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

doi:10.1093/nar/gkw1047

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)

Gene Regulation and Expression

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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 language	English
Pages (from-to)	3437-3447
Number of pages	11
Journal	Nucleic Acids Research
Volume	45
Issue number	6
Early online date	24 Nov 2016
DOIs	https://doi.org/10.1093/nar/gkw1047
Publication status	Published - 7 Apr 2017

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10.1093/nar/gkw1047Licence: CC BY-NC

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© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
Final published version, 5.39 MBLicence: CC BY-NC

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

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",

note = "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.",

year = "2017",

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doi = "10.1093/nar/gkw1047",

language = "English",

volume = "45",

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journal = "Nucleic Acids Research",

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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

C2 - 27899605

SN - 0305-1048

VL - 45

SP - 3437

EP - 3447

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - 6

ER -

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

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