Structural modeling of RNase P RNA of the hyperthermophilic archaeon Pyrococcus horikoshii OT3

Zwieb, Christian W; Nakao, Yûji; Nakashima, Takashi; Takagi, Hisanori; Goda, Shuichiro; Andersen, Ellen Juul; Kakuta, Yoshimitsu; Kimura, Makoto

doi:10.1016/j.bbrc.2011.09.098

Cited by 13 publications

(19 citation statements)

References 40 publications

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“…Accordingly, in the absence of an available high-resolution structure of eukaryotic RNase P, the locations and structures of the conserved core elements in bacterial RNase P can serve as a first approximation for the locations of the corresponding elements in eukaryotic enzymes. The resulting outline of the core elements of the RNA component is similar to that in the recently proposed model of the RNA component of archaeal RNase P (Zwieb et al 2011).…”

Section: D Mapping Of Rna-protein Interactions In Yeast Rnase Psupporting

confidence: 76%

Structural organizations of yeast RNase P and RNase MRP holoenzymes as revealed by UV-crosslinking studies of RNA–protein interactions

Khanova¹,

Esakova²,

Perederina³

et al. 2012

RNA

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Eukaryotic ribonuclease (RNase) P and RNase MRP are closely related ribonucleoprotein complexes involved in the metabolism of various RNA molecules including tRNA, rRNA, and some mRNAs. While evolutionarily related to bacterial RNase P, eukaryotic enzymes of the RNase P/MRP family are much more complex. Saccharomyces cerevisiae RNase P consists of a catalytic RNA component and nine essential proteins; yeast RNase MRP has an RNA component resembling that in RNase P and 10 essential proteins, most of which are shared with RNase P. The structural organizations of eukaryotic RNases P/MRP are not clear. Here we present the results of RNA-protein UV crosslinking studies performed on RNase P and RNase MRP holoenzymes isolated from yeast. The results indicate locations of specific protein-binding sites in the RNA components of RNase P and RNase MRP and shed light on the structural organizations of these large ribonucleoprotein complexes.

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Section: D Mapping Of Rna-protein Interactions In Yeast Rnase Psupporting

confidence: 76%

Structural organizations of yeast RNase P and RNase MRP holoenzymes as revealed by UV-crosslinking studies of RNA–protein interactions

Khanova¹,

Esakova²,

Perederina³

et al. 2012

RNA

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“…We found recently that PhoPop5 and PhoRpp30 specifically bind to SL3 and SL16 in the C-domain of PhopRNA (15). It is known that residues C252-G258 connecting P16 interact with a single-strand region (residues C55-G61) to form P6 (19). It is thus likely that PhoPop5PhoRpp30 recognizes a specific structure of SL16 formed in P6.…”

Section: Resultsmentioning

confidence: 99%

“…We found further that the PhoPop5PhoRpp30 complex specifically recognizes SL3 and SL16 (15). In the PhopRNA model structure (19), SL3 is approximately 65 Å away from SL16 (Fig. 4A).…”

Section: A 3-d Model Of Phopop5 and Phorpp30 In Complex With Phoprnamentioning

confidence: 91%

“…Comparative analysis of the RNase P RNA sequences and existing crystallographic structural information of the bacterial RNase P RNAs were combined to generate a phylogenetically supported 3-D model of PhopRNA (19). The crystal structure of PhoPop5 in complex with PhoRpp30 was solved previously (Protein Data Bank accession code 2CZV) (7).…”

Section: Modelling Of Phopop5phorpp30 Bound Phoprnamentioning

confidence: 99%

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Functional implication of archaeal homologues of human RNase P protein pair Pop5 and Rpp30

Hamasaki

Hazeyama

Iwasaki³

et al. 2015

J Biochem

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PhoPop5 and PhoRpp30 in the hyperthermophilic archaeon Pyrococcus horikoshii, homologues of human ribonuclease P (RNase P) proteins hPop5 and Rpp30, respectively, fold into a heterotetramer [PhoRpp 30(PhoPop5) 2 PhoRpp30], which plays a crucial role in the activation of RNase P RNA (PhopRNA). Here, we examined the functional implication of PhoPop5 and PhoRpp30 in the tetramer. Surface plasmon resonance (SPR) analysis revealed that the tetramer strongly interacts with an oligonucleotide including the nucleotide sequence of a stem-loop SL3 in PhopRNA. In contrast, PhoPop5 had markedly reduced affinity to SL3, whereas PhoRpp30 had little affinity to SL3. SPR studies of PhoPop5 mutants further revealed that the C-terminal helix (a4) in PhoPop5 functions as a molecular recognition element for SL3. Moreover, gel filtration indicated that PhoRpp30 exists as a monomer, whereas PhoPop5 is an oligomer in solution, suggesting that PhoRpp30 assists PhoPop5 in attaining a functionally active conformation by shielding hydrophobic surfaces of PhoPop5. These results, together with available data, allow us to generate a structural and mechanistic model for the PhopRNA activation by PhoPop5 and PhoRpp30, in which the two Cterminal helices (a4) of PhoPop5 in the tetramer whose formation is assisted by PhoRpp30 act as binding elements and bridge SL3 and SL16 in PhopRNA.Keywords: archaea/proteinRNA interaction/ Pyrococcus horikoshii/ribonuclease P/surface plasmon resonance.Abbreviations: 3-D, three-dimensional; PhopRNA, ribonuclease P RNA from P. horikoshii; pre-tRNA, precursor tRNA; RNase P, ribonuclease P; RNP, ribonucleoprotein; RRM, RNA recognition motif; SL3, stem-loop containing P3 helix; SL16, stem-loop containing P16 helix; SPR, surface plasmon resonance.Ribonuclease P (RNase P) is a ubiquitous trans-acting ribozyme that catalyses the processing of 5 0 leader sequences from tRNA precursors (pre-tRNA) and other noncoding RNAs in all living cells (1, 2). In contrast to eubacterial RNase P RNAs, the RNA components in archaea and eukaryotes alone have little catalytic activity in vitro and function in cooperation with protein subunits in substrate recognition and catalysis (3). Hence, archaeal and eukaryotic RNase Ps may serve as a model ribonucleoprotein (RNP) for studying how a functional RNA can be activated by protein cofactors and how the RNP enzymes catalyse biological processes.We earlier found that RNase P RNA (PhopRNA) and five proteins in the hyperthermophilic archaeon Pyrococcus horikoshii OT3 reconstituted RNase P activity that exhibits enzymatic properties like those of the authentic enzyme (4, 5). The P. horikoshii RNase P proteins were designated PhoPop5, PhoRpp21, PhoRpp29, PhoRpp30 and PhoRpp38, according to their sequence homology with the human RNase P proteins hPop5, Rpp21, Rpp29, Rpp30 and Rpp38, respectively (6). Biochemical and structural studies revealed that PhoPop5 and PhoRpp21 form a complex with PhoRpp30 and PhoRpp29, and the resulting complexes, PhoPop5PhoRpp30 and Pho Rpp21PhoRpp29, are involved i...

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“…McClain (2010) Methanocaldococcus jannaschii Endo-and exoribonucleolytic activity Levy et al (2011) Pyrococcus horikoshii Catalytic process Zwieb et al (2011) World J Microbiol Biotechnol immobilized A. clavatus cells have also been studied. Reducing glucose, peptone and soybean concentrations of the medium stimulated the RNase production from immobilized cells by 2.3 and 2.5 times higher than that of free cells in a bioreactor and flasks, respectively (Manolov 1992b).…”

Section: Substrate Recognitionmentioning

confidence: 99%

Microbial ribonucleases (RNases): production and application potential

Hameş

Demir

2015

World J Microbiol Biotechnol

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Ribonuclease (RNase) is hydrolytic enzyme that catalyzes the cleavage of phosphodiester bonds in RNA. RNases play an important role in the metabolism of cellular RNAs, such as mRNA and rRNA or tRNA maturation. Besides their cellular roles, RNases possess biological activity, cell stimulating properties, cytotoxicity and genotoxicity. Cytotoxic effect of particular microbial RNases was comparable to that of animal derived counterparts. In this respect, microbial RNases have a therapeutic potential as anti-tumor drugs. The significant development of DNA vaccines and the progress of gene therapy trials increased the need for RNases in downstream processes. In addition, RNases are used in different fields, such as food industry for single cell protein preparations, and in some molecular biological studies for the synthesis of specific nucleotides, identifying RNA metabolism and the relationship between protein structure and function. In some cases, the use of bovine or other animal-derived RNases have increased the difficulties due to the safety and regulatory issues. Microbial RNases have promising potential mainly for pharmaceutical purposes as well as downstream processing. Therefore, an effort has been given to determination of optimum fermentation conditions to maximize RNase production from different bacterial and fungal producers. Also immobilization or strain development experiments have been carried out.

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Structural modeling of RNase P RNA of the hyperthermophilic archaeon Pyrococcus horikoshii OT3

Cited by 13 publications

References 40 publications

Structural organizations of yeast RNase P and RNase MRP holoenzymes as revealed by UV-crosslinking studies of RNA–protein interactions

Structural organizations of yeast RNase P and RNase MRP holoenzymes as revealed by UV-crosslinking studies of RNA–protein interactions

Functional implication of archaeal homologues of human RNase P protein pair Pop5 and Rpp30

Microbial ribonucleases (RNases): production and application potential

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