Minimal protein-only RNase P structure reveals insights into tRNA precursor recognition and catalysis

Teramoto, Takamasa; Koyasu, Takeshi; Adachi, Naruhiko; Kawasaki, Masato; Moriya, Toshio; Numata, T.; Senda, Toshiya; Kakuta, Yoshimitsu

doi:10.1016/j.jbc.2021.101028

Cited by 14 publications

(23 citation statements)

References 38 publications

(44 reference statements)

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Section: Prokaryotic Minimal Protein-only Rnase Psmentioning

confidence: 99%

“…Recent cryo-EM studies of HARPs from A. aeolicus and Halorhodospira halophila demonstrate that they adopt a different architecture than eukaryotic PRORPs [61,62]. They assemble into large dodecameric assemblies comprised of hexamers of dimers, wherein two monomers dimerise via their spike helix or protruding helix (SH/PrH) microdomains, and the resulting dimers interact side by side to form a superhelical assembly (Figure 3) [61,62]. The overall fold of the individual monomers is distinct from the nuclease domain of eukaryotic PRORPs, and instead shows similarities to different members of the PIN family, for example, the VapC4 toxin from Pyrococcus horikoshii [40,60,61,63,64].…”

Section: Prokaryotic Minimal Protein-only Rnase Psmentioning

confidence: 99%

“…They assemble into large dodecameric assemblies comprised of hexamers of dimers, wherein two monomers dimerise via their spike helix or protruding helix (SH/PrH) microdomains, and the resulting dimers interact side by side to form a superhelical assembly (Figure 3) [61,62]. The overall fold of the individual monomers is distinct from the nuclease domain of eukaryotic PRORPs, and instead shows similarities to different members of the PIN family, for example, the VapC4 toxin from Pyrococcus horikoshii [40,60,61,63,64]. This suggests that HARPs may have an independent evolutionary origin from eukaryotic PRORPs [61,62].…”

Section: Prokaryotic Minimal Protein-only Rnase Psmentioning

confidence: 99%

“…The overall fold of the individual monomers is distinct from the nuclease domain of eukaryotic PRORPs, and instead shows similarities to different members of the PIN family, for example, the VapC4 toxin from Pyrococcus horikoshii [40,60,61,63,64]. This suggests that HARPs may have an independent evolutionary origin from eukaryotic PRORPs [61,62]. Biochemical experiments show that the oligomerisation of HARPs is necessary for their RNase P activity [62], and it has been proposed that two adjacent dimers may cooperate to mediate processing of a single tRNA molecule [61,62].…”

Section: Prokaryotic Minimal Protein-only Rnase Psmentioning

confidence: 99%

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Structural and mechanistic basis of RNA processing by protein-only ribonuclease P enzymes

Bhatta¹,

Hillen²

2022

Trends in Biochemical Sciences

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Section: Prokaryotic Minimal Protein-only Rnase Psmentioning

confidence: 99%

Section: Prokaryotic Minimal Protein-only Rnase Psmentioning

confidence: 99%

Section: Prokaryotic Minimal Protein-only Rnase Psmentioning

confidence: 99%

Section: Prokaryotic Minimal Protein-only Rnase Psmentioning

confidence: 99%

See 2 more Smart Citations

Structural and mechanistic basis of RNA processing by protein-only ribonuclease P enzymes

Bhatta¹,

Hillen²

2022

Trends in Biochemical Sciences

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“…Moreover, the protein-only HARPs found in prokaryotes are smaller enzymes than plant PRORPs and lack a PPR-equivalent domain [15]. As shown by the recent structures from A. aeolicus and H. halophila, HARPs form homododecamers with two adjacent subunits required for processing a single pre-tRNA [42,43]. Recognition of pre-tRNAs by HARPs is achieved through a manner similar to plant PRORPs and RNase P RNP [42].…”

Section: Universal Recognition Of Pre-trnas By Rnase P Holoenzymes From a Structural Point Of Viewmentioning

confidence: 99%

The Dynamic Network of RNP RNase P Subunits

Shaukat

Kaliatsi

Skeparnias

et al. 2021

IJMS

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Ribonuclease P (RNase P) is an important ribonucleoprotein (RNP), responsible for the maturation of the 5′ end of precursor tRNAs (pre-tRNAs). In all organisms, the cleavage activity of a single phosphodiester bond adjacent to the first nucleotide of the acceptor stem is indispensable for cell viability and lies within an essential catalytic RNA subunit. Although RNase P is a ribozyme, its kinetic efficiency in vivo, as well as its structural variability and complexity throughout evolution, requires the presence of one protein subunit in bacteria to several protein partners in archaea and eukaryotes. Moreover, the existence of protein-only RNase P (PRORP) enzymes in several organisms and organelles suggests a more complex evolutionary timeline than previously thought. Recent detailed structures of bacterial, archaeal, human and mitochondrial RNase P complexes suggest that, although apparently dissimilar enzymes, they all recognize pre-tRNAs through conserved interactions. Interestingly, individual protein subunits of the human nuclear and mitochondrial holoenzymes have additional functions and contribute to a dynamic network of elaborate interactions and cellular processes. Herein, we summarize the role of each RNase P subunit with a focus on the human nuclear RNP and its putative role in flawless gene expression in light of recent structural studies.

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Multiple structural flavors of RNase P in precursor tRNA processing

Sridhara

2024

WIREs RNA

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The precursor transfer RNAs (pre‐tRNAs) require extensive processing to generate mature tRNAs possessing proper fold, structural stability, and functionality required to sustain cellular viability. The road to tRNA maturation follows an ordered process: 5′‐processing, 3′‐processing, modifications at specific sites, if any, and 3′‐CCA addition before aminoacylation and recruitment to the cellular protein synthesis machinery. Ribonuclease P (RNase P) is a universally conserved endonuclease in all domains of life, performing the hydrolysis of pre‐tRNA sequences at the 5′ end by the removal of phosphodiester linkages between nucleotides at position −1 and +1. Except for an archaeal species: Nanoarchaeum equitans where tRNAs are transcribed from leaderless‐position +1, RNase P is indispensable for life and displays fundamental variations in terms of enzyme subunit composition, mechanism of substrate recognition and active site architecture, utilizing in all cases a two metal ion‐mediated conserved catalytic reaction. While the canonical RNA‐based ribonucleoprotein RNase P has been well‐known to occur in bacteria, archaea, and eukaryotes, the occurrence of RNA‐free protein‐only RNase P in eukaryotes and RNA‐free homologs of Aquifex RNase P in prokaryotes has been discovered more recently. This review aims to provide a comprehensive overview of structural diversity displayed by various RNA‐based and RNA‐free RNase P holoenzymes towards harnessing critical RNA–protein and protein–protein interactions in achieving conserved pre‐tRNA processing functionality. Furthermore, alternate roles and functional interchangeability of RNase P are discussed in the context of its employability in several clinical and biotechnological applications.This article is categorized under: RNA Processing > tRNA Processing RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Interactions with Proteins and Other Molecules > RNA‐Protein Complexes

show abstract

Minimal protein-only RNase P structure reveals insights into tRNA precursor recognition and catalysis

Cited by 14 publications

References 38 publications

Structural and mechanistic basis of RNA processing by protein-only ribonuclease P enzymes

Structural and mechanistic basis of RNA processing by protein-only ribonuclease P enzymes

The Dynamic Network of RNP RNase P Subunits

Multiple structural flavors of RNase P in precursor tRNA processing

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