Details of a Researcher - Yoshikawa, Harunori

Papers - Yoshikawa, Harunori

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Human nucleolar protein Nop52 (RRP1/NNP-1) is involved in site 2 cleavage in internal transcribed spacer 1 of pre-rRNAs at early stages of ribosome biogenesis

Harunori Yoshikawa, Hideaki Ishikawa, Keiichi Izumikawa, Yutaka Miura, Toshiya Hayano, Toshiaki Isobe, Richard J. Simpson, Nobuhiro Takahashi

NUCLEIC ACIDS RESEARCH (OXFORD UNIV PRESS) 43 ( 11 ) 5524 - 5536 2015.06

Accepted, ISSN 0305-1048

During the early steps of ribosome biogenesis in mammals, the two ribosomal subunits 40S and 60S are produced via splitting of the large 90S pre-ribosomal particle (90S) into pre-40S and pre-60S pre-ribosomal particles (pre-40S and pre-60S). We previously proposed that replacement of fibrillarin by Nop52 (RRP1/NNP-1) for the binding to p32 (C1QBP) is a key event that drives this splitting process. However, how the replacement by RRP1 is coupled with the endo- and/or exo-ribonucleolytic cleavage of pre-rRNA remains unknown. In this study, we demonstrate that RRP1 deficiency suppressed site 2 cleavage on ITS1 of 47S/45S, 41S and 36S pre-rRNAs in human cells. RRP1 was also present in 90S and was localized in the dense fibrillar component of the nucleolus dependently on active RNA polymerase I transcription. In addition, double knockdown of XRN2 and RRP1 revealed that RRP1 accelerated the site 2 cleavage of 47S, 45S and 41S pre-rRNAs. These data suggest that RRP1 is involved not only in competitive binding with fibrillarin to C1QBP on 90S but also in site 2 cleavage in ITS1 of pre-rRNAs at early stages of human ribosome biogenesis; thus, it is likely that RRP1 integrates the cleavage of site 2 with the physical split of 90S into pre-40S and pre-60S.

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Comprehensive Analysis of RNA–Protein Complex Using Mass Spectrometry-Based Technology

Keiichi IZUMIKAWA, Hideaki ISHIKAWA, Harunori YOSHIKAWA, Toshiaki ISOBE, Nobuhiro TAKAHASHI

KAGAKU TO SEIBUTSU (Japan Society for Bioscience, Biotechnology, and Agrochemistry) 53 ( 12 ) 850 - 859 2015

ISSN 0453-073X

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Human cell growth regulator Ly-1 antibody reactive homologue accelerates processing of preribosomal RNA

Naoki Miyazawa, Harunori Yoshikawa, Satomi Magae, Hideaki Ishikawa, Keiichi Izumikawa, Goro Terukina, Ai Suzuki, Sally Nakamura-Fujiyama, Yutaka Miura, Toshiya Hayano, Wataru Komatsu, Toshiaki Isobe, Nobuhiro Takahashi

GENES TO CELLS (WILEY-BLACKWELL) 19 ( 4 ) 273 - 286 2014.04

Accepted, ISSN 1356-9597

Ribosome biogenesis is an essential process for cell growth and proliferation and is enhanced in cancer and embryonic stem cells. Mouse Ly-1 antibody reactive clone product (Lyar) is expressed at very high levels in many tumor, leukemia or embryonic stem cells; is a novel nucleolar protein with zinc-finger DNA-binding motifs and is involved in cell growth regulation. However, cellular function of Lyar remains unexplored. Here, we show that human homologue of Lyar (LYAR) accelerates ribosome biogenesis at the level of processing of preribosomal RNA (pre-rRNA). We show that LYAR is excluded from the nucleolus after actinomycin D treatment and is present in preribosomal fraction of the nuclear extract as well as in the fractions with 40S, 60S and 90S sedimentation coefficients. LYAR is required for processing of 47S/45S, 32S, 30S and 21S pre-rRNAs. In addition, we show that over-expression of LYAR increases cell proliferation without affecting the expression of c-Myc or p53. Combined, these results suggest that some rapidly growing cells enhance ribosome biogenesis by increasing the expression of LYAR.

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Identification of truncated forms of U1 snRNA reveals a novel RNA degradation pathway during snRNP biogenesis

Hideaki Ishikawa, Yuko Nobe, Keiichi Izumikawa, Harunori Yoshikawa, Naoki Miyazawa, Goro Terukina, Natsuki Kurokawa, Masato Taoka, Yoshio Yamauchi, Hiroshi Nakayama, Toshiaki Isobe, Nobuhiro Takahashi

NUCLEIC ACIDS RESEARCH (OXFORD UNIV PRESS) 42 ( 4 ) 2708 - 2724 2014.02

Accepted, ISSN 0305-1048

The U1 small nuclear ribonucleoprotein (snRNP) plays pivotal roles in pre-mRNA splicing and in regulating mRNA length and isoform expression; however, the mechanism of U1 snRNA quality control remains undetermined. Here, we describe a novel surveillance pathway for U1 snRNP biogenesis. Mass spectrometry-based RNA analysis showed that a small population of SMN complexes contains truncated forms of U1 snRNA (U1-tfs) lacking the Sm-binding site and stem loop 4 but containing a 7-monomethylguanosine 5' cap and a methylated first adenosine base. U1-tfs form a unique SMN complex, are shunted to processing bodies and have a turnover rate faster than that of mature U1 snRNA. U1-tfs are formed partly from the transcripts of U1 genes and partly from those lacking the 3' box elements or having defective SL4 coding regions. We propose that U1 snRNP biogenesis is under strict quality control: U1 transcripts are surveyed at the 3'-terminal region and U1-tfs are diverted from the normal U1 snRNP biogenesis pathway.

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Friend of Prmt1, FOP is a novel component of the nuclear SMN complex isolated using biotin affinity purification

Keiichi Izumikawa, Hideaki Ishikawa, Harunori Yoshikawa, Goro Terukina, Naoki Miyazawa, Hiroshi Nakayama, Yuko Nobe, Masato Taoka, Yoshio Yamauchi, Sjaak Philipsen, Toshiaki Isobe, Nobuhiro Takahashi

Journal of Proteomics and Bioinformatics (OMICS Publishing Group) 7 ( 4 ) 2014

Accepted, ISSN 0974-276X

SMN (survival motor neuron protein) complexes are essential for the biogenesis of uridine-rich small nuclear ribonucleoproteins (UsnRNPs). During the biogenesis, the SMN complexes bound to UsnRNPs are transported from the cytoplasm to the nucleus, and moved to Cajal body (bodies)/Gems (Cajal/Gems) where the SMN complexes- UsnRNPs are subjected to additional chemical modifications and dissociated to the SMN complexes and the mature UsnRNPs. Although the mature UsnRNPs are assembled into spliceosome with newly transcribed pre-mRNA in the perichromatin fibrils at the chromatin, the role of the dissociated nuclear SMN complexes remains undetermined. In this study, we identified Friend of Prmt1 (FOP
chromatin target of Prmt1, CHTOP
C1orf77) as a novel component of the nuclear SMN complexes by the biotin affinity purification, coupled with the mass spectrometry-based protein identification. FOP was associated with SMN, Gemines 2, 3, 4, 6, and 8, unrip, and fragile X mental retardation 1 protein (FMR1), as well as with U5and U6 snRNAs in the nucleus, but not with Sm proteins, Gemin5, coilin, and U1 and U2snRNAs. Using the quantitative proteomic method with SILAC coupled with RNA interference, we also showed that FOP is required for the association of the SMN complexes with hnRNPs, histone proteins, and various RNA-binding proteins. It is reported that FOP localizes mainly in the nuclear speckles, binds chromatin, and plays a role in mRNA transcriptional regulation. Our present data suggest that the nuclear SMN complex containing FOP participates in the process of mRNA post-transcriptional regulation. © 2013 Izumikawa K, et al.

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Human cell growth regulator LYAR is highly expressed in many tumors and accelerates ribosome biogenesis

Yoshikawa Harunori, Miyazawa Naoki, Magae Satomi, Ishikawa Hideaki, Izumikawa Keiichi, Terukina Goro, Miura Yutaka, Hayano Toshiya, Isobe Toshiaki, Watanabe Ryo, Aburatani Hiroyuki, Takahashi Nobuhiro

Abstracts for Annual Meeting of Japanese Proteomics Society (Japanese Proteomics Society (Japan Human Proteome Organisation)) 2014 78 - 78 2014

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Functional analysis of a novel component of the nuclear complex associated with survival motor neuron protein

Izumikawa Keiichi, Ishikawa Hideaki, Yoshikawa Harunori, Terukina Goro, Nobe Yuko, Nakayama Hiroshi, Taoka Masato, Yamauchi Yoshio, Isobe Toshiaki, Takahashi Nobuhiro

Abstracts for Annual Meeting of Japanese Proteomics Society (Japanese Proteomics Society (Japan Human Proteome Organisation)) 2014 76 - 76 2014

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Ribonucleoproteomics based approach identified U1-tfs in SMN-associated RNP complex and discovered a novel U1 snRNA metabolic pathway in human cell

Ishikawa Hideaki, Izumikawa Keiichi, Yoshikawa Harunori, Nobe Yuko, Yamauchi Yoshio, Taoka Masato, Nakayama Hiroshi, Isobe Toshiaki, Takahashi Nobuhiro

Abstracts for Annual Meeting of Japanese Proteomics Society (Japanese Proteomics Society (Japan Human Proteome Organisation)) 2014 79 - 79 2014

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Ribonucleoproteomic analysis on RNA modification and turnover

H Ishikawa, K Izumikawa, H Yoshikawa, Y Nobe, Y Yamauchi, M Taoka, H Nakayama, T Isobe, N Takahashi

Abstracts for Annual Meeting of Japanese Proteomics Society (Japanese Proteomics Society (Japan Human Proteome Organisation)) 2014 36 - 36 2014

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[The regulatory mechanism underlying ribosomal subunit synthesis].

Yoshikawa, H., Izumikawa, K., Ishikawa, H., Takahashi, N.

Seikagaku. The Journal of Japanese Biochemical Society 85 ( 10 ) 861—870 2013

Accepted

Identification of a novel SMN1-associated RNP complex containing short form of U1 snRNA

Ishikawa Hideaki, Yoshikawa Harunori, Izumikawa Keiichi, Miura Yutaka, Taoka Masato, Nobe Yuko, Yamauchi Yoshio, Nakayama Hiroshi, Isobe Toshiaki, Takahashi Nobuhiro

Abstracts for Annual Meeting of Japanese Proteomics Society (Japanese Proteomics Society (Japan Human Proteome Organisation)) 2012 128 - 128 2012

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Molecular mechanism by which RNA helicase II/Guα regulates ribosome biogenesis

Yasumura Taiju, Yoshikawa Harunori, Ooshima Hitoshi, Benigno Valdez, Takahashi Nobuhiro

Abstracts for Annual Meeting of Japanese Proteomics Society (Japanese Proteomics Society (Japan Human Proteome Organisation)) 2012 129 - 129 2012

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Human cell growth regulator LYAR is highly expressed in many tumors and accelerates ribosome biogenesis.

Miyazawa Naoki, Yoshikawa Harunori, Magae Emi, Ishikawa Hideaki, Izumikawa Keiichi, Terukina Goro, Suzuki Ai, Fujiyama-Nakamura Sally, Miura Yutaka, Hayano Toshiya, Isobe Toshiaki, Watanabe Akira, Aburatani Hiroyuki, Takahashi Nobuhiro

Abstracts for Annual Meeting of Japanese Proteomics Society (Japanese Proteomics Society (Japan Human Proteome Organisation)) 2012 171 - 171 2012

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The role of nucleolar protein Nop52 in the pre-rRNA processing during human ribosome biogenesis revealed by proteomic approach

Yoshikawa Harunori, Kawasaki Miyuki, Hayano Toshiya, Izumikawa Keiichi, Ishikawa Hideaki, Miura Yutaka, Yamauchi Yoshio, Isobe Toshiaki, Takahashi Nobuhiro

Abstracts for Annual Meeting of Japanese Proteomics Society (Japanese Proteomics Society (Japan Human Proteome Organisation)) 2012 181 - 181 2012

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Splicing Factor 2-Associated Protein p32 Participates in Ribosome Biogenesis by Regulating the Binding of Nop52 and Fibrillarin to Preribosome Particles

Harunori Yoshikawa, Wataru Komatsu, Toshiya Hayano, Yutaka Miura, Keiichi Homma, Keiichi Izumikawa, Hideaki Ishikawa, Naoki Miyazawa, Hiroyuki Tachikawa, Yoshio Yamauchi, Toshiaki Isobe, Nobuhiro Takahashi

MOLECULAR & CELLULAR PROTEOMICS (AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC) 10 ( 8 ) M110.006148 2011.08

Accepted, ISSN 1535-9476

Ribosome biogenesis starts with transcription of the large ribosomal RNA precursor (47S pre-rRNA), which soon combines with numerous factors to form the 90S preribosome in the nucleolus. Although the subsequent separation of the pre-90S particle into pre-40S and pre-60S particles is critical for the production process of mature small and large ribosomal subunits, its molecular mechanisms remain undetermined. Here, we present evidence that p32, fibrillarin (FBL), and Nop52 play key roles in this separation step. Mass-based analyses combined with immunoblotting showed that p32 associated with 155 proteins including 31 rRNA-processing factors (of which nine were components of small subunit processome, and six were those of RIX1 complex), 13 chromatin remodeling components, and six general transcription factors required for RNA polymerase III-mediated transcription. Of these, a late rRNA-processing factor Nop52 interacted directly with p32. Immunocytochemical analyses demonstrated that p32 colocalized with an early rRNA-processing factor FBL or Nop52 in the nucleolus and Cajal bodies, but was excluded from the nucleolus after actinomycin D treatment. p32 was present in the pre-ribosomal fractions prepared by cell fractionation or separated by ultracentrifugation of the nuclear extract. p32 also associated with pre-rRNAs including 47S/45S and 32S pre-rRNAs. Furthermore, knockdown of p32 with a small interfering RNA slowed the early processing from 47S/45S pre-rRNAs to 18S rRNA and 32S pre-rRNA. Finally, Nop52 was found to compete with FBL for binding to p32 probably in the nucleolus. Given the fact that FBL and Nop52 are associated with pre-ribosome particles distinctly different from each other, we suggest that p32 is a new rRNA maturation factor involved in the remodeling from pre-90S particles to pre-40S and pre-60S particles that requires the exchange of FBL for Nop52. Molecular & Cellular Proteomics 10: 10.1074/mcp.M110.006148, 1-23, 2011.

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Parvulin (Par14), a Peptidyl-Prolyl cis-trans Isomerase, Is a Novel rRNA Processing Factor That Evolved in the Metazoan Lineage

Sally Fujiyama-Nakamura, Harunori Yoshikawa, Keiichi Homma, Toshiya Hayano, Teruko Tsujimura-Takahashi, Keiichi Izumikawa, Hideaki Ishikawa, Naoki Miyazawa, Mitsuaki Yanagida, Yutaka Miura, Takashi Shinkawa, Yoshio Yamauchi, Toshiaki Isobe, Nobuhiro Takahashi

MOLECULAR & CELLULAR PROTEOMICS (AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC) 8 ( 7 ) 1552 - 1565 2009.07

Accepted, ISSN 1535-9476

Although parvulin (Par14/eukaryotic parvulin homolog), a peptidyl-prolyl cis-trans isomerase, is found associated with the preribosomal ribonucleoprotein (pre-rRNP) complexes, its roles in ribosome biogenesis remain undetermined. In this study, we describe a comprehensive proteomics analysis of the Par14-associated pre-rRNP complexes using LC-MS/MS and a knockdown analysis of Par14. Together with our previous results, we finally identified 115 protein components of the complexes, including 39 ribosomal proteins and 54 potential trans-acting factors whose yeast homologs are found in the pre-rRNP complexes formed at various stages of ribosome biogenesis. We give evidence that, although Par14 exists in both the phosphorylated and unphosphorylated forms in the cell, only the latter form is associated with the pre-40 S and pre-60 S ribosomal complexes. We also show that Par14 co-localizes with the nucleolar protein B23 during the interphase and in the spindle apparatus during mitosis and that actinomycin D treatment results in the exclusion of Par14 from the nucleolus. Finally we demonstrate that knockdown of Par14 mRNA decelerates the processing of pre-rRNA to 18 and 28 S rRNAs. We propose that Par14 is a component of the pre-rRNA complexes and functions as an rRNA processing factor in ribosome biogenesis. As the amino acid sequence of Par14 including that in the amino-terminal pre-rRNP binding region is conserved only in metazoan homologs, we suggest that its roles in ribosome biogenesis have evolved in the metazoan lineage. Molecular & Cellular Proteomics 8: 1552-1565, 2009.

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