関: RNase P

WordNet

the 16th letter of the Roman alphabet (同)p
a transferase that catalyzes the hydrolysis of ribonucleic acid (同)ribonucleinase, RNase
a river in western Thailand; a major tributary of the Chao Phraya (同)Ping River

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parking
phosphorusの化学記号
palladiumの化学記号

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出典(authority):フリー百科事典『ウィキペディア（Wikipedia）』「2014/01/16 23:49:50」(JST)

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Crystal structure of a bacterial ribonuclease P holoenzyme in complex with tRNA (yellow), showing metal ions involved in catalysis (pink spheres), PDB 3Q1R

Archaeal RNase P class T
Predicted secondary structure and sequence conservation of the small form of Archaeal RNase P found in the Thermoproteaceae
Identifiers
Symbol	RNaseP_arch_t
Rfam	TBD
Other data
RNA type	Gene; ribozyme
Domain(s)	Archaea
GO	0008033 0004526 0030680
SO	0000386

Ribonuclease P (EC 3.1.26.5, RNase P) is a type of ribonuclease which cleaves RNA. RNase P is unique from other RNases in that it is a ribozyme – a ribonucleic acid that acts as a catalyst in the same way that a protein based enzyme would. Its function is to cleave off an extra, or precursor, sequence of RNA on tRNA molecules.^[1] Further RNase P is one of two known multiple turnover ribozymes in nature (the other being the ribosome), the discovery of which earned Sidney Altman and Thomas Cech the Nobel Prize in Chemistry in 1989: in the 1970s, Altman discovered the existence of precursor tRNA with flanking sequences and was the first to characterize RNase P and its activity in processing of the 5' leader sequence of precursor tRNA. Recent findings also reveal that RNase P has a new function.^[2] It has been shown that human nuclear RNase P is required for the normal and efficient transcription of various small noncoding RNAs, such as tRNA, 5S rRNA, SRP RNA and U6 snRNA genes,^[3] which are transcribed by RNA polymerase III, one of three major nuclear RNA polymerases in human cells.

In bacteria[edit]

Bacterial RNase P has two components: an RNA chain, called M1 RNA, and a polypeptide chain, or protein, called C5 protein.^[4]^[5] In vivo, both components are necessary for the ribozyme to function properly, but in vitro, the M1 RNA can act alone as a catalyst.^[1] The primary role of the C5 protein is to enhance the substrate binding affinity and the catalytic rate of the M1 RNA enzyme probably by increasing the metal ion affinity in the active site. The crystal structure of a bacterial RNase P holoenzyme with tRNA has been recently resolved, showing how the large, coaxially stacked helical domains of the RNase P RNA engage in shape selective recognition of the pre-tRNA target. This crystal structure confirms earlier models of substrate recognition and catalysis, identifies the location of the active site, and shows how the protein component increases RNase P functionality.^[6]^[7]

Bacterial RNase P class A and B[edit]

Ribonuclease P (RNase P) is a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterised activity is the generation of mature 5'-ends of tRNAs by cleaving the 5'-leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins (RNP). RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous—helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs.

In archaea[edit]

In archaea, RNase P ribonucleoproteins consist of 4-5 protein subunits that are associated with RNA. As revealed by in vitro reconstitution experiments these protein subunits are individually dispensable for tRNA processing that is essentially mediated by the RNA component.^[8]^[9]^[10] The structures of protein subunits of archaeal RNase P have been resolved by x-ray crystallography and NMR, thus revealing new protein domains and folding fundamental for function.

Isolated eukaryotic RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous—helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs.

Using comparative genomics and improved computational methods, a radically minimized form of the RNase P RNA, dubbed "Type T", has been found in all complete genomes in the crenarchaeal phylogenetic family Thermoproteaceae, including species in the genera Pyrobaculum, Caldivirga and Vulcanisaeta.^[11] All retain a conventional catalytic domain, but lack a recognizable specificity domain. 5′ tRNA processing activity of the RNA alone was experimentally confirmed. The Pyrobaculum and Caldivirga RNase P RNAs are the smallest naturally occurring form yet discovered to function as trans-acting ribozymes.^[11] Loss of the specificity domain in these RNAs suggests potential altered substrate specificity.

It has recently been argued that the archaebacteriium Nanoarchaeum equitans does not possess RNase P. Computational and experimental studies failed to find evidence for its existence. In this organism the tRNA promoter is close to the tRNA gene and it is thought that transcription starts at the first base of the tRNA thus removing the requirement for RNase P.^[12]

In eukaryotes[edit]

Further information: Nuclear RNase P

In eukaryotes, such as humans and yeast, most RNase P consists of an RNA chain that is structurally similar to that found in bacteria ^[13] as well as nine to ten associated proteins (as opposed to the single bacterial RNase P protein, C5).^[2]^[14] Five of these protein subunits exhibit homology to archaeal counterparts. These protein subunits of RNase P are shared with RNase MRP,^[14]^[15]^[16] a catalytic ribonucleoprotein involved in processing of ribosomal RNA in the nucleolus.^[17] RNase P from eukaryotes was only recently demonstrated to be a ribozyme.^[18] Accordingly, the numerous protein subunits of eucaryal RNase P have a minor contribution to tRNA processing per se,^[19] while they seem to be essential for the function of RNase P and RNase MRP in other biological settings, such as gene transcription and the cell cycle.^[3]^[20] Despite the bacterial origins of mitochondria and chloroplasts, plastids from higher animals and plants do not appear to contain an RNA-based RNase P. It has been shown that human mitochondrial RNase P is a protein and does not contain RNA.^[21] Spinach chloroplast RNase P has also been shown to function without an RNA subunit.^[22]

References[edit]

^ ^a ^b Guerrier-Takada C, Gardiner K, Marsh T, Pace N, Altman S (1983). "The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme". Cell 35 (3 Pt 2): 849–57. doi:10.1016/0092-8674(83)90117-4. PMID 6197186.
^ ^a ^b Jarrous N, Reiner R (2007). "Human RNase P: a tRNA-processing enzyme and transcription factor". Nucleic Acids Res. 35 (11): 3519–24. doi:10.1093/nar/gkm071. PMC 1920233. PMID 17483522.
^ ^a ^b Reiner R, Ben-Asouli Y, Krilovetzky I, Jarrous N (2006). "A role for the catalytic ribonucleoprotein RNase P in RNA polymerase III transcription". Genes Dev. 20 (12): 1621–35. doi:10.1101/gad.386706. PMC 1482482. PMID 16778078.
^ Evans D, Marquez SM, Pace NR (2006). "RNase P: interface of the RNA and protein worlds". Trends Biochem. Sci. 31 (6): 333–41. doi:10.1016/j.tibs.2006.04.007. PMID 16679018.
^ Tsai HY, Masquida B, Biswas R, Westhof E, Gopalan V (2003). "Molecular modeling of the three-dimensional structure of the bacterial RNase P holoenzyme". J. Mol. Biol. 325 (4): 661–75. doi:10.1016/S0022-2836(02)01267-6. PMID 12507471.
^ Reiter N, Osterman A, Torres-Larios A, Swinger KK, Pan T, Mondragon A, Nicholas J.; Osterman, Amy; Torres-Larios, Alfredo; Swinger, Kerren K.; Pan, Tao; Mondragón, Alfonso (2010). "Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA". Nature 468 (7325): 784–789. doi:10.1038/nature09516. PMC 3058908. PMID 21076397.
^ Masquida B, Westhof E, B.; Westhof, E. (2011). "RNase P: At last, the key finds its lock". RNA 17 (9): 1615–1618. doi:10.1261/rna.2841511. PMC 3162327. PMID 21803972.
^ Hall TA, Brown JW (2002). "Archaeal RNase P has multiple protein subunits homologous to eukaryotic nuclear RNase P proteins". RNA 8 (3): 296–306. doi:10.1017/S1355838202028492. PMC 1370252. PMID 12003490.
^ Fukuhara H, Kifusa M, Watanabe M, Terada A, Honda T, Numata T, Kakuta Y, Kimura M (2006). "A fifth protein subunit Ph1496p elevates the optimum temperature for the ribonuclease P activity from Pyrococcus horikoshii OT3". Biochem. Biophys. Res. Commun. 343 (3): 956–64. doi:10.1016/j.bbrc.2006.02.192. PMID 16574071.
^ Tsai HY, Pulukkunat DK, Woznick WK, Gopalan V (2006). "Functional reconstitution and characterization of Pyrococcus furiosus RNase P". Proc. Natl. Acad. Sci. U.S.A. 103 (44): 16147–52. doi:10.1073/pnas.0608000103. PMC 1637551. PMID 17053064.
^ ^a ^b Lai LB, Chan PP, Cozen AE, et al. (December 2010). "Discovery of a minimal form of RNase P in Pyrobaculum". Proc. Natl. Acad. Sci. U.S.A. 107 (52): 22493–8. doi:10.1073/pnas.1013969107. PMC 3012483. PMID 21135215. Cite uses deprecated parameters (help)
^ Randau L, Schröder I, Söll D (May 2008). "Life without RNase P". Nature 453 (7191): 120–3. doi:10.1038/nature06833. PMID 18451863. Cite uses deprecated parameters (help)
^ Marquez SM, Chen JL, Evans D, Pace NR (2006). "Structure and Function of Eukaryotic Ribonuclease P RNA". Mol. Cell 24 (3): 445–56. doi:10.1016/j.molcel.2006.09.011. PMC 1716732. PMID 17081993.
^ ^a ^b Chamberlain JR, Lee Y, Lane WS, Engelke DR (1998). "Purification and characterization of the nuclear RNase P holoenzyme complex reveals extensive subunit overlap with RNase MRP". Genes Dev. 12 (11): 1678–90. doi:10.1101/gad.12.11.1678. PMC 316871. PMID 9620854.
^ Salinas K, Wierzbicki S, Zhou L, Schmitt ME (2005). "Characterization and purification of Saccharomyces cerevisiae RNase MRP reveals a new unique protein component". J. Biol. Chem. 280 (12): 11352–60. doi:10.1074/jbc.M409568200. PMID 15637077.
^ Welting TJ, Kikkert BJ, van Venrooij WJ, Pruijn GJ (2006). "Differential association of protein subunits with the human RNase MRP and RNase P complexes". RNA 12 (7): 1373–82. doi:10.1261/rna.2293906. PMC 1484433. PMID 16723659.
^ Clayton DA (2001). "A big development for a small RNA". Nature 410 (6824): 29, 31. doi:10.1038/35065191. PMID 11242026.
^ Kikovska E, Svärd SG, Kirsebom LA (2007). "Eukaryotic RNase P RNA mediates cleavage in the absence of protein". Proc. Natl. Acad. Sci. U.S.A. 104 (7): 2062–7. doi:10.1073/pnas.0607326104. PMC 1892975. PMID 17284611.
^ Willkomm DK, Hartmann RK (2007). "An important piece of the RNase P jigsaw solved". Trends Biochem. Sci. 32 (6): 247–50. doi:10.1016/j.tibs.2007.04.005. PMID 17485211.
^ Gill T, Cai T, Aulds J, Wierzbicki S, Schmitt ME (2004). "RNase MRP Cleaves the CLB2 mRNA To Promote Cell Cycle Progression: Novel Method of mRNA Degradation". Mol. Cell. Biol. 24 (3): 945–53. doi:10.1128/MCB.24.3.945-953.2004. PMC 321458. PMID 14729943.
^ J. Holzmann, P. Frank, E. Löffler, K. Bennett, C. Gerner & W. Rossmanith (2008). "RNase P without RNA: Identification and functional reconstitution of the human mitochondrial tRNA processing enzyme". Cell 135 (3): 462–474. doi:10.1016/j.cell.2008.09.013. PMID 18984158.
^ B. C. Thomas, X. Li, & P. Gegenheimer (2000). "Chloroplast ribonuclease P does not utilize the ribozyme-type pre-tRNA cleavage mechanism". RNA 6 (4): 545–553. doi:10.1017/S1355838200991465. PMID 10786845.

External links[edit]

RNase P Database at ncsu.edu
Page for Nuclear RNase P at Rfam
Page for Archaeal RNase P at Rfam
Page for Bacterial RNase P class A at Rfam
Page for Bacterial RNase P class B at Rfam

RNase P at the US National Library of Medicine Medical Subject Headings (MeSH)
EC 3.1.26.5

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English Journal

Initial steps in RNA processing and ribosome assembly occur at mitochondrial DNA nucleoids.

Bogenhagen DF1, Martin DW2, Koller A3.Author information 1Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA. Electronic address: daniel.bogenhagen@stonybrook.edu.2Department of Medicine, Stony Brook University, Stony Brook, NY 11794-8160, USA; Proteomics Center, Stony Brook University, Stony Brook, NY 11794-8691, USA.3Proteomics Center, Stony Brook University, Stony Brook, NY 11794-8691, USA.AbstractMammalian mitochondrial DNA (mtDNA) resides in compact nucleoids, where it is replicated and transcribed into long primary transcripts processed to generate rRNAs, tRNAs, and mRNAs encoding 13 proteins. This situation differs from bacteria and eukaryotic nucleoli, which have dedicated rRNA transcription units. The assembly of rRNAs into mitoribosomes has received little study. We show that mitochondrial RNA processing enzymes involved in tRNA excision, ribonuclease P (RNase P) and ELAC2, as well as a subset of nascent mitochondrial ribosomal proteins (MRPs) associate with nucleoids to initiate RNA processing and ribosome assembly. SILAC pulse-chase labeling experiments show that nascent MRPs recruited to the nucleoid fraction were highly labeled after the pulse in a transcription-dependent manner and decreased in labeling intensity during the chase. These results provide insight into the landscape of binding events required for mitochondrial ribosome assembly and firmly establish the mtDNA nucleoid as a control center for mitochondrial biogenesis.
Cell metabolism.Cell Metab.2014 Apr 1;19(4):618-29. doi: 10.1016/j.cmet.2014.03.013.
Mammalian mitochondrial DNA (mtDNA) resides in compact nucleoids, where it is replicated and transcribed into long primary transcripts processed to generate rRNAs, tRNAs, and mRNAs encoding 13 proteins. This situation differs from bacteria and eukaryotic nucleoli, which have dedicated rRNA transcri
PMID 24703694

Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5'-ends of primary transcripts.

Schwientek P1, Neshat A2, Kalinowski J2, Klein A3, Rückert C2, Schneiker-Bekel S4, Wendler S4, Stoye J5, Pühler A6.Author information 1Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; Genome Informatics Research Group, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany.2Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany.3Bayer HealthCare AG, Friedrich-Ebert-Str. 475, 42117 Wuppertal, Germany.4Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany.5Genome Informatics Research Group, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany; Institute for Bioinformatics, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany.6Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany. Electronic address: Puehler@CeBiTec.Uni-Bielefeld.de.AbstractActinoplanes sp. SE50/110 is the producer of the alpha-glucosidase inhibitor acarbose, which is an economically relevant and potent drug in the treatment of type-2 diabetes mellitus. In this study, we present the detection of transcription start sites on this genome by sequencing enriched 5'-ends of primary transcripts. Altogether, 1427 putative transcription start sites were initially identified. With help of the annotated genome sequence, 661 transcription start sites were found to belong to the leader region of protein-coding genes with the surprising result that roughly 20% of these genes rank among the class of leaderless transcripts. Next, conserved promoter motifs were identified for protein-coding genes with and without leader sequences. The mapped transcription start sites were finally used to improve the annotation of the Actinoplanes sp. SE50/110 genome sequence. Concerning protein-coding genes, 41 translation start sites were corrected and 9 novel protein-coding genes could be identified. In addition to this, 122 previously undetermined non-coding RNA (ncRNA) genes of Actinoplanes sp. SE50/110 were defined. Focusing on antisense transcription start sites located within coding genes or their leader sequences, it was discovered that 96 of those ncRNA genes belong to the class of antisense RNA (asRNA) genes. The remaining 26 ncRNA genes were found outside of known protein-coding genes. Four chosen examples of prominent ncRNA genes, namely the transfer messenger RNA gene ssrA, the ribonuclease P class A RNA gene rnpB, the cobalamin riboswitch RNA gene cobRS, and the selenocysteine-specific tRNA gene selC, are presented in more detail. This study demonstrates that sequencing of enriched 5'-ends of primary transcripts and the identification of transcription start sites are valuable tools for advanced genome annotation of Actinoplanes sp. SE50/110 and most probably also for other bacteria.
Journal of biotechnology.J Biotechnol.2014 Mar 15. pii: S0168-1656(14)00116-3. doi: 10.1016/j.jbiotec.2014.03.013. [Epub ahead of print]
Actinoplanes sp. SE50/110 is the producer of the alpha-glucosidase inhibitor acarbose, which is an economically relevant and potent drug in the treatment of type-2 diabetes mellitus. In this study, we present the detection of transcription start sites on this genome by sequencing enriched 5'-ends of
PMID 24642337

Mutation or knock-down of 17β-hydroxysteroid dehydrogenase type 10 cause loss of MRPP1 and impaired processing of mitochondrial heavy strand transcripts.

Deutschmann AJ1, Amberger A, Zavadil C, Steinbeisser H, Mayr JA, Feichtinger RG, Oerum S, Yue WW, Zschocke J.Author information 1Division of Human Genetics, Innsbruck Medical University, Innsbruck 6020, Austria.Abstract17β-Hydroxysteroid dehydrogenase type 10 (HSD10) is multifunctional protein coded by the X-chromosomal HSD17B10 gene. Mutations in this gene cause HSD10 disease characterized by progressive neurological abnormalities and cardiomyopathy. Disease progression and severity of symptoms is unrelated to the protein's dehydrogenase activity. Recently, it was shown that HSD10 is an essential component of mitochondrial Ribonuclease P (RNase P), an enzyme required for mitochondrial tRNA processing, but little is known about the role of HSD10 in RNase P function. RNase P consists of three different proteins MRPP1, MRPP2 (HSD10) and MRPP3, each of which is essential for RNase P function. Here, we show that HSD10 protein levels are significantly reduced in fibroblasts from patients carrying the HSD17B10 mutation p.R130C. A reduction in HSD10 levels was accompanied by a reduction in MRPP1 protein but not MRPP3 protein. In HSD10 knock-down cells, MRPP1 protein content was also reduced, indicating that HSD10 is important for the maintenance of normal MRPP1 protein levels. Ectopic expression of HSD10 partially restored RNA processing in HSD10 knock-down cells and fibroblasts, and also expression of MRPP1 protein was restored to values comparable to controls. In both, patient fibroblasts and HSD10 knock-down cells, there was evidence of impaired processing of precursor tRNA transcripts of the mitochondrial heavy strand but not the light strand compared with controls. Our findings indicate that HSD10 is important for the maintenance of the MRPP1-HSD10 subcomplex of RNase P and that loss of HSD10 causes impaired mitochondrial precursor transcript processing which may explain mitochondrial dysfunction observed in HSD10 disease.
Human molecular genetics.Hum Mol Genet.2014 Feb 26. [Epub ahead of print]
17β-Hydroxysteroid dehydrogenase type 10 (HSD10) is multifunctional protein coded by the X-chromosomal HSD17B10 gene. Mutations in this gene cause HSD10 disease characterized by progressive neurological abnormalities and cardiomyopathy. Disease progression and severity of symptoms is unrelated to t
PMID 24549042

Japanese Journal

Identification of the specific interactors of the human lariat RNA debranching enzyme 1 protein.

Masaki So,Yoshimoto Rei,Kaida Daisuke,Hata Asuka,Satoh Takayuki,Ohno Mutsuhito,Kataoka Naoyuki
International journal of molecular sciences 16(2), 3705-3721, 2015-02-09
… This protein is well conserved among many species and shows the highest similarity to yeast Drn1, so it is designated as human Dbr1 associated ribonuclease 1 (hDrn1). …
NAID 120005555507

シアル酸結合レクチン(SBL)のマウス白血病細胞に対するアポトーシス誘導機構

小川由起子,藤井佑樹,菅原栄紀,細野雅佑,立田岳生,仁田一雄,小出康裕, ,大関泰裕
日本女性科学者の会学術誌 15(1), 39-45, 2015
ウシガエル未受精卵に発見されたシアル酸結合レクチン (SBL) は、リボヌクレアーゼ活性を有し、がん細胞特異的に細胞に傷害を与える、興味深い作用を持ったレクチンである。SBLがマウス白血病P388細胞に起こした細胞死は、細胞表面のシアル酸を除くと失われ、がん細胞表面糖鎖のシアル酸を持つリガンド糖鎖との結合が必須と判明した。SBLはリガンドに結合すると細胞中のカスパーゼ-8とカスパーゼ-3を活性化さ …
NAID 130005063872

Mutagenesis of the Novel Hericium erinaceus Ribonuclease, RNase He1, Reveals Critical Responsible Residues for Enzyme Stability and Activity

Kobayashi Hiroko,Motoyoshi Naomi,Itagaki Tadashi [他]
Biological & pharmaceutical bulletin 37(11), 1843-1847, 2014-11
NAID 40020248141

「リボヌクレアーゼP」

Archaeal RNase P
	Predicted secondary structure and sequence conservation of Archaeal RNase P
Identifiers
Symbol	RNaseP_arch
Rfam	RF00373
	Other data
RNA type	Gene; ribozyme
Domain(s)	Archaea
GO	0008033 0004526 0030680
SO	0000386

Bacterial RNase P class B
	Predicted secondary structure and sequence conservation of RNaseP_bact_b
Identifiers
Symbol	RNaseP_bact_b
Rfam	RF00011
	Other data
RNA type	Gene; ribozyme
Domain(s)	Bacteria
GO	0008033 0004526 0030680
SO	0000386

Bacterial RNase P class A
	Predicted secondary structure and sequence conservation of RNaseP_bact_a
Identifiers
Symbol	RNaseP_bact_a
Rfam	RF00010
	Other data
RNA type	Gene; ribozyme
Domain(s)	Bacteria
GO	0008033 0004526 0030680
SO	0000386