1
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Gutierrez RF, Ciol H, Carrillo Barra AL, Leonardo DA, Avaca-Crusca JS, Thiemann OH, Zanchin NIT, Araujo APU. Assigning roles in Chlamydomonas ribosome biogenesis: The conserved factor NIP7. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141045. [PMID: 39216654 DOI: 10.1016/j.bbapap.2024.141045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/31/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024]
Abstract
Ribosome biogenesis (RB) is a highly conserved process across eukaryotes that results in the assembly of functional ribosomal subunits. Studies in Saccharomyces cerevisiae and Homo sapiens have identified numerous RB factors (RBFs), including the NIP7 protein, which is involved in late-stage pre-60S ribosomal maturation. NIP7 expression has also been observed in Chlamydomonas reinhardtii, highlighting its evolutionary significance. This study aimed to characterize the function of the NIP7 protein from C. reinhardtii (CrNip7) through protein complementation assays and a paromomycin resistance test, assessing its ability to complement the role of NIP7 in yeast. Protein interaction studies were conducted via yeast two-hybrid assay to identify potential protein partners of CrNip7. Additionally, rRNA modeling analysis was performed using the predicted structure of CrNip7 to investigate its interaction with rRNA. The study revealed that CrNip7 can complement the role of NIP7 in yeast, implicating CrNip7 in the biogenesis of the 60S ribosomal subunit. Furthermore, two possible partner proteins of CrNip7, UNC-p and G-patch, were identified through yeast two-hybrid assay. The potential of these proteins to interact with CrNip7 was explored through in silico analyses. Furthermore, nucleic acid interaction was also evaluated, indicating the involvement of the N- and C-terminal domains of CrNIP7 in interacting with rRNA. Collectively, our findings provide valuable insights into the RBFs CrNip7, offering novel information for comparative studies on RB among eukaryotic model organisms, shedding light on its evolutionary conservation and functional role across species.
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Affiliation(s)
- Raissa Ferreira Gutierrez
- São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo 13560-970, PO Box 369, Brazil
| | - Heloisa Ciol
- São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo 13560-970, PO Box 369, Brazil
| | - Angélica L Carrillo Barra
- São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo 13560-970, PO Box 369, Brazil
| | - Diego Antonio Leonardo
- São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo 13560-970, PO Box 369, Brazil
| | - Juliana S Avaca-Crusca
- São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo 13560-970, PO Box 369, Brazil
| | - Otavio H Thiemann
- São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo 13560-970, PO Box 369, Brazil
| | | | - Ana P Ulian Araujo
- São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo 13560-970, PO Box 369, Brazil.
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2
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Bagatelli FFM, de Luna Vitorino FN, da Cunha JPC, Oliveira CC. The ribosome assembly factor Nop53 has a structural role in the formation of nuclear pre-60S intermediates, affecting late maturation events. Nucleic Acids Res 2021; 49:7053-7074. [PMID: 34125911 PMCID: PMC8266606 DOI: 10.1093/nar/gkab494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/18/2021] [Accepted: 05/24/2021] [Indexed: 12/19/2022] Open
Abstract
Eukaryotic ribosome biogenesis is an elaborate process during which ribosomal proteins assemble with the pre-rRNA while it is being processed and folded. Hundreds of assembly factors (AF) are required and transiently recruited to assist the sequential remodeling events. One of the most intricate ones is the stepwise removal of the internal transcribed spacer 2 (ITS2), between the 5.8S and 25S rRNAs, that constitutes together with five AFs the pre-60S ‘foot’. In the transition from nucleolus to nucleoplasm, Nop53 replaces Erb1 at the basis of the foot and recruits the RNA exosome for the ITS2 cleavage and foot disassembly. Here we comprehensively analyze the impact of Nop53 recruitment on the pre-60S compositional changes. We show that depletion of Nop53, different from nop53 mutants lacking the exosome-interacting motif, not only causes retention of the unprocessed foot in late pre-60S intermediates but also affects the transition from nucleolar state E particle to subsequent nuclear stages. Additionally, we reveal that Nop53 depletion causes the impairment of late maturation events such as Yvh1 recruitment. In light of recently described pre-60S cryo-EM structures, our results provide biochemical evidence for the structural role of Nop53 rearranging and stabilizing the foot interface to assist the Nog2 particle formation.
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Affiliation(s)
- Felipe F M Bagatelli
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP 05508-000, Brazil
| | - Francisca N de Luna Vitorino
- Laboratory of Cell Cycle, Butantan Institute, São Paulo, SP 05503-900, Brazil.,Center of Toxins, Immune-Response and Cell Signaling, Butantan Institute, São Paulo, SP 05503-900, Brazil
| | - Julia P C da Cunha
- Laboratory of Cell Cycle, Butantan Institute, São Paulo, SP 05503-900, Brazil.,Center of Toxins, Immune-Response and Cell Signaling, Butantan Institute, São Paulo, SP 05503-900, Brazil
| | - Carla C Oliveira
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP 05508-000, Brazil
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3
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Cepeda LPP, Bagatelli FFM, Santos RM, Santos MDM, Nogueira FCS, Oliveira CC. The ribosome assembly factor Nop53 controls association of the RNA exosome with pre-60S particles in yeast. J Biol Chem 2019; 294:19365-19380. [PMID: 31662437 DOI: 10.1074/jbc.ra119.010193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/22/2019] [Indexed: 12/24/2022] Open
Abstract
Eukaryotic ribosomal biogenesis is a high-energy-demanding and complex process that requires hundreds of trans-acting factors to dynamically build the highly-organized 40S and 60S subunits. Each ribonucleoprotein complex comprises specific rRNAs and ribosomal proteins that are organized into functional domains. The RNA exosome complex plays a crucial role as one of the pre-60S-processing factors, because it is the RNase responsible for processing the 7S pre-rRNA to the mature 5.8S rRNA. The yeast pre-60S assembly factor Nop53 has previously been shown to associate with the nucleoplasmic pre-60S in a region containing the "foot" structure assembled around the 3' end of the 7S pre-rRNA. Nop53 interacts with 25S rRNA and with several 60S assembly factors, including the RNA exosome, specifically, with its catalytic subunit Rrp6 and with the exosome-associated RNA helicase Mtr4. Nop53 is therefore considered the adaptor responsible for recruiting the exosome complex for 7S processing. Here, using proteomics-based approaches in budding yeast to analyze the effects of Nop53 on the exosome interactome, we found that the exosome binds pre-ribosomal complexes early during the ribosome maturation pathway. We also identified interactions through which Nop53 modulates exosome activity in the context of 60S maturation and provide evidence that in addition to recruiting the exosome, Nop53 may also be important for positioning the exosome during 7S processing. On the basis of these findings, we propose that the exosome is recruited much earlier during ribosome assembly than previously thought, suggesting the existence of additional interactions that remain to be described.
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Affiliation(s)
- Leidy Paola P Cepeda
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, 05508-000 São Paulo, SP, Brazil
| | - Felipe F M Bagatelli
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, 05508-000 São Paulo, SP, Brazil
| | - Renata M Santos
- Proteomics Unit and Laboratory of Proteomics/LADETEC, Federal University of Rio de Janeiro, 22410-001 Rio de Janeiro (RJ), Brazil
| | - Marlon D M Santos
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Curitiba, PR, CEP 81350-010, Brazil
| | - Fabio C S Nogueira
- Proteomics Unit and Laboratory of Proteomics/LADETEC, Federal University of Rio de Janeiro, 22410-001 Rio de Janeiro (RJ), Brazil
| | - Carla C Oliveira
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, 05508-000 São Paulo, SP, Brazil
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4
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Cao SN, Yuan Y, Qin YH, Zhang MZ, de Figueiredo P, Li GH, Qin QM. The pre-rRNA processing factor Nop53 regulates fungal development and pathogenesis via mediating production of reactive oxygen species. Environ Microbiol 2018; 20:1531-1549. [PMID: 29488307 DOI: 10.1111/1462-2920.14082] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 02/20/2018] [Accepted: 02/21/2018] [Indexed: 11/28/2022]
Abstract
Botrytis cinerea is a necrotrophic plant fungal pathogen that annually causes enormous economic losses worldwide. The ribosome is an organelle for cellular protein biosynthesis. However, little is known about how the ribosome operates as a machine to mediate microbial pathogenesis. Here, we demonstrate that Nop53, a late-acting factor for 60S ribosomal subunit maturation, is crucial for the pathogen's development and virulence. BcNop53 is functionally equivalent to yeast nop53p. Complementation of BcNOP53 completely restored the growth defect of the yeast Δnop53 mutant. BcNop53 is located in nuclei and disruption of BcNOP53 also dramatically impaired pathogen growth. Deletion of BcNOP53 blocked infection structure formation and abolished virulence of the pathogen, possibly due to reduced production of reactive oxygen species. Moreover, loss of BcNOP53 impaired pathogen conidiation and stress adaptation, altered conidial and sclerotial morphology, retarded conidium and sclerotium germination as well as reduced the activities of cell-wall degradation-associated enzymes. Sclerotium production was, however, increased. Complementation with the wild-type BcNOP53 allele rescued defects found in the ΔBcnop53 mutant. Our work establishes a systematic elucidation of Nop53 in regulating microbial development and pathogenesis, provides novel insights into ribosomal processes that regulate fungal pathogenesis, and may open up new targets for addressing fungal diseases.
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Affiliation(s)
- Sheng-Nan Cao
- College of Plant Sciences, Jilin University, Changchun 130062, China
| | - Ye Yuan
- College of Plant Sciences, Jilin University, Changchun 130062, China.,Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun 130062, China
| | - Yu Haity Qin
- College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ming-Zhe Zhang
- College of Plant Sciences, Jilin University, Changchun 130062, China
| | - Paul de Figueiredo
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, College Station, TX 77843, USA.,Norman Borlaug Center, Texas A&M University, College Station, TX 77843, USA.,Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Gui-Hua Li
- College of Plant Sciences, Jilin University, Changchun 130062, China
| | - Qing-Ming Qin
- College of Plant Sciences, Jilin University, Changchun 130062, China.,Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun 130062, China
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5
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Meng W, Han SC, Li CC, Dong HJ, Wang XJ. Multifunctional viral protein γ34.5 manipulates nucleolar protein NOP53 for optimal viral replication of HSV-1. Cell Death Dis 2018; 9:103. [PMID: 29367603 PMCID: PMC5833762 DOI: 10.1038/s41419-017-0116-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/25/2017] [Accepted: 10/27/2017] [Indexed: 12/14/2022]
Abstract
To ensure efficient virus replication, herpes simplex virus type 1 (HSV-1) encodes several viral proteins to counter host defense response upon infection. Among these proteins, the multifunctional viral protein γ34.5 crucially interferes with or disrupts several antiviral pathways at multiple levels. The current study shows that γ34.5 utilizes nucleolar protein NOP53 to facilitate the dephosphorylation of eukaryotic initiation factor eIF2α for efficient viral translation. Our study shows that: (1) ectopic expression of NOP53 greatly increases the intracellular and extracellular viral yields of HSV-1 (wild strain F) in type I interferon-deficient Vero cells, and more subtly promotes viral replication of γ34.5 deletion mutant virus HSV-1/Δγ34.5. (2) NOP53 is migrated from nuclei in HSV-1/F infected cells, but is redistributed incompletely after infection by either HSV-1/Δγ34.5 or ICP4 deletion mutant virus HSV-1/d120 (replication inadequate). Ectopic expression of γ34.5, consequently, induces cytoplasmic translocation of NOP53 in response to HSV-1/Δγ34.5 infection. (3) Increase of NOP53, in two forms of transient transfection and in vitro expression, attenuates the phosphorylation level of eIF2α in HSV-1/F infected cells, but fails to affect eIF2α phosphorylation induced by HSV-1/Δγ34.5 infection. (4) Knockdown of NOP53, which impairs the specific interaction between γ34.5 and protein phosphatase PP1α, disrupts the ability of γ34.5 to maintain HSV-1 virulence. (5) NOP53 knockdown also significantly reduces tissue damage and decreases viral yield in livers of HSV-1 infected mice. Our findings expand the understanding of the underlying mechanism by which viral protein γ34.5 induces NOP53 redistribution; cytoplasmic NOP53 facilitates γ34.5 recruitment of PP1α to dephosphorylate eIF2α, for optimal viral replication. This paper also demonstrates that blocking the specific interaction between γ34.5 and PP1α would be a useful approach for the development of antiviral agents.
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Affiliation(s)
- Wen Meng
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, 100193, Beijing, China
| | - Shi-Chong Han
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, 100193, Beijing, China
| | - Cui-Cui Li
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, 100193, Beijing, China
| | - Hui-Jun Dong
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, 100193, Beijing, China
| | - Xiao-Jia Wang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, 100193, Beijing, China.
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6
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Falk S, Tants JN, Basquin J, Thoms M, Hurt E, Sattler M, Conti E. Structural insights into the interaction of the nuclear exosome helicase Mtr4 with the preribosomal protein Nop53. RNA (NEW YORK, N.Y.) 2017; 23:1780-1787. [PMID: 28883156 PMCID: PMC5688999 DOI: 10.1261/rna.062901.117] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 09/05/2017] [Indexed: 05/24/2023]
Abstract
The nuclear exosome and the associated RNA helicase Mtr4 participate in the processing of several ribonucleoprotein particles (RNP), including the maturation of the large ribosomal subunit (60S). S. cerevisiae Mtr4 interacts directly with Nop53, a ribosomal biogenesis factor present in late pre-60S particles containing precursors of the 5.8S rRNA. The Mtr4-Nop53 interaction plays a pivotal role in the maturation of the 5.8S rRNA, providing a physical link between the nuclear exosome and the pre-60S RNP. An analogous interaction between Mtr4 and another ribosome biogenesis factor, Utp18, directs the exosome to an earlier preribosomal particle. Nop53 and Utp18 contain a similar Mtr4-binding motif known as the arch-interacting motif (AIM). Here, we report the 3.2 Å resolution crystal structure of S. cerevisiae Mtr4 bound to the interacting region of Nop53, revealing how the KOW domain of the helicase recognizes the AIM sequence of Nop53 with a network of hydrophobic and electrostatic interactions. The AIM-interacting residues are conserved in Mtr4 and are not present in the related cytoplasmic helicase Ski2, rationalizing the specificity and versatility of Mtr4 in the recognition of different AIM-containing proteins. Using nuclear magnetic resonance (NMR), we show that the KOW domain of Mtr4 can simultaneously bind an AIM-containing protein and a structured RNA at adjacent surfaces, suggesting how it can dock onto RNPs. The KOW domains of exosome-associated helicases thus appear to have evolved from the KOW domains of ribosomal proteins and to function as RNP-binding modules in the context of the nuclear exosome.
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Affiliation(s)
- Sebastian Falk
- Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, D-82152 Martinsried, Germany
| | - Jan-Niklas Tants
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, 85748 Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Jerôme Basquin
- Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, D-82152 Martinsried, Germany
| | - Matthias Thoms
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Ed Hurt
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Michael Sattler
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, 85748 Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Elena Conti
- Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, D-82152 Martinsried, Germany
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7
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Chen W, Xie Z, Yang F, Ye K. Stepwise assembly of the earliest precursors of large ribosomal subunits in yeast. Nucleic Acids Res 2017; 45:6837-6847. [PMID: 28402444 PMCID: PMC5499802 DOI: 10.1093/nar/gkx254] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/04/2017] [Indexed: 12/15/2022] Open
Abstract
Small ribosomal subunits are co-transcriptionally assembled on the nascent precursor rRNA in Saccharomyces cerevisiae. It is unknown how the highly intertwined structure of 60S large ribosomal subunits is initially formed. Here, we affinity purified and analyzed a series of pre-60S particles assembled in vivo on plasmid-encoded pre-rRNA fragments of increasing lengths, revealing a spatiotemporal assembly map for 34 trans-acting assembly factors (AFs), 30 ribosomal proteins and 5S rRNA. The gradual association of AFs and ribosomal proteins with the pre-rRNA fragments strongly supports that the pre-60S is co-transcriptionally, rather than post-transcriptionally, assembled. The internal and external transcribed spacers ITS1, ITS2 and 3΄ ETS in pre-rRNA must be processed in pre-60S. We show that the processing machineries for ITS1 and ITS2 are primarily recruited by the 5΄ and 3΄ halves of pre-27S RNA, respectively. Nevertheless, processing of both ITS1 and ITS2 requires a complete 25S region. The 3΄ ETS plays a minor role in ribosome assembly, but is important for efficient rRNA processing and ribosome maturation. We also identified a distinct pre-60S state occurring before ITS2 processing. Our data reveal the elusive co-transcriptional assembly pathway of large ribosomal subunit.
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Affiliation(s)
- Wu Chen
- College of Biological Sciences, China Agricultural University, Beijing 100193, China.,National Institute of Biological Sciences, Beijing 102206, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhensheng Xie
- Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fuquan Yang
- Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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8
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Kayama K, Watanabe S, Takafuji T, Tsuji T, Hironaka K, Matsumoto M, Nakayama KI, Enari M, Kohno T, Shiraishi K, Kiyono T, Yoshida K, Sugimoto N, Fujita M. GRWD1 negatively regulates p53 via the RPL11-MDM2 pathway and promotes tumorigenesis. EMBO Rep 2016; 18:123-137. [PMID: 27856536 DOI: 10.15252/embr.201642444] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Revised: 10/19/2016] [Accepted: 10/21/2016] [Indexed: 01/11/2023] Open
Abstract
The ribosomal protein L11 (RPL11) binds and inhibits the MDM2 ubiquitin ligase, thereby promoting p53 stability. Thus, RPL11 acts as a tumor suppressor. Here, we show that GRWD1 (glutamate-rich WD40 repeat containing 1) physically and functionally interacts with RPL11. GRWD1 is localized to nucleoli and is released into the nucleoplasm upon nucleolar stress. Silencing of GRWD1 increases p53 induction by nucleolar stress, whereas overexpression of GRWD1 reduces p53 induction. Furthermore, GRWD1 overexpression competitively inhibits the RPL11-MDM2 interaction and alleviates RPL11-mediated suppression of MDM2 ubiquitin ligase activity toward p53. These effects are mediated by the N-terminal region of GRWD1, including the acidic domain. Finally, we show that GRWD1 overexpression in combination with HPV16 E7 and activated KRAS confers anchorage-independent growth and tumorigenic capacity on normal human fibroblasts. Consistent with this, GRWD1 overexpression is associated with poor prognosis in cancer patients. Taken together, our results suggest that GRWD1 is a novel negative regulator of p53 and a potential oncogene.
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Affiliation(s)
- Kota Kayama
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Shinya Watanabe
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Takuya Takafuji
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Takahiro Tsuji
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Kensuke Hironaka
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Masaki Matsumoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Masato Enari
- Division of Refractory and Advancer Cancer, National Cancer Center Research Institute, Tokyo, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Tohru Kiyono
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tokyo, Japan
| | - Kazumasa Yoshida
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Nozomi Sugimoto
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Masatoshi Fujita
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
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9
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Thoms M, Thomson E, Baßler J, Gnädig M, Griesel S, Hurt E. The Exosome Is Recruited to RNA Substrates through Specific Adaptor Proteins. Cell 2015; 162:1029-38. [PMID: 26317469 DOI: 10.1016/j.cell.2015.07.060] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 05/18/2015] [Accepted: 07/02/2015] [Indexed: 12/15/2022]
Abstract
The exosome regulates the processing, degradation, and surveillance of a plethora of RNA species. However, little is known about how the exosome recognizes and is recruited to its diverse substrates. We report the identification of adaptor proteins that recruit the exosome-associated helicase, Mtr4, to unique RNA substrates. Nop53, the yeast homolog of the tumor suppressor PICT1, targets Mtr4 to pre-ribosomal particles for exosome-mediated processing, while a second adaptor Utp18 recruits Mtr4 to cleaved rRNA fragments destined for degradation by the exosome. Both Nop53 and Utp18 contain the same consensus motif, through which they dock to the "arch" domain of Mtr4 and target it to specific substrates. These findings show that the exosome employs a general mechanism of recruitment to defined substrates and that this process is regulated through adaptor proteins.
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Affiliation(s)
- Matthias Thoms
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, Heidelberg 69120, Germany
| | - Emma Thomson
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, Heidelberg 69120, Germany
| | - Jochen Baßler
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, Heidelberg 69120, Germany
| | - Marén Gnädig
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, Heidelberg 69120, Germany
| | - Sabine Griesel
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, Heidelberg 69120, Germany
| | - Ed Hurt
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, Heidelberg 69120, Germany.
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10
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Zhang XR, Qin Z, Zhang X, Hu Y. Arabidopsis SMALL ORGAN 4, a homolog of yeast NOP53, regulates cell proliferation rate during organ growth. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:810-818. [PMID: 26310197 DOI: 10.1111/jipb.12424] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 08/23/2015] [Indexed: 06/04/2023]
Abstract
Cell proliferation is a fundamental event essential for plant organogenesis and contributes greatly to the final organ size. Although the control of cell proliferation in plants has been extensively studied, how the plant sets the cell number required for a single organ is largely elusive. Here, we describe the Arabidopsis SMALL ORGAN 4 (SMO4) that functions in the regulation of cell proliferation rate and thus final organ size. The smo4 mutant exhibits a reduced size of organs due to the decreased cell number, and further analysis reveals that such phenotype results from a retardation of the cell cycle progression during organ development. SMO4 encodes a homolog of NUCLEOLAR PROTEIN 53 (NOP53) in Saccharomyces cerevisiae and is expressed primarily in tissues undergoing cell proliferation. Nevertheless, further complementation tests show that SMO4 could not rescue the lethal defect of NOP53 mutant of S. cerevisiae. These results define SMO4 as an important regulator of cell proliferation during organ growth and suggest that SMO4 might have been evolutionarily divergent from NOP53.
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Affiliation(s)
- Xiao-Ran Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhixiang Qin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiao Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100093, China
| | - Yuxin Hu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- National Center for Plant Gene Research, Beijing, 100093, China
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11
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Prieto MB, Georg RC, Gonzales-Zubiate FA, Luz JS, Oliveira CC. Nop17 is a key R2TP factor for the assembly and maturation of box C/D snoRNP complex. BMC Mol Biol 2015; 16:7. [PMID: 25888478 PMCID: PMC4377001 DOI: 10.1186/s12867-015-0037-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 02/24/2015] [Indexed: 11/24/2022] Open
Abstract
Background Box C/D snoRNPs are responsible for rRNA methylation and processing, and are formed by snoRNAs and four conserved proteins, Nop1, Nop56, Nop58 and Snu13. The snoRNP assembly is a stepwise process, involving other protein complexes, among which the R2TP and Hsp90 chaperone. Nop17, also known as Pih1, has been shown to be a constituent of the R2TP (Rvb1, Rvb2, Tah1, Pih1) and to participate in box C/D snoRNP assembly by its interaction with Nop58. The molecular function of Nop17, however, has not yet been described. Results To shed light on the role played by Nop17 in the maturation of snoRNP, here we analyzed the interactions domains of Nop58 – Nop17 – Tah1 and the importance of ATP to the interaction between Nop17 and the ATPase Rvb1/2. Conclusions Based on the results shown here, we propose a model for the assembly of box C/D snoRNP, according to which R2TP complex is important for reducing the affinity of Nop58 for snoRNA, and for the binding of the other snoRNP subunits. Electronic supplementary material The online version of this article (doi:10.1186/s12867-015-0037-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marcela B Prieto
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000, São Paulo, SP, Brazil.
| | - Raphaela C Georg
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000, São Paulo, SP, Brazil. .,Present address: Department of Biochemistry and Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil.
| | - Fernando A Gonzales-Zubiate
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000, São Paulo, SP, Brazil.
| | - Juliana S Luz
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000, São Paulo, SP, Brazil. .,Present address: Department of Biological Sciences, School of Pharmacy, São Paulo State University, Araraquara, Brazil.
| | - Carla C Oliveira
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000, São Paulo, SP, Brazil.
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12
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Borodianskiy-Shteinberg T, Kalt I, Kipper S, Nachum N, Katz S, Pauker MH, Barda-Saad M, Gerber D, Sarid R. The Nucleolar PICT-1/GLTSCR2 Protein Forms Homo-Oligomers. J Mol Biol 2014; 426:2363-78. [DOI: 10.1016/j.jmb.2014.04.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 04/02/2014] [Accepted: 04/07/2014] [Indexed: 01/05/2023]
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13
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Woolford JL, Baserga SJ. Ribosome biogenesis in the yeast Saccharomyces cerevisiae. Genetics 2013; 195:643-81. [PMID: 24190922 PMCID: PMC3813855 DOI: 10.1534/genetics.113.153197] [Citation(s) in RCA: 558] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 08/26/2013] [Indexed: 01/09/2023] Open
Abstract
Ribosomes are highly conserved ribonucleoprotein nanomachines that translate information in the genome to create the proteome in all cells. In yeast these complex particles contain four RNAs (>5400 nucleotides) and 79 different proteins. During the past 25 years, studies in yeast have led the way to understanding how these molecules are assembled into ribosomes in vivo. Assembly begins with transcription of ribosomal RNA in the nucleolus, where the RNA then undergoes complex pathways of folding, coupled with nucleotide modification, removal of spacer sequences, and binding to ribosomal proteins. More than 200 assembly factors and 76 small nucleolar RNAs transiently associate with assembling ribosomes, to enable their accurate and efficient construction. Following export of preribosomes from the nucleus to the cytoplasm, they undergo final stages of maturation before entering the pool of functioning ribosomes. Elaborate mechanisms exist to monitor the formation of correct structural and functional neighborhoods within ribosomes and to destroy preribosomes that fail to assemble properly. Studies of yeast ribosome biogenesis provide useful models for ribosomopathies, diseases in humans that result from failure to properly assemble ribosomes.
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Affiliation(s)
- John L. Woolford
- Department of Biological Sciences, Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Susan J. Baserga
- Molecular Biophysics and Biochemistry, Genetics and Therapeutic Radiology, Yale University, New Haven, Connecticut 06520-8024
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14
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Ohmayer U, Gamalinda M, Sauert M, Ossowski J, Pöll G, Linnemann J, Hierlmeier T, Perez-Fernandez J, Kumcuoglu B, Leger-Silvestre I, Faubladier M, Griesenbeck J, Woolford J, Tschochner H, Milkereit P. Studies on the assembly characteristics of large subunit ribosomal proteins in S. cerevisae. PLoS One 2013; 8:e68412. [PMID: 23874617 PMCID: PMC3707915 DOI: 10.1371/journal.pone.0068412] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 05/29/2013] [Indexed: 11/18/2022] Open
Abstract
During the assembly process of ribosomal subunits, their structural components, the ribosomal RNAs (rRNAs) and the ribosomal proteins (r-proteins) have to join together in a highly dynamic and defined manner to enable the efficient formation of functional ribosomes. In this work, the assembly of large ribosomal subunit (LSU) r-proteins from the eukaryote S. cerevisiae was systematically investigated. Groups of LSU r-proteins with specific assembly characteristics were detected by comparing the protein composition of affinity purified early, middle, late or mature LSU (precursor) particles by semi-quantitative mass spectrometry. The impact of yeast LSU r-proteins rpL25, rpL2, rpL43, and rpL21 on the composition of intermediate to late nuclear LSU precursors was analyzed in more detail. Effects of these proteins on the assembly states of other r-proteins and on the transient LSU precursor association of several ribosome biogenesis factors, including Nog2, Rsa4 and Nop53, are discussed.
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Affiliation(s)
- Uli Ohmayer
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | - Michael Gamalinda
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Martina Sauert
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | - Julius Ossowski
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | - Gisela Pöll
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | - Jan Linnemann
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | - Thomas Hierlmeier
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | | | - Beril Kumcuoglu
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Isabelle Leger-Silvestre
- Laboratoire de Biologie Moléculaire Eucaryote, UMR 5099, Universite Paul Sabatier, Toulouse, France
| | - Marlène Faubladier
- Laboratoire de Biologie Moléculaire Eucaryote, UMR 5099, Universite Paul Sabatier, Toulouse, France
| | | | - John Woolford
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Herbert Tschochner
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | - Philipp Milkereit
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
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15
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Bernstein J, Toth EA. Yeast nuclear RNA processing. World J Biol Chem 2012; 3:7-26. [PMID: 22312453 PMCID: PMC3272586 DOI: 10.4331/wjbc.v3.i1.7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Revised: 11/27/2011] [Accepted: 12/04/2011] [Indexed: 02/05/2023] Open
Abstract
Nuclear RNA processing requires dynamic and intricately regulated machinery composed of multiple enzymes and their cofactors. In this review, we summarize recent experiments using Saccharomyces cerevisiae as a model system that have yielded important insights regarding the conversion of pre-RNAs to functional RNAs, and the elimination of aberrant RNAs and unneeded intermediates from the nuclear RNA pool. Much progress has been made recently in describing the 3D structure of many elements of the nuclear degradation machinery and its cofactors. Similarly, the regulatory mechanisms that govern RNA processing are gradually coming into focus. Such advances invariably generate many new questions, which we highlight in this review.
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Affiliation(s)
- Jade Bernstein
- Jade Bernstein, Eric A Toth, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, United States
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16
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Kakihara Y, Houry WA. The R2TP complex: Discovery and functions. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1823:101-7. [DOI: 10.1016/j.bbamcr.2011.08.016] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 08/30/2011] [Accepted: 08/30/2011] [Indexed: 10/17/2022]
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17
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Morello LG, Coltri PP, Quaresma AJC, Simabuco FM, Silva TCL, Singh G, Nickerson JA, Oliveira CC, Moore MJ, Zanchin NIT. The human nucleolar protein FTSJ3 associates with NIP7 and functions in pre-rRNA processing. PLoS One 2011; 6:e29174. [PMID: 22195017 PMCID: PMC3241699 DOI: 10.1371/journal.pone.0029174] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 11/22/2011] [Indexed: 12/22/2022] Open
Abstract
NIP7 is one of the many trans-acting factors required for eukaryotic ribosome biogenesis, which interacts with nascent pre-ribosomal particles and dissociates as they complete maturation and are exported to the cytoplasm. By using conditional knockdown, we have shown previously that yeast Nip7p is required primarily for 60S subunit synthesis while human NIP7 is involved in the biogenesis of 40S subunit. This raised the possibility that human NIP7 interacts with a different set of proteins as compared to the yeast protein. By using the yeast two-hybrid system we identified FTSJ3, a putative ortholog of yeast Spb1p, as a human NIP7-interacting protein. A functional association between NIP7 and FTSJ3 is further supported by colocalization and coimmunoprecipitation analyses. Conditional knockdown revealed that depletion of FTSJ3 affects cell proliferation and causes pre-rRNA processing defects. The major pre-rRNA processing defect involves accumulation of the 34S pre-rRNA encompassing from site A′ to site 2b. Accumulation of this pre-rRNA indicates that processing of sites A0, 1 and 2 are slower in cells depleted of FTSJ3 and implicates FTSJ3 in the pathway leading to 18S rRNA maturation as observed previously for NIP7. The results presented in this work indicate a close functional interaction between NIP7 and FTSJ3 during pre-rRNA processing and show that FTSJ3 participates in ribosome synthesis in human cells.
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Affiliation(s)
- Luis G. Morello
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
- Department of Biochemistry and Molecular Pharmacology and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | | | - Alexandre J. C. Quaresma
- Department of Cell Biology and Cancer Center, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Fernando M. Simabuco
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Tereza C. L. Silva
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Guramrit Singh
- Department of Biochemistry and Molecular Pharmacology and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jeffrey A. Nickerson
- Department of Cell Biology and Cancer Center, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Carla C. Oliveira
- Department of Biochemistry, University of São Paulo, São Paulo, Brazil
| | - Melissa J. Moore
- Department of Biochemistry and Molecular Pharmacology and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Nilson I. T. Zanchin
- Instituto Carlos Chagas, Fundação Instituto Oswaldo Cruz, Curitiba, Paraná, Brazil
- * E-mail:
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18
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Makhnevych T, Houry WA. The role of Hsp90 in protein complex assembly. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2011; 1823:674-82. [PMID: 21945180 DOI: 10.1016/j.bbamcr.2011.09.001] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 09/01/2011] [Accepted: 09/02/2011] [Indexed: 12/16/2022]
Abstract
Hsp90 is a ubiquitous and essential molecular chaperone that plays central roles in many signaling and other cellular pathways. The in vivo and in vitro activity of Hsp90 depends on its association with a wide variety of cochaperones and cofactors, which form large multi-protein complexes involved in folding client proteins. Based on our proteomic work mapping the molecular chaperone interaction networks in yeast, especially that of Hsp90, as well as, on experiments and results presented in the published literature, one major role of Hsp90 appears to be the promotion and maintenance of proper assembly of protein complexes. To highlight this role of Hsp90, the effect of the chaperone on the assembly of the following seven complexes is discussed in this review: snoRNP, RNA polymerase II, phosphatidylinositol-3 kinase-related protein kinase (PIKK), telomere complex, kinetochore, RNA induced silencing complexes (RISC), and 26S proteasome. For some complexes, it is observed that Hsp90 mediates complex assembly by stabilizing an unstable protein subunit and facilitating its incorporation into the complex; for other complexes, Hsp90 promotes change in the composition of that complex. In all cases, Hsp90 does not appear to be part of the final assembled complex. This article is part of a Special Issue entitled:Heat Shock Protein 90 (HSP90).
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Affiliation(s)
- Taras Makhnevych
- Department of Biochemsitry, University of Toronto, Toronto, Canada
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19
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Santos MCT, Goldfeder MB, Zanchin NIT, Oliveira CC. The essential nucleolar yeast protein Nop8p controls the exosome function during 60S ribosomal subunit maturation. PLoS One 2011; 6:e21686. [PMID: 21747919 PMCID: PMC3126838 DOI: 10.1371/journal.pone.0021686] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Accepted: 06/08/2011] [Indexed: 11/19/2022] Open
Abstract
The yeast nucleolar protein Nop8p has previously been shown to interact with Nip7p and to be required for 60S ribosomal subunit formation. Although depletion of Nop8p in yeast cells leads to premature degradation of rRNAs, the biochemical mechanism responsible for this phenotype is still not known. In this work, we show that the Nop8p amino-terminal region mediates interaction with the 5.8S rRNA, while its carboxyl-terminal portion interacts with Nip7p and can partially complement the growth defect of the conditional mutant strain Δnop8/GAL::NOP8. Interestingly, Nop8p mediates association of Nip7p to pre-ribosomal particles. Nop8p also interacts with the exosome subunit Rrp6p and inhibits the complex activity in vitro, suggesting that the decrease in 60S ribosomal subunit levels detected upon depletion of Nop8p may result from degradation of pre-rRNAs by the exosome. These results strongly indicate that Nop8p may control the exosome function during pre-rRNA processing.
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Affiliation(s)
- Marcia C. T. Santos
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Mauricio B. Goldfeder
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Nilson I. T. Zanchin
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, São Paulo, Brazil
- Faculdade de Ciências Aplicadas, Universidade Estadual de Campinas, Limeira, São Paulo, Brazil
| | - Carla C. Oliveira
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
- * E-mail:
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20
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Im CH, Hwang SM, Son YS, Heo JB, Bang WY, Suwastika IN, Shiina T, Bahk JD. Nuclear/nucleolar GTPase 2 proteins as a subfamily of YlqF/YawG GTPases function in pre-60S ribosomal subunit maturation of mono- and dicotyledonous plants. J Biol Chem 2011; 286:8620-8632. [PMID: 21205822 DOI: 10.1074/jbc.m110.200816] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The YlqF/YawG families are important GTPases involved in ribosome biogenesis, cell proliferation, or cell growth, however, no plant homologs have yet to be characterized. Here we isolated rice (Oryza sativa) and Arabidopsis nuclear/nucleolar GTPase 2 (OsNug2 and AtNug2, respectively) that belong to the YawG subfamily and characterized them for pre-60S ribosomal subunit maturation. They showed typical intrinsic YlqF/YawG family GTPase activities in bacteria and yeasts with k(cat) values 0.12 ± 0.007 min(-1) (n = 6) and 0.087 ± 0.002 min(-1) (n = 4), respectively, and addition of 60S ribosomal subunits stimulated their activities in vitro. In addition, OsNug2 rescued the lethality of the yeast nug2 null mutant through recovery of 25S pre-rRNA processing. By yeast two-hybrid screening five clones, including a putative one of 60S ribosomal proteins, OsL10a, were isolated. Subcellular localization and pulldown assays resulted in that the N-terminal region of OsNug2 is sufficient for nucleolar/nuclear targeting and association with OsL10a. OsNug2 is physically associated with pre-60S ribosomal complexes highly enriched in the 25S, 5.8S, and 5S rRNA, and its interaction was stimulated by exogenous GTP. Furthermore, the AtNug2 knockdown mutant constructed by the RNAi method showed defective growth on the medium containing cycloheximide. Expression pattern analysis revealed that the distribution of AtNug2 mainly in the meristematic region underlies its potential role in active plant growth. Finally, it is concluded that Nug2/Nog2p GTPase from mono- and didicotyledonous plants is linked to the pre-60S ribosome complex and actively processed 27S into 25S during the ribosomal large subunit maturation process, i.e. prior to export to the cytoplasm.
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Affiliation(s)
- Chak Han Im
- From the Division of Applied Life Sciences (BK21), Graduate School of Gyeongsang National University, Jinju 660-701, Korea
| | - Sung Min Hwang
- From the Division of Applied Life Sciences (BK21), Graduate School of Gyeongsang National University, Jinju 660-701, Korea
| | - Young Sim Son
- From the Division of Applied Life Sciences (BK21), Graduate School of Gyeongsang National University, Jinju 660-701, Korea
| | - Jae Bok Heo
- From the Division of Applied Life Sciences (BK21), Graduate School of Gyeongsang National University, Jinju 660-701, Korea
| | - Woo Young Bang
- From the Division of Applied Life Sciences (BK21), Graduate School of Gyeongsang National University, Jinju 660-701, Korea
| | - I Nengah Suwastika
- the Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan, and
| | - Takashi Shiina
- the Graduate School of Human and Environmental Sciences, Kyoto Prefectural University, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Jeong Dong Bahk
- From the Division of Applied Life Sciences (BK21), Graduate School of Gyeongsang National University, Jinju 660-701, Korea,.
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21
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Cloutier P, Coulombe B. New insights into the biogenesis of nuclear RNA polymerases? Biochem Cell Biol 2010; 88:211-21. [PMID: 20453924 DOI: 10.1139/o09-173] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
More than 30 years of research on nuclear RNA polymerases (RNAP I, II, and III) has uncovered numerous factors that regulate the activity of these enzymes during the transcription reaction. However, very little is known about the machinery that regulates the fate of RNAPs before or after transcription. In particular, the mechanisms of biogenesis of the 3 nuclear RNAPs, which comprise both common and specific subunits, remains mostly uncharacterized and the proteins involved are yet to be discovered. Using protein affinity purification coupled to mass spectrometry (AP-MS), we recently unraveled a high-density interaction network formed by nuclear RNAP subunits from the soluble fraction of human cell extracts. Validation of the dataset using a machine learning approach trained to minimize the rate of false positives and false negatives yielded a high-confidence dataset and uncovered novel interactors that regulate the RNAP II transcription machinery, including a set of proteins we named the RNAP II-associated proteins (RPAPs). One of the RPAPs, RPAP3, is part of an 11-subunit complex we termed the RPAP3/R2TP/prefoldin-like complex. Here, we review the literature on the subunits of this complex, which points to a role in nuclear RNAP biogenesis.
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Affiliation(s)
- Philippe Cloutier
- Laboratory of Gene Transcription and Proteomics, Institut de recherches cliniques de Montreal, 110 avenue des Pins Ouest, Montreal, QC H2W 1R7, Canada
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22
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Morello LG, Hesling C, Coltri PP, Castilho BA, Rimokh R, Zanchin NIT. The NIP7 protein is required for accurate pre-rRNA processing in human cells. Nucleic Acids Res 2010; 39:648-65. [PMID: 20798176 PMCID: PMC3025556 DOI: 10.1093/nar/gkq758] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Eukaryotic ribosome biogenesis requires the function of a large number of trans-acting factors which interact transiently with the nascent pre-rRNA and dissociate as the ribosomal subunits proceed to maturation and export to the cytoplasm. Loss-of-function mutations in human trans-acting factors or ribosome components may lead to genetic syndromes. In a previous study, we have shown association between the SBDS (Shwachman-Bodian-Diamond syndrome) and NIP7 proteins and that downregulation of SBDS in HEK293 affects gene expression at the transcriptional and translational levels. In this study, we show that downregulation of NIP7 affects pre-rRNA processing, causing an imbalance of the 40S/60S subunit ratio. We also identified defects at the pre-rRNA processing level with a decrease of the 34S pre-rRNA concentration and an increase of the 26S and 21S pre-rRNA concentrations, indicating that processing at site 2 is particularly slower in NIP7-depleted cells and showing that NIP7 is required for maturation of the 18S rRNA. The NIP7 protein is restricted to the nuclear compartment and co-sediments with complexes with molecular masses in the range of 40S-80S, suggesting an association to nucleolar pre-ribosomal particles. Downregulation of NIP7 affects cell proliferation, consistently with an important role for NIP7 in rRNA biosynthesis in human cells.
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Affiliation(s)
- Luis G Morello
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas SP, Brazil
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23
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Eckert K, Saliou JM, Monlezun L, Vigouroux A, Atmane N, Caillat C, Quevillon-Chéruel S, Madiona K, Nicaise M, Lazereg S, Van Dorsselaer A, Sanglier-Cianférani S, Meyer P, Moréra S. The Pih1-Tah1 cochaperone complex inhibits Hsp90 molecular chaperone ATPase activity. J Biol Chem 2010; 285:31304-12. [PMID: 20663878 DOI: 10.1074/jbc.m110.138263] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Hsp90 (heat shock protein 90) is an ATP-dependent molecular chaperone regulated by collaborating proteins called cochaperones. This machinery is involved in the conformational activation of client proteins like signaling kinases, transcription factors, or ribonucleoproteins (RNP) such as telomerase. TPR (TetratricoPeptide Repeat)-containing protein associated with Hsp90 (Tah1) and protein interacting with Hsp90 (Pih1) have been identified in Saccharomyces cerevisiae as two Hsp90 cochaperones involved in chromatin remodeling complexes and small nucleolar RNP maturation. Tah1 possesses a minimal TPR domain and binds specifically to the Hsp90 C terminus, whereas Pih1 displays no homology to other protein motifs and has been involved in core RNP protein interaction. While Pih1 alone was unstable and was degraded from its N terminus, we showed that Pih1 and Tah1 form a stable heterodimeric complex that regulates Hsp90 ATPase activity. We used different biophysical approaches such as analytical ultracentrifugation, microcalorimetry, and noncovalent mass spectrometry to characterize the Pih1-Tah1 complex and its interaction with Hsp90. We showed that the Pih1-Tah1 heterodimer binds to Hsp90 with a similar affinity and the same stoichiometry as Tah1 alone. However, the Pih1-Tah1 complex antagonizes Tah1 activity on Hsp90 and inhibits the chaperone ATPase activity. We further identified the region within Pih1 responsible for interaction with Tah1 and inhibition of Hsp90, allowing us to suggest an interaction model for the Pih1-Tah1/Hsp90 complex. These results, together with previous reports, suggest a role for the Pih1-Tah1 cochaperone complex in the recruitment of client proteins such as core RNP proteins to Hsp90.
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Affiliation(s)
- Kelvin Eckert
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, 91198 Gif-sur-Yvette, France
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24
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Luz JS, Ramos CRR, Santos MCT, Coltri PP, Palhano FL, Foguel D, Zanchin NIT, Oliveira CC. Identification of archaeal proteins that affect the exosome function in vitro. BMC BIOCHEMISTRY 2010; 11:22. [PMID: 20507607 PMCID: PMC2890523 DOI: 10.1186/1471-2091-11-22] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Accepted: 05/27/2010] [Indexed: 11/17/2022]
Abstract
Background The archaeal exosome is formed by a hexameric RNase PH ring and three RNA binding subunits and has been shown to bind and degrade RNA in vitro. Despite extensive studies on the eukaryotic exosome and on the proteins interacting with this complex, little information is yet available on the identification and function of archaeal exosome regulatory factors. Results Here, we show that the proteins PaSBDS and PaNip7, which bind preferentially to poly-A and AU-rich RNAs, respectively, affect the Pyrococcus abyssi exosome activity in vitro. PaSBDS inhibits slightly degradation of a poly-rA substrate, while PaNip7 strongly inhibits the degradation of poly-A and poly-AU by the exosome. The exosome inhibition by PaNip7 appears to depend at least partially on its interaction with RNA, since mutants of PaNip7 that no longer bind RNA, inhibit the exosome less strongly. We also show that FITC-labeled PaNip7 associates with the exosome in the absence of substrate RNA. Conclusions Given the high structural homology between the archaeal and eukaryotic proteins, the effect of archaeal Nip7 and SBDS on the exosome provides a model for an evolutionarily conserved exosome control mechanism.
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Affiliation(s)
- Juliana S Luz
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, 05508-000, São Paulo, SP, Brazil
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25
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Goldfeder MB, Oliveira CC. Utp25p, a nucleolar Saccharomyces cerevisiae protein, interacts with U3 snoRNP subunits and affects processing of the 35S pre-rRNA. FEBS J 2010; 277:2838-52. [PMID: 20528918 DOI: 10.1111/j.1742-4658.2010.07701.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In eukaryotes, pre-rRNA processing depends on a large number of nonribosomal trans-acting factors that form intriguingly organized complexes. Two intermediate complexes, pre-40S and pre-60S, are formed at the early stages of 35S pre-rRNA processing and give rise to the mature ribosome subunits. Each of these complexes contains specific pre-rRNAs, some ribosomal proteins and processing factors. The novel yeast protein Utp25p has previously been identified in the nucleolus, an indication that this protein could be involved in ribosome biogenesis. Here we show that Utp25p interacts with the SSU processome proteins Sas10p and Mpp10p, and affects 18S rRNA maturation. Depletion of Utp25p leads to accumulation of the pre-rRNA 35S and the aberrant rRNA 23S, and to a severe reduction in 40S ribosomal subunit levels. Our results indicate that Utp25p is a novel SSU processome subunit involved in pre-40S maturation.
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26
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Granato DC, Machado-Santelli GM, Oliveira CC. Nop53p interacts with 5.8S rRNA co-transcriptionally, and regulates processing of pre-rRNA by the exosome. FEBS J 2008; 275:4164-78. [PMID: 18631361 DOI: 10.1111/j.1742-4658.2008.06565.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In eukaryotes, pre-rRNA processing depends on a large number of nonribosomal trans-acting factors that form intriguingly organized complexes. One of the early stages of pre-rRNA processing includes formation of the two intermediate complexes pre-40S and pre-60S, which then form the mature ribosome subunits. Each of these complexes contains specific pre-rRNAs, ribosomal proteins and processing factors. The yeast nucleolar protein Nop53p has previously been identified in the pre-60S complex and shown to affect pre-rRNA processing by directly binding to 5.8S rRNA, and to interact with Nop17p and Nip7p, which are also involved in this process. Here we show that Nop53p binds 5.8S rRNA co-transcriptionally through its N-terminal region, and that this protein portion can also partially complement growth of the conditional mutant strain Deltanop53/GAL::NOP53. Nop53p interacts with Rrp6p and activates the exosome in vitro. These results indicate that Nop53p may recruit the exosome to 7S pre-rRNA for processing. Consistent with this observation and similar to the observed in exosome mutants, depletion of Nop53p leads to accumulation of polyadenylated pre-rRNAs.
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Affiliation(s)
- Daniela C Granato
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Brazil
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27
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Zhao R, Kakihara Y, Gribun A, Huen J, Yang G, Khanna M, Costanzo M, Brost RL, Boone C, Hughes TR, Yip CM, Houry WA. Molecular chaperone Hsp90 stabilizes Pih1/Nop17 to maintain R2TP complex activity that regulates snoRNA accumulation. ACTA ACUST UNITED AC 2008; 180:563-78. [PMID: 18268103 PMCID: PMC2234237 DOI: 10.1083/jcb.200709061] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Hsp90 is a highly conserved molecular chaperone that is involved in modulating a multitude of cellular processes. In this study, we identify a function for the chaperone in RNA processing and maintenance. This functionality of Hsp90 involves two recently identified interactors of the chaperone: Tah1 and Pih1/Nop17. Tah1 is a small protein containing tetratricopeptide repeats, whereas Pih1 is found to be an unstable protein. Tah1 and Pih1 bind to the essential helicases Rvb1 and Rvb2 to form the R2TP complex, which we demonstrate is required for the correct accumulation of box C/D small nucleolar ribonucleoproteins. Together with the Tah1 cofactor, Hsp90 functions to stabilize Pih1. As a consequence, the chaperone is shown to affect box C/D accumulation and maintenance, especially under stress conditions. Hsp90 and R2TP proteins are also involved in the proper accumulation of box H/ACA small nucleolar RNAs.
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Affiliation(s)
- Rongmin Zhao
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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28
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Coltri PP, Guimarães BG, Granato DC, Luz JS, Teixeira EC, Oliveira CC, Zanchin NIT. Structural insights into the interaction of the Nip7 PUA domain with polyuridine RNA. Biochemistry 2007; 46:14177-87. [PMID: 18001138 DOI: 10.1021/bi7015876] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The conserved protein Nip7 is involved in ribosome biogenesis, being required for proper 27S pre-rRNA processing and 60S ribosome subunit assembly in Saccharomyces cerevisiae. Yeast Nip7p interacts with nucleolar proteins and with the exosome subunit Rrp43p, but its molecular function remains to be determined. Solution of the Pyrococcus abyssi Nip7 (PaNip7) crystal structure revealed a monomeric protein composed by two alpha-beta domains. The N-terminal domain is formed by a five-stranded antiparallel beta-sheet surrounded by three alpha-helices and a 310 helix while the C-terminal, a mixed beta-sheet domain composed by strands beta8 to beta12, one alpha-helix, and a 310 helix, corresponds to the conserved PUA domain (after Pseudo-Uridine synthases and Archaeosine-specific transglycosylases). By combining structural analyses and RNA interaction assays, we assessed the ability of both yeast and archaeal Nip7 orthologues to interact with RNA. Structural alignment of the PaNip7 PUA domain with the RNA-interacting surface of the ArcTGT (archaeosine tRNA-guanine transglycosylase) PUA domain indicated that in the archaeal PUA domain positively charged residues (R151, R152, K155, and K158) are involved in RNA interaction. However, equivalent positions are occupied by mostly hydrophobic residues (A/G160, I161, F164, and A167) in eukaryotic Nip7 orthologues. Both proteins can bind specifically to polyuridine, and RNA interaction requires specific residues of the PUA domain as determined by site-directed mutagenesis. This work provides experimental verification that the PUA domain mediates Nip7 interaction with RNA and reveals that the preference for interaction with polyuridine sequences is conserved in Archaea and eukaryotic Nip7 proteins.
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Affiliation(s)
- Patrícia P Coltri
- Center for Structural Molecular Biology, Brazilian Synchrotron Light Laboratory, LNLS, Rua Giuseppe Maximo Scolfaro 10000, P.O. Box 6192, CEP13083-970, Campinas SP, Brazil
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29
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Liu GY, Xiong YZ. Isolation, sequence analysis and expression profile of a novel porcine gene, NIP7, differentially expressed in the Longissimus dorsi muscle tissues from Meishan, Meishan x Large White cross and Large White pigs. Mol Biol Rep 2006; 34:213-9. [PMID: 17187224 DOI: 10.1007/s11033-006-9035-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2006] [Accepted: 10/27/2006] [Indexed: 10/23/2022]
Abstract
In order to detect the molecular mechanism of heterosis in pigs, the mRNA differential display technique was performed to investigate the differences in gene expression in the Longissimus dorsi muscle tissues from Meishan, Meishan x Large White cross and Large White pigs. One novel gene that was differentially expressed was identified using semi-quantitative reverse transcriptase polymerase chain reaction (RT-PCR) and its complete cDNA sequence was obtained using the rapid amplification of cDNA ends (RACE) method. The nucleotide sequence of the gene is not homologous to any of the known porcine genes. The sequence prediction analysis revealed that the open reading frame of this gene encodes a protein of 180 amino acids that contains the conserved putative RNA-binding domain in PseudoUridine synthase and Archaeosine transglycosylase (PUA) and has high homology with the 60S ribosome subunit biogenesis protein NIP7 homolog of three species--human (98%), mouse (97%) and rat (96%)--so that it can be defined as swine 60S ribosome subunit biogenesis protein NIP7 homolog (NIP7). The tissue expression analysis indicated that the swine NIP7 gene is over expressed in muscle, heart, liver, fat, kidney, and lung, but weakly expressed in small intestine, ovary, and spleen. The genomic DNA sequence of swine NIP7 gene was finally amplified and result revealed that the swine NIP7 gene contains five exons and four introns. Our experiment is the first to establish the primary foundation for further research on the swine NIP7 gene.
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Affiliation(s)
- G Y Liu
- Key Laboratory of Animal Nutrition and Feed of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China.
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30
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Abstract
The exosome complex of 3'-->5' exonucleases is an important component of the RNA-processing machinery in eukaryotes. This complex functions in the accurate processing of nuclear RNA precursors and in the degradation of RNAs in both the nucleus and the cytoplasm. However, it has been unclear how different classes of substrate are distinguished from one another. Recent studies now provide insights into the regulation and structure of the exosome, and they reveal striking similarities between the process of RNA degradation in bacteria and eukaryotes.
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Affiliation(s)
- Jonathan Houseley
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, UK.
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31
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Current awareness on yeast. Yeast 2006. [DOI: 10.1002/yea.1285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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32
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Luz JS, Georg RC, Gomes CH, Machado-Santelli GM, Oliveira CC. Sdo1p, the yeast orthologue of Shwachman-Bodian-Diamond syndrome protein, binds RNA and interacts with nuclear rRNA-processing factors. Yeast 1990; 26:287-98. [DOI: 10.1002/yea.1668] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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