Extra-structural elements in the RNA recognition motif in archaeal Pop5 play a crucial role in the activation of RNase P RNA from Pyrococcus horikoshii OT3

Hazeyama, Kohsuke; Ishihara, Masato; Ueda, Taro; Nishimoto, Etsuko; Nakashima, Takashi; Kakuta, Yoshimitsu; Kimura, Makoto

doi:10.1016/j.bbrc.2013.09.140

Cited by 8 publications

(13 citation statements)

References 21 publications

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“…Deletion of the loop between the two helices (α1 and αμ2) in PhoPop5 caused heterodimerization with PhoRpp30, 12) and the reconstituted particle containing the deletion mutant PhoPop5 exhibited significantly reduced nuclease activity. 12,13) These results suggest that the heterotetrameric formation of PhoPop5 and PhoRpp30 is essential for activation of the C-domain in PhopRNA.…”

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confidence: 86%

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On archaeal homologs of the human RNase P proteins Pop5 and Rpp30 in the hyperthermophilic archaeon Thermococcus kodakarensis

Suematsu

Ueda

Nakashima

et al. 2015

Bioscience, Biotechnology, and Biochemistry

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The ribonuclease P (RNase P) proteins TkoPop5 and TkoRpp30, homologs of human Pop5 and Rpp30, respectively, in the hyperthermophilic archaeon Thermococcus kodakarensis were prepared and characterized with respect to pre-tRNA cleavage activity using the reconstitution system of the well-studied Pyrococcus horikoshii RNase P. The reconstituted particle containing TkoPop5 in place of the P. horikoshii counterpart PhoPop5 retained pre-tRNA cleavage activity comparable to that of the reconstituted P. horikoshii RNase P, while that containing TkoRpp30 instead of its corresponding protein PhoRpp30 had slightly lower activity than the P. horikoshii RNase P. Moreover, we determined crystal structures of TkoRpp30 alone and in complex with TkoPop5. Like their P. horikoshii counterparts, whose structures were solved previously, TkoRpp30 and TkoPop5 fold into TIM barrel and RRM-like fold, respectively. This finding demonstrates that RNase P proteins in T. kodakarensis and P. horikoshii are interchangeable and that their three-dimensional structures are highly conserved.

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confidence: 86%

“…Previous mutational analyses of the corresponding residues in P. horikoshii found their association with reduced pretRNA cleavage activity of the reconstituted particles. 13,14) It is thus assumed that the concave surfaces formed by two interfaces of TkoPop5 and TkoRpp30 are involved in the interaction with TkopRNA.…”

Section: Structural Descriptionmentioning

confidence: 99%

On archaeal homologs of the human RNase P proteins Pop5 and Rpp30 in the hyperthermophilic archaeon Thermococcus kodakarensis

Suematsu

Ueda

Nakashima

et al. 2015

Bioscience, Biotechnology, and Biochemistry

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“…The deletion mutant ÁL43-48, in which the residues 4348 including Glu44 and Glu48 in PhoPop5 were deleted, and the C-terminal truncated mutant (Á14 C) of PhoPop5 were prepared as described previously (7,14). Mutants of PhoRpp30, in which Arg90, Arg107, Lys123, Arg176, Asp180 and Lys196 in PhoRpp30 were individually replaced by Ala, were prepared as described previously (16).…”

Section: Preparation Of Proteins and Rnasmentioning

confidence: 99%

“…PhoPop5 dimerizes through hydrogen bonding interaction from the loop between a1 and a2 helices. The reconstituted particle containing the PhoPop5 mutant termed ÁL43-48, in which the a1a2 loop in PhoPop5 was deleted, had significantly reduced pre-tRNA cleavage activity (7,14). Furthermore, reconstitution experiments indicated that deletion of the C-terminal helices a4 and a5 (3 10 -helix) significantly influenced the pre-tRNA cleavage activity, whereas that of a5 had little effect on this activity (14).…”

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confidence: 99%

“…The reconstituted particle containing the PhoPop5 mutant termed ÁL43-48, in which the a1a2 loop in PhoPop5 was deleted, had significantly reduced pre-tRNA cleavage activity (7,14). Furthermore, reconstitution experiments indicated that deletion of the C-terminal helices a4 and a5 (3 10 -helix) significantly influenced the pre-tRNA cleavage activity, whereas that of a5 had little effect on this activity (14). These results indicate that the heterotetrameric structure is essential for activation of PhopRNA, and that C-terminal helix a4 in PhoPop5 plays a crucial role in the activation of PhopRNA.…”

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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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Structure and Function of Archaeal Ribonuclease P

Kimura

Oshima

Gao

et al. 2017

RNA Metabolism and Gene Expression in Archaea

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Extra-structural elements in the RNA recognition motif in archaeal Pop5 play a crucial role in the activation of RNase P RNA from Pyrococcus horikoshii OT3

Cited by 8 publications

References 21 publications

On archaeal homologs of the human RNase P proteins Pop5 and Rpp30 in the hyperthermophilic archaeon Thermococcus kodakarensis

On archaeal homologs of the human RNase P proteins Pop5 and Rpp30 in the hyperthermophilic archaeon Thermococcus kodakarensis

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

Structure and Function of Archaeal Ribonuclease P

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