A fifth protein subunit Ph1496p elevates the optimum temperature for the ribonuclease P activity from Pyrococcus horikoshii OT3

Fukuhara, Hideo; Kifusa, Mayumi; Watanabe, Mitsutoshi; Terada, Atsushi; Honda, Takashi; Numata, T.; Kakuta, Yoshimitsu; Kimura, Makoto

doi:10.1016/j.bbrc.2006.02.192

Cited by 61 publications

(92 citation statements)

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“…Subsequently, a fifth protein, PhoRpp38 (an archaeal homolog of human Rpp38), was found to be involved in elevating the optimal temperature of the reconstituted particle (R-5P). 23) Although these results indicate that PhopRNA and five protein subunits reconstitute a RNase P that exhibits enzymatic properties of the authentic enzyme, we could not exclude the possibility of the presence of additional protein components in P. horikoshii RNase P, due to a lack of information about protein subunits of authentic RNase P.…”

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confidence: 77%

“…Cloning and expression of the resulting DNA fragment were done in a manner identical to those described for expression of P. horikoshii RNase P proteins. 21,23) E. coli lysate overproducing PhoAlba in 50 mM Tris-HCl (pH 7.0), containing 200 mM NaCl, was first heated at 80 C for 40 min, and then the supernatant was applied onto a SP-Sepharose FF column (1:5 Â 12 cm) equilibrated with 50 mM TrisHCl (pH 7.0), containing 200 mM NaCl. The protein was eluted with a linear gradient from 0.2 to 1.2 M NaCl in the starting buffer, and the purified protein was dialyzed against 50 mM Tris-HCl (pH 7.0) buffer, containing 200 mM NaCl, 10 mM MgCl 2 , and 200 mM arginine hydrochloride.…”

Section: Methodsmentioning

confidence: 99%

“…The RNA-binding capacity of PhoAlba for PhopRNA and pre-tRNA Tyr was tested by gel shift assay, as described previously. 21,23) The involvement of PhoAlba in pre-tRNA processing activity was analyzed as follows: reconstituted particles R-5P and R-4P, composed of PhopRNA and four and five proteins respectively, were prepared, and then an equimolar amount of PhoAlba was added. The pretRNA processing activity for R-5P and R-4P was analyzed at 55 C and 70 C respectively for the indicated periods of time using in vitro transcribed 32 P-labelled P. horikoshii pre-tRNA Tyr , as described previously.…”

Section: Methodsmentioning

confidence: 99%

“…The pretRNA processing activity for R-5P and R-4P was analyzed at 55 C and 70 C respectively for the indicated periods of time using in vitro transcribed 32 P-labelled P. horikoshii pre-tRNA Tyr , as described previously. 21,23) The optimum temperature of the reconstituted R-4P and PhoAlba was analyzed as described above, except that the activity was measured at various temperatures. Reaction products were separated on 15% polyacrylamide denaturing gels, and then visualized using a PhosphorImager, FLA-5000 (Fuji Film, Tokyo).…”

Section: Methodsmentioning

confidence: 99%

“…Five RNase P proteins (PhoPop5, PhoRpp21, PhoRpp29, PhoRpp30, and PhoRpp38), PhopRNA, and 32 P-labeled pre-tRNA Tyr in P. horikoshii were prepared as described previously. 21,23) All nucleotide sequence data were cited in the P. horikoshii OT3 genome database (http://www.bio.nite.go.jp). All other chemicals were of analytical grade for biochemical use.…”

Section: Methodsmentioning

confidence: 99%

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Crystal Structure and Functional Analysis of an Archaeal Chromatin Protein Alba from the Hyperthermophilic ArchaeonPyrococcus horikoshiiOT3

Hada

Nakashima

Osawa

et al. 2008

Bioscience, Biotechnology, and Biochemistry

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mentioning

confidence: 77%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 3 more Smart Citations

Crystal Structure and Functional Analysis of an Archaeal Chromatin Protein Alba from the Hyperthermophilic ArchaeonPyrococcus horikoshiiOT3

Hada

Nakashima

Osawa

et al. 2008

Bioscience, Biotechnology, and Biochemistry

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Homologs of aquifex aeolicus protein‐only RNase P are not the major RNase P activities in the archaea haloferax volcanii and methanosarcina mazei

et al. 2019

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The mature 5′‐ends of tRNAs are generated by RNase P in all domains of life. The ancient form of the enzyme is a ribonucleoprotein consisting of a catalytic RNA and one or more protein subunits. However, in the hyperthermophilic bacterium Aquifex aeolicus and close relatives, RNase P is a protein‐only enzyme consisting of a single type of polypeptide (Aq_880, ~23 kDa). In many archaea, homologs of Aq_880 were identified (termed HARPs for Homologs of Aquifex RNase P) in addition to the RNA‐based RNase P, raising the question about the functions of HARP and the classical RNase P in these archaea. Here we investigated HARPs from two euryarchaeotes, Haloferax volcanii and Methanosarcina mazei. Archaeal strains with HARP gene knockouts showed no growth phenotypes under standard conditions, temperature and salt stress (H. volcanii) or nitrogen deficiency (M. mazei). Recombinant H. volcanii and M. mazei HARPs were basically able to catalyse specific tRNA 5′‐end maturation in vitro. Furthermore, M. mazei HARP was able to rescue growth of an Escherichia coli RNase P depletion strain with comparable efficiency as Aq_880, while H. volcanii HARP was unable to do so. In conclusion, both archaeal HARPs showed the capacity (in at least one functional assay) to act as RNases P. However, the ease to obtain knockouts of the singular HARP genes and the lack of growth phenotypes upon HARP gene deletion contrasts with the findings that the canonical RNase P RNA gene cannot be deleted in H. volcanii, and a knockdown of RNase P RNA in H. volcanii results in severe tRNA processing defects. We conclude that archaeal HARPs do not make a major contribution to global tRNA 5′‐end maturation in archaea, but may well exert a specialised, yet unknown function in (t)RNA metabolism. © 2019 IUBMB Life, 2019 © 2019 IUBMB Life, 71(8):1109–1116, 2019

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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

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A fifth protein subunit Ph1496p elevates the optimum temperature for the ribonuclease P activity from Pyrococcus horikoshii OT3

Cited by 61 publications

References 39 publications

Crystal Structure and Functional Analysis of an Archaeal Chromatin Protein Alba from the Hyperthermophilic ArchaeonPyrococcus horikoshiiOT3

Crystal Structure and Functional Analysis of an Archaeal Chromatin Protein Alba from the Hyperthermophilic ArchaeonPyrococcus horikoshiiOT3

Homologs of aquifex aeolicus protein‐only RNase P are not the major RNase P activities in the archaea haloferax volcanii and methanosarcina mazei

Multiple structural flavors of RNase P in precursor tRNA processing

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