Poly(A)-specific ribonuclease regulates the processing of small-subunit rRNAs in human cells

Hideaki Ishikawa, Harunori Yoshikawa, Keiichi Izumikawa, Yutaka Miura, Masato Taoka, Yuko Nobe, Yoshio Yamauchi, Hiroshi Nakayama, Richard J. Simpson, Toshiaki Isobe, Nobuhiro Takahashi (Lead / Corresponding author)

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Abstract

Ribosome biogenesis occurs successively in the nucleolus, nucleoplasm, and cytoplasm. Maturation of the ribosomal small subunit is completed in the cytoplasm by incorporation of a particular class of ribosomal proteins and final cleavage of 18S-E pre-rRNA (18S-E). Here, we show that poly(A)-specific ribonuclease (PARN) participates in steps leading to 18S-E maturation in human cells. We found PARN as a novel component of the pre-40S particle pulled down with the pre-ribosome factor LTV1 or Bystin. Reverse pull-down analysis revealed that PARN is a constitutive component of the Bystin-associated pre-40S particle. Knockdown of PARN or exogenous expression of an enzyme-dead PARN mutant (D28A) accumulated 18S-E in both the cytoplasm and nucleus. Moreover, expression of D28A accumulated 18S-E in Bystin-associated pre-40S particles, suggesting that the enzymatic activity of PARN is necessary for the release of 18S-E from Bystin-associated pre-40S particles. Finally, RNase H-based fragmentation analysis and 3'-sequence analysis of 18S-E species present in cells expressing wild-type PARN or D28A suggested that PARN degrades the extended regions encompassing nucleotides 5-44 at the 3' end of mature 18S rRNA. Our results reveal a novel role for PARN in ribosome biogenesis in human cells.

Original languageEnglish
Pages (from-to)3437-3447
Number of pages11
JournalNucleic Acids Research
Volume45
Issue number6
Early online date24 Nov 2016
DOIs
Publication statusPublished - 7 Apr 2017

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Ribosomes
Cytoplasm
Small Ribosome Subunits
Ribonuclease H
Ribosomal Proteins
RNA Precursors
Sequence Analysis
Nucleotides
Enzymes
poly(A)-specific ribonuclease

Cite this

Ishikawa, Hideaki ; Yoshikawa, Harunori ; Izumikawa, Keiichi ; Miura, Yutaka ; Taoka, Masato ; Nobe, Yuko ; Yamauchi, Yoshio ; Nakayama, Hiroshi ; Simpson, Richard J. ; Isobe, Toshiaki ; Takahashi, Nobuhiro. / Poly(A)-specific ribonuclease regulates the processing of small-subunit rRNAs in human cells. In: Nucleic Acids Research. 2017 ; Vol. 45, No. 6. pp. 3437-3447.
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abstract = "Ribosome biogenesis occurs successively in the nucleolus, nucleoplasm, and cytoplasm. Maturation of the ribosomal small subunit is completed in the cytoplasm by incorporation of a particular class of ribosomal proteins and final cleavage of 18S-E pre-rRNA (18S-E). Here, we show that poly(A)-specific ribonuclease (PARN) participates in steps leading to 18S-E maturation in human cells. We found PARN as a novel component of the pre-40S particle pulled down with the pre-ribosome factor LTV1 or Bystin. Reverse pull-down analysis revealed that PARN is a constitutive component of the Bystin-associated pre-40S particle. Knockdown of PARN or exogenous expression of an enzyme-dead PARN mutant (D28A) accumulated 18S-E in both the cytoplasm and nucleus. Moreover, expression of D28A accumulated 18S-E in Bystin-associated pre-40S particles, suggesting that the enzymatic activity of PARN is necessary for the release of 18S-E from Bystin-associated pre-40S particles. Finally, RNase H-based fragmentation analysis and 3'-sequence analysis of 18S-E species present in cells expressing wild-type PARN or D28A suggested that PARN degrades the extended regions encompassing nucleotides 5-44 at the 3' end of mature 18S rRNA. Our results reveal a novel role for PARN in ribosome biogenesis in human cells.",
author = "Hideaki Ishikawa and Harunori Yoshikawa and Keiichi Izumikawa and Yutaka Miura and Masato Taoka and Yuko Nobe and Yoshio Yamauchi and Hiroshi Nakayama and Simpson, {Richard J.} and Toshiaki Isobe and Nobuhiro Takahashi",
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Ishikawa, H, Yoshikawa, H, Izumikawa, K, Miura, Y, Taoka, M, Nobe, Y, Yamauchi, Y, Nakayama, H, Simpson, RJ, Isobe, T & Takahashi, N 2017, 'Poly(A)-specific ribonuclease regulates the processing of small-subunit rRNAs in human cells', Nucleic Acids Research, vol. 45, no. 6, pp. 3437-3447. https://doi.org/10.1093/nar/gkw1047

Poly(A)-specific ribonuclease regulates the processing of small-subunit rRNAs in human cells. / Ishikawa, Hideaki; Yoshikawa, Harunori; Izumikawa, Keiichi; Miura, Yutaka; Taoka, Masato; Nobe, Yuko; Yamauchi, Yoshio; Nakayama, Hiroshi; Simpson, Richard J.; Isobe, Toshiaki; Takahashi, Nobuhiro (Lead / Corresponding author).

In: Nucleic Acids Research, Vol. 45, No. 6, 07.04.2017, p. 3437-3447.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Poly(A)-specific ribonuclease regulates the processing of small-subunit rRNAs in human cells

AU - Ishikawa, Hideaki

AU - Yoshikawa, Harunori

AU - Izumikawa, Keiichi

AU - Miura, Yutaka

AU - Taoka, Masato

AU - Nobe, Yuko

AU - Yamauchi, Yoshio

AU - Nakayama, Hiroshi

AU - Simpson, Richard J.

AU - Isobe, Toshiaki

AU - Takahashi, Nobuhiro

N1 - Core Research for Evolutional Science and Technology (CREST) from the Japan Science and Technology Agency (JST) [13415564]; Grant-in-Aid for Scientific Research, Ministry of Education, Culture, Sports, Science & Technology of Japan (MEXT) [24241075]; Global Innovation Research Organization of Tokyo University of Agriculture & Technology. Funding for open access charge: CREST/JST.

PY - 2017/4/7

Y1 - 2017/4/7

N2 - Ribosome biogenesis occurs successively in the nucleolus, nucleoplasm, and cytoplasm. Maturation of the ribosomal small subunit is completed in the cytoplasm by incorporation of a particular class of ribosomal proteins and final cleavage of 18S-E pre-rRNA (18S-E). Here, we show that poly(A)-specific ribonuclease (PARN) participates in steps leading to 18S-E maturation in human cells. We found PARN as a novel component of the pre-40S particle pulled down with the pre-ribosome factor LTV1 or Bystin. Reverse pull-down analysis revealed that PARN is a constitutive component of the Bystin-associated pre-40S particle. Knockdown of PARN or exogenous expression of an enzyme-dead PARN mutant (D28A) accumulated 18S-E in both the cytoplasm and nucleus. Moreover, expression of D28A accumulated 18S-E in Bystin-associated pre-40S particles, suggesting that the enzymatic activity of PARN is necessary for the release of 18S-E from Bystin-associated pre-40S particles. Finally, RNase H-based fragmentation analysis and 3'-sequence analysis of 18S-E species present in cells expressing wild-type PARN or D28A suggested that PARN degrades the extended regions encompassing nucleotides 5-44 at the 3' end of mature 18S rRNA. Our results reveal a novel role for PARN in ribosome biogenesis in human cells.

AB - Ribosome biogenesis occurs successively in the nucleolus, nucleoplasm, and cytoplasm. Maturation of the ribosomal small subunit is completed in the cytoplasm by incorporation of a particular class of ribosomal proteins and final cleavage of 18S-E pre-rRNA (18S-E). Here, we show that poly(A)-specific ribonuclease (PARN) participates in steps leading to 18S-E maturation in human cells. We found PARN as a novel component of the pre-40S particle pulled down with the pre-ribosome factor LTV1 or Bystin. Reverse pull-down analysis revealed that PARN is a constitutive component of the Bystin-associated pre-40S particle. Knockdown of PARN or exogenous expression of an enzyme-dead PARN mutant (D28A) accumulated 18S-E in both the cytoplasm and nucleus. Moreover, expression of D28A accumulated 18S-E in Bystin-associated pre-40S particles, suggesting that the enzymatic activity of PARN is necessary for the release of 18S-E from Bystin-associated pre-40S particles. Finally, RNase H-based fragmentation analysis and 3'-sequence analysis of 18S-E species present in cells expressing wild-type PARN or D28A suggested that PARN degrades the extended regions encompassing nucleotides 5-44 at the 3' end of mature 18S rRNA. Our results reveal a novel role for PARN in ribosome biogenesis in human cells.

UR - http://nar.oxfordjournals.org/content/early/2016/11/28/nar.gkw1047.full

U2 - 10.1093/nar/gkw1047

DO - 10.1093/nar/gkw1047

M3 - Article

VL - 45

SP - 3437

EP - 3447

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

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ER -