-based anchors and a eukaryal-like protein-aided stabilization mechanism. The 3′-RCCA sequence of tRNA, which is a key recognition element for bacterial RNase P, is dispensable for tRNA recognition by Mja RNase P. The overall organization of Mja RNase P, particularly within the active site, is similar to those of bacterial and eukaryal RNase Ps, suggesting a universal catalytic mechanism for all RNase Ps.

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“…This suggested electrostatic repulsion effects between enzyme and substrate RNAs upon disruption of the L18-P8 contact. Kirsebom and coworkers probed Eco WT and mL18 (5'-CUUG) P RNA with Pb 2+ ions and RNase T1 (Mao et al, 2018). They observed structural changes in P11 and at the junction between P14 and P11 in the S-domain of the mL18 mutant RNA with disrupted L18-P8 interaction.…”

Section: Discussionmentioning

confidence: 99%

“…In addition, there was a change in RNase T1 susceptibility at helix P5 in the C-domain, close to the active site. Generally, higher Pb 2+ concentrations were required for the mL18 versus WT P RNA to induce backbone hydrolysis at high affinity metal ion binding sites (Mao et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

“…This was analyzed with a substrate carrying a protonable 2'-NH 2 group at nt -1 near the canonical cleavage site. The mL18 mutation caused changes in the fraction of substrate that was cleaved at the canonical cleavage (-1/+1) site at different pH values (Mao et al, 2018). The authors proposed that the L18-P8 interaction acts as structural mediator between the substrate (T stem-loop) binding region in the S-domain and the active center of the C-domain.…”

Section: Discussionmentioning

confidence: 99%

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Comparative study on tertiary contacts and folding of RNase P RNAs from a psychrophilic, a mesophilic/radiation-resistant, and a thermophilic bacterium

Marszalkowski

Werner

Feltens

et al. 2021

RNA

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In most bacterial type A RNase P RNAs (P RNAs), two major loop-helix tertiary contacts (L8-P4 and L18-P8) help to orient the two independently folding S-and C-domains for concerted recognition of precursor tRNA substrates. Here, we analyze the effects of mutations in these tertiary contacts in P RNAs from three different species: (i) the psychrophilic bacterium Pseudoalteromonas translucida (Ptr), (ii) the mesophilic radiation-resistant bacterium Deinococcus radiodurans (Dra), and (iii) the thermophilic bacterium Thermus thermophilus (Tth). We show by UV melting experiments that simultaneous disruption of these two interdomain contacts has a stabilizing effect on all three P RNAs. This can be inferred from reduced RNA unfolding at lower temperatures and a more concerted unfolding at higher temperatures. Thus, when the two domains tightly interact via the tertiary contacts, one domain facilitates structural transitions in the other. P RNA mutants with disrupted interdomain contacts showed severe kinetic defects that were most pronounced upon simultaneous disruption of the L8-P4 and L18-P8 contacts. At 37°C, the mildest effects were observed for the thermostable Tth RNA. A third interdomain contact, L9-P1, makes only a minor contribution to P RNA tertiary folding. Furthermore, D. radiodurans RNase P RNA forms an additional pseudoknot structure between the P9 and P12 of its S-domain. This interaction was found to be particularly crucial for RNase P holoenzyme activity at near-physiological Mg 2+ concentrations (2 mM). We further analyzed an exceptionally stable folding trap of the G,C-rich Tth P RNA.

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Critical domain interactions for type A RNase P RNA catalysis with and without the specificity domain

Cited by 11 publications

References 54 publications

Modular Architecture of Bacterial RNase P Ribozymes as a Structural Platform for RNA Nanostructure Design

Modular Architecture of Bacterial RNase P Ribozymes as a Structural Platform for RNA Nanostructure Design

Cryo-electron microscopy structure of an archaeal ribonuclease P holoenzyme

Comparative study on tertiary contacts and folding of RNase P RNAs from a psychrophilic, a mesophilic/radiation-resistant, and a thermophilic bacterium

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