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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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McCormick CA, Qiu Y, Fanari O, Liu Y, Bloch D, Klink IN, Meseonznik M, Jain M, Wanunu M, Rouhanifard SH. mRNA psi profiling using nanopore DRS reveals cell type-specific pseudouridylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.593203. [PMID: 38766185 PMCID: PMC11100687 DOI: 10.1101/2024.05.08.593203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Pseudouridine (psi) is one of the most abundant human mRNA modifications generated from the isomerization of uridine via psi synthases, including TRUB1 and PUS7. Nanopore direct RNA sequencing combined with our recent tool, Mod-p ID, enables psi mapping, transcriptome-wide, without chemical derivatization of the input RNA and/or conversion to cDNA. This method is sensitive for detecting changes in positional psi occupancies across cell types, which can inform our understanding of the impact on gene expression. We sequenced, mapped, and compared the positional psi occupancy across six immortalized human cell lines derived from diverse tissue types. We found that lung-derived cells have the highest proportion of psi, while liver-derived cells have the lowest. Further, among a list of highly conserved sites across cell types, most are TRUB1 substrates and fall within the coding sequence. We find that these conserved psi positions correspond to higher levels of protein expression than expected, suggesting translation regulation. Interestingly, we identify cell type-specific sites of psi modification in ubiquitously expressed genes. We validate these sites by ruling out single-nucleotide variants, analyzing current traces, and performing enzymatic knockdowns of psi synthases. Finally, we characterize sites with multiple psi modifications on the same transcript (hypermodification type II) and found that these can be conserved or cell type specific. Among these, we discovered examples of multiple psi modifications within the same k-mer for the first time and analyzed the effect on current distribution. Our data support the hypothesis that motif sequence and the presence of psi synthase are insufficient to drive modifications, that psi modifications contribute to regulating translation and that cell type-specific trans-acting factors play a major role in driving pseudouridylation.
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Affiliation(s)
| | - Yuchen Qiu
- Dept. of Bioengineering, Northeastern University, Boston, MA
| | | | - Yifang Liu
- Dept. of Bioengineering, Northeastern University, Boston, MA
| | - Dylan Bloch
- Dept. of Bioengineering, Northeastern University, Boston, MA
| | - Isabel N Klink
- Dept. of Bioengineering, Northeastern University, Boston, MA
| | | | - Miten Jain
- Dept. of Bioengineering, Northeastern University, Boston, MA
- Dept. of Physics, Northeastern University, Boston, MA
| | - Meni Wanunu
- Dept. of Bioengineering, Northeastern University, Boston, MA
- Dept. of Physics, Northeastern University, Boston, MA
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3
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Scudero OB, Santiago VF, Palmisano G, Simabuco FM, Ventura AM. The respiratory syncytial virus M2-2 protein is targeted for proteasome degradation and inhibits translation and stress granules assembly. PLoS One 2023; 18:e0289100. [PMID: 37490507 PMCID: PMC10368288 DOI: 10.1371/journal.pone.0289100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/12/2023] [Indexed: 07/27/2023] Open
Abstract
The M2-2 protein from the respiratory syncytial virus (RSV) is a 10 kDa protein expressed by the second ORF of the viral gene M2. During infection, M2-2 has been described as the polymerase cofactor responsible for promoting genome replication, which occurs by the induction of changes in interactions between the polymerase and other viral proteins at early stages of infection. Despite its well-explored role in the regulation of the polymerase activity, little has been made to investigate the relationship of M2-2 with cellular proteins. A previous report showed poor recruitment of M2-2 to viral structures, with the protein being mainly localized to the nucleus and cytoplasmic granules. To unravel which other functions M2-2 exerts during infection, we performed proteomic analysis of co-immunoprecipitated cellular partners, identifying enrichment of proteins involved with regulation of translation, protein folding and mRNA splicing. In approaches based on these data, we found that M2-2 expression downregulates eiF2α phosphorylation and inhibits both translation and stress granules assembly. Finally, we also verified that M2-2 is targeted for proteasome degradation, being localized to granules composed of defective ribosomal products at the cytoplasm. These results suggest that besides its functions in the replicative complex, M2-2 may exert additional functions to contribute to successful RSV infection.
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Affiliation(s)
- Orlando Bonito Scudero
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Verônica Feijoli Santiago
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Fernando Moreira Simabuco
- Multidisciplinary Laboratory of Food and Health, School of Applied Sciences, University of Campinas, Limeira, São Paulo, Brazil
- Department of Biochemistry, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Armando Morais Ventura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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4
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Scull CE, Twa G, Zhang Y, Yang NJ, Hunter RN, Augelli-Szafran CE, Schneider DA. Small Molecule RBI2 Disrupts Ribosome Biogenesis through Pre-rRNA Depletion. Cancers (Basel) 2023; 15:3303. [PMID: 37444413 PMCID: PMC10340317 DOI: 10.3390/cancers15133303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Cancer cells are especially sensitive to perturbations in ribosome biogenesis as they rely on finely tuned protein homeostasis to facilitate their rapid growth and proliferation. While ribosome synthesis and cancer have a well-established relationship, ribosome biogenesis has only recently drawn interest as a cancer therapeutic target. In this study, we exploited the relationship between ribosome biogenesis and cancer cell proliferation by using a potent ribosome biogenesis inhibitor, RBI2 (Ribosome Biogenesis Inhibitor 2), to perturb cancer cell growth and viability. We demonstrate herein that RBI2 significantly decreases cell viability in malignant melanoma cells and breast cancer cell lines. Treatment with RBI2 dramatically and rapidly decreased ribosomal RNA (rRNA) synthesis, without affecting the occupancy of RNA polymerase I (Pol I) on the ribosomal DNA template. Next-generation RNA sequencing (RNA-seq) revealed that RBI2 and previously described ribosome biogenesis inhibitor CX-5461 induce distinct changes in the transcriptome. An investigation of the content of the pre-rRNAs through RT-qPCR revealed an increase in the polyadenylation of cellular rRNA after treatment with RBI2, constituting a known pathway by which rRNA degradation occurs. Northern blotting revealed that RBI2 does not appear to impair or alter rRNA processing. Collectively, these data suggest that RBI2 inhibits rRNA synthesis differently from other previously described ribosome biogenesis inhibitors, potentially acting through a novel pathway that upregulates the turnover of premature rRNAs.
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Affiliation(s)
- Catherine E. Scull
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Guy Twa
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Yinfeng Zhang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Naiheng J. Yang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | | | - David A. Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Ford BL, Wei T, Liu H, Scull CE, Najmi SM, Pitts S, Fan W, Schneider DA, Laiho M. Expression of RNA polymerase I catalytic core is influenced by RPA12. PLoS One 2023; 18:e0285660. [PMID: 37167337 PMCID: PMC10174586 DOI: 10.1371/journal.pone.0285660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 04/27/2023] [Indexed: 05/13/2023] Open
Abstract
RNA Polymerase I (Pol I) has recently been recognized as a cancer therapeutic target. The activity of this enzyme is essential for ribosome biogenesis and is universally activated in cancers. The enzymatic activity of this multi-subunit complex resides in its catalytic core composed of RPA194, RPA135, and RPA12, a subunit with functions in RNA cleavage, transcription initiation and elongation. Here we explore whether RPA12 influences the regulation of RPA194 in human cancer cells. We use a specific small-molecule Pol I inhibitor BMH-21 that inhibits transcription initiation, elongation and ultimately activates the degradation of Pol I catalytic subunit RPA194. We show that silencing RPA12 causes alterations in the expression and localization of Pol I subunits RPA194 and RPA135. Furthermore, we find that despite these alterations not only does the Pol I core complex between RPA194 and RPA135 remain intact upon RPA12 knockdown, but the transcription of Pol I and its engagement with chromatin remain unaffected. The BMH-21-mediated degradation of RPA194 was independent of RPA12 suggesting that RPA12 affects the basal expression, but not the drug-inducible turnover of RPA194. These studies add to knowledge defining regulatory factors for the expression of this Pol I catalytic subunit.
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Affiliation(s)
- Brittany L. Ford
- Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
- Department of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Ting Wei
- Department of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Hester Liu
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Catherine E. Scull
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Saman M. Najmi
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Stephanie Pitts
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Wenjun Fan
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - David A. Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Marikki Laiho
- Department of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
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6
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Dörner K, Ruggeri C, Zemp I, Kutay U. Ribosome biogenesis factors-from names to functions. EMBO J 2023; 42:e112699. [PMID: 36762427 PMCID: PMC10068337 DOI: 10.15252/embj.2022112699] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/13/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
The assembly of ribosomal subunits is a highly orchestrated process that involves a huge cohort of accessory factors. Most eukaryotic ribosome biogenesis factors were first identified by genetic screens and proteomic approaches of pre-ribosomal particles in Saccharomyces cerevisiae. Later, research on human ribosome synthesis not only demonstrated that the requirement for many of these factors is conserved in evolution, but also revealed the involvement of additional players, reflecting a more complex assembly pathway in mammalian cells. Yet, it remained a challenge for the field to assign a function to many of the identified factors and to reveal their molecular mode of action. Over the past decade, structural, biochemical, and cellular studies have largely filled this gap in knowledge and led to a detailed understanding of the molecular role that many of the players have during the stepwise process of ribosome maturation. Such detailed knowledge of the function of ribosome biogenesis factors will be key to further understand and better treat diseases linked to disturbed ribosome assembly, including ribosomopathies, as well as different types of cancer.
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Affiliation(s)
- Kerstin Dörner
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,Molecular Life Sciences Ph.D. Program, Zurich, Switzerland
| | - Chiara Ruggeri
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,RNA Biology Ph.D. Program, Zurich, Switzerland
| | - Ivo Zemp
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Ulrike Kutay
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
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7
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Guan M, Ji W, Xu Y, Yan L, Chen D, Li S, Zhang X. Molecular fingerprints of polar narcotic chemicals based on heterozygous essential gene knockout library in Saccharomyces cerevisiae. CHEMOSPHERE 2022; 308:136343. [PMID: 36087727 DOI: 10.1016/j.chemosphere.2022.136343] [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: 04/10/2022] [Revised: 08/02/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Cytotoxicity of non-polar narcotic chemicals can be predicted by quantitative structure activity relationship (QSAR) models, but the polar narcotic chemicals' actual cytotoxicity exceeds the predicted values by their chemical structures. This discrepancy indicates that the molecular mechanism by which polar narcotic chemicals exert their toxicity is unclear. Taking advantage of Saccharomyces cerevisiae (yeast) functional genome-wide heterozygous essential gene knockout mutants, we here have identified the specific molecular fingerprints of two main chemical structure groups (phenols and anilines) of polar narcotic chemicals (dichlorophen (DCP), 4-chlorophenol (4-CP), 2, 4, 6-trichlorophenol (TCP), 3, 4-dichloroaniline (DCA) and N-methylaniline (NMA)) and one non-polar narcotic chemical 2, 2, 2-trichloroethanol (TCE). Especially, we identify 33, 57, 54, 46, 59 and 53 responsive strains through exposure to TCE, DCP, 4-CP, TCP, DCA and NMA with three test concentrations, respectively, revealing that these polar narcotic chemicals have more responsive strains than the non-polar narcotic chemical. Remarkably, we find that the molecular fingerprints of polar narcotic chemicals in different chemical structure groups are obviously varied, particularly phenols and anilines have their own specific molecular fingerprints. Interestingly, our results demonstrate that the molecular toxicity mechanisms of anilines are associated with DNA replication, but phenols are related with pathway of RNA degradation. Additionally, we find that the two knockout strains (SME1 and DIS3) and the three knockout strains (TSC11, RSP5 and HSF1) can specifically respond to exposure to phenols and anilines, respectively. Thus, they may be served as potential biomarkers to distinguish phenols from anilines. Collectively, our works demonstrate that the functional genomic platform of yeast essential gene mutants can not only act as an effective tool to identify key specific molecular fingerprints for polar narcotic chemicals, but also help to understand the molecular mechanisms of polar narcotic chemicals.
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Affiliation(s)
- Miao Guan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, Jiangsu, 210023, China.
| | - Wenya Ji
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, Jiangsu, 210023, China
| | - Yue Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, Jiangsu, 210023, China
| | - Lu Yan
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, China
| | - Dong Chen
- Jiangsu Provincial Academy of Environmental Science, 176 North Jiangdong Rd., Nanjing, Jiangsu, 210036, China
| | - Shengjie Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, Jiangsu, 210023, China; School of Food Science, Nanjing Xiaozhuang University, Jiangsu, Nanjing, 211171, China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, China.
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8
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Venturi G, Zacchini F, Vaccari CL, Trerè D, Montanaro L. Primer extension coupled with fragment analysis for rapid and quantitative evaluation of 5.8S rRNA isoforms. PLoS One 2021; 16:e0261476. [PMID: 34932578 PMCID: PMC8691633 DOI: 10.1371/journal.pone.0261476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/02/2021] [Indexed: 11/30/2022] Open
Abstract
The ribosomal RNA 5.8S is one of the four rRNAs that constitute ribosomes. In human cells, like in all eukaryotes, it derives from the extensive processing of a long precursor containing the sequence of 18S, 5.8S and 28S rRNAs. It has been confirmed also in human cells the presence of three isoforms of 5.8S rRNA: one more abundant called 5.8S short, one called 5.8S long bearing 5 extra-nucleotides at its 5’ end and one 10 nucleotide shorter called 5.8S cropped. So far, little is known about 5.8S long specific role in cell biology and its function in human pathology. The lack of studies on the three 5.8S isoforms could be due to the techniques usually applied to study ribosome biogenesis, such as Northern blot with radioactively labelled probes, that require strict protective measures, and abundant and high-quality samples. To overcome this issue, we optimized a method that combines primer extension with a fluorescently labeled reverse primer designed on the 3’ of 5.8S rRNA sequence and fragment analysis. The resulting electropherogram shows the peaks corresponding to the three isoforms of 5.8S rRNA. The estimation of the area underneath the peaks allows to directly quantify the isoforms and to express their relative abundance. The relative abundance of 5.8S long and 5.8S short remains constant using scalar dilution of RNA and in samples subjected to partial degradation. 5.8S cropped abundance varies significantly in lower concentrate RNA samples. This method allows to analyze rapidly and safely the abundance of 5.8S rRNA isoforms in samples that have been so far considered not suitable such as poorly concentrated samples, RNA derived from frozen tissue or unique samples.
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Affiliation(s)
- Giulia Venturi
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum—Università di Bologna, Bologna, Italia
- Centro di Ricerca Biomedica Applicata–CRBA, Università̀ di Bologna, Policlinico di Sant’Orsola, Bologna, Italia
| | - Federico Zacchini
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum—Università di Bologna, Bologna, Italia
- Centro di Ricerca Biomedica Applicata–CRBA, Università̀ di Bologna, Policlinico di Sant’Orsola, Bologna, Italia
| | - Cinzia Lucia Vaccari
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum—Università di Bologna, Bologna, Italia
- Centro di Ricerca Biomedica Applicata–CRBA, Università̀ di Bologna, Policlinico di Sant’Orsola, Bologna, Italia
| | - Davide Trerè
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum—Università di Bologna, Bologna, Italia
- Programma Dipartimentale di Medicina di Laboratorio, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italia
| | - Lorenzo Montanaro
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum—Università di Bologna, Bologna, Italia
- Centro di Ricerca Biomedica Applicata–CRBA, Università̀ di Bologna, Policlinico di Sant’Orsola, Bologna, Italia
- Programma Dipartimentale di Medicina di Laboratorio, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italia
- * E-mail:
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9
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Wu T, Nance J, Chu F, Fazzio TG. Characterization of R-Loop-Interacting Proteins in Embryonic Stem Cells Reveals Roles in rRNA Processing and Gene Expression. Mol Cell Proteomics 2021; 20:100142. [PMID: 34478875 PMCID: PMC8461376 DOI: 10.1016/j.mcpro.2021.100142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 08/21/2021] [Accepted: 08/25/2021] [Indexed: 12/14/2022] Open
Abstract
Chromatin-associated RNAs have diverse roles in the nucleus. However, their mechanisms of action are poorly understood, in part because of the inability to identify proteins that specifically associate with chromatin-bound RNAs. Here, we address this problem for a subset of chromatin-associated RNAs that form R-loops-RNA-DNA hybrid structures that include a displaced strand of ssDNA. R-loops generally form cotranscriptionally and have important roles in regulation of gene expression, immunoglobulin class switching, and other processes. However, unresolved R-loops can lead to DNA damage and chromosome instability. To identify factors that may bind and regulate R-loop accumulation or mediate R-loop-dependent functions, we used a comparative immunoprecipitation/MS approach, with and without RNA-protein crosslinking, to identify a stringent set of R-loop-binding proteins in mouse embryonic stem cells. We identified 364 R-loop-interacting proteins, which were highly enriched for proteins with predicted RNA-binding functions. We characterized several R-loop-interacting proteins of the DEAD-box family of RNA helicases and found that these proteins localize to the nucleolus and, to a lesser degree, the nucleus. Consistent with their localization patterns, we found that these helicases are required for rRNA processing and regulation of gene expression. Surprisingly, depletion of these helicases resulted in misregulation of highly overlapping sets of protein-coding genes, including many genes that function in differentiation and development. We conclude that R-loop-interacting DEAD-box helicases have nonredundant roles that are critical for maintaining the normal embryonic stem cell transcriptome.
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Affiliation(s)
- Tong Wu
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jennifer Nance
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Feixia Chu
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Thomas G Fazzio
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.
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10
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Understanding the proteome encoded by "non-coding RNAs": new insights into human genome. SCIENCE CHINA. LIFE SCIENCES 2020; 63:986-995. [PMID: 32318910 DOI: 10.1007/s11427-019-1677-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/12/2020] [Indexed: 01/19/2023]
Abstract
A great number of non-coding RNAs (ncRNAs) account for the majority of the genome. The translation of these ncRNAs has been noted but seriously underestimated due to both technological and theoretical limitations. Based on the development of ribosome profiling (Ribo-seq), full length translating RNA analysis (RNC-seq) and mass spectrometry technology, more and more ncRNAs are being found to be translated in different organism, and some of them can produce functional peptides. While recently, not only individual new functional proteins, but also a new proteome have been experimentally discovered to be encoded by endogenous lncRNAs and circRNAs. These new proteins are of biological significance, suggesting the connection of the translation of ncRNAs to human physiology and diseases. Therefore, an in-depth and systematic understanding of the coding capabilities of ncRNAs is necessary for basic biology and medicine. In this review, we summarize the advances in the field of discovering this new proteome, i.e. "ncRNA-coded" proteins.
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11
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Zhang Y, Tao Y, Ji H, Li W, Guo X, Ng DM, Haleem M, Xi Y, Dong C, Zhao J, Zhang L, Zhang X, Xie Y, Dai X, Liao Q. Genome-wide identification of the essential protein-coding genes and long non-coding RNAs for human pan-cancer. Bioinformatics 2020; 35:4344-4349. [PMID: 30923830 DOI: 10.1093/bioinformatics/btz230] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 01/17/2019] [Accepted: 03/26/2019] [Indexed: 01/11/2023] Open
Abstract
MOTIVATION Genome-scale CRISPR/Cas9 system has been a democratized gene editing technique and widely used to investigate gene functions in some biological processes and diseases especially cancers. Aiming to characterize gene aberrations and assess their effects on cancer, we designed a pipeline to identify the essential genes for pan-cancer. METHODS CRISPR screening data were used to identify the essential genes that were collected from published data and integrated by Robust Rank Aggregation algorithm. Then, hypergeometrics test and random walks with restart (RWR) were used to predict additional essential genes on broader scale. Finally, the expression status and potential roles of these genes were explored based on TCGA portal and regulatory network analysis. RESULTS We collected 926 samples from 10 CRISPR-based screening studies involving 33 different types of cancer to identify cancer-essential genes, which consists of 799 protein-coding genes (PCGs) and 97 long non-coding RNAs (lncRNAs). Then, we constructed a 'bi-colored' network with both PCGs and lncRNAs and applied it to predict additional essential genes including 495 PCGs and 280 lncRNAs on a broader scale using hypergeometrics test and RWR. After obtaining all essential genes, we further investigated their potential roles in cancer and found that essential genes have higher and more stable expression levels, and are associated with multiple cancer-associated biological processes and survival time. The regulatory network analysis detected two intriguing modules of essential genes participating in the regulation of cell cycle and ribosome biogenesis in cancer. AVAILABILITY AND IMPLEMENTATION . SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yuwei Zhang
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, Zhejiang, China
| | - Yang Tao
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, Zhejiang, China
| | - Huihui Ji
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Zhejiang, Ningbo, China
| | - Wei Li
- Center for Genetic Medicine Research, Children's National Medical Center, Department of Genomics and Precision Medicine, George Washington University, Washington, DC, USA
| | - Xingli Guo
- School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi Province 710071, China
| | - Derry Minyao Ng
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, Zhejiang, China
| | - Maria Haleem
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, Zhejiang, China
| | - Yang Xi
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Zhejiang, Ningbo, China
| | - Changzheng Dong
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, Zhejiang, China
| | - Jinshun Zhao
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, Zhejiang, China
| | - Lina Zhang
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, Zhejiang, China
| | - Xiaohong Zhang
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, Zhejiang, China
| | - Yangyang Xie
- Anorectal Surgery, Ningbo Second Hospital, Ningbo, China
| | - Xiaoyu Dai
- Anorectal Surgery, Ningbo Second Hospital, Ningbo, China
| | - Qi Liao
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, Zhejiang, China
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12
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Figueiredo VC, Englund DA, Vechetti IJ, Alimov A, Peterson CA, McCarthy JJ. Phosphorylation of eukaryotic initiation factor 4E is dispensable for skeletal muscle hypertrophy. Am J Physiol Cell Physiol 2019; 317:C1247-C1255. [PMID: 31596607 PMCID: PMC6962521 DOI: 10.1152/ajpcell.00380.2019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/09/2019] [Accepted: 10/09/2019] [Indexed: 11/22/2022]
Abstract
The eukaryotic initiation factor 4E (eIF4E) is a major mRNA cap-binding protein that has a central role in translation initiation. Ser209 is the single phosphorylation site within eIF4E and modulates its activity in response to MAPK pathway activation. It has been reported that phosphorylation of eIF4E at Ser209 promotes translation of key mRNAs, such as cyclin D1, that regulate ribosome biogenesis. We hypothesized that phosphorylation at Ser209 is required for skeletal muscle growth in response to a hypertrophic stimulus by promoting ribosome biogenesis. To test this hypothesis, wild-type (WT) and eIF4E knocked-in (KI) mice were subjected to synergist ablation to induce muscle hypertrophy of the plantaris muscle as the result of mechanical overload; in the KI mouse, Ser209 of eIF4E was replaced with a nonphosphorylatable alanine. Contrary to our hypothesis, we observed no difference in the magnitude of hypertrophy between WT and KI groups in response to 14 days of mechanical overload induced by synergist ablation. Similarly, the increases in cyclin D1 protein levels, ribosome biogenesis, and translational capacity did not differ between WT and KI groups. Based on these findings, we conclude that phosphorylation of eIF4E at Ser209 is dispensable for skeletal muscle hypertrophy in response to mechanical overload.
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Affiliation(s)
- Vandre C Figueiredo
- Department of Rehabilitation Sciences, College of Health Sciences, University of Kentucky, Lexington, Kentucky
- Center for Muscle Biology, University of Kentucky, Lexington, Kentucky
| | - Davis A Englund
- Department of Rehabilitation Sciences, College of Health Sciences, University of Kentucky, Lexington, Kentucky
- Center for Muscle Biology, University of Kentucky, Lexington, Kentucky
| | - Ivan J Vechetti
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, Kentucky
- Center for Muscle Biology, University of Kentucky, Lexington, Kentucky
| | - Alexander Alimov
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, Kentucky
- Center for Muscle Biology, University of Kentucky, Lexington, Kentucky
| | - Charlotte A Peterson
- Department of Rehabilitation Sciences, College of Health Sciences, University of Kentucky, Lexington, Kentucky
- Center for Muscle Biology, University of Kentucky, Lexington, Kentucky
| | - John J McCarthy
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, Kentucky
- Center for Muscle Biology, University of Kentucky, Lexington, Kentucky
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13
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Kuppers DA, Arora S, Lim Y, Lim AR, Carter LM, Corrin PD, Plaisier CL, Basom R, Delrow JJ, Wang S, Hansen He H, Torok-Storb B, Hsieh AC, Paddison PJ. N 6-methyladenosine mRNA marking promotes selective translation of regulons required for human erythropoiesis. Nat Commun 2019; 10:4596. [PMID: 31601799 PMCID: PMC6787028 DOI: 10.1038/s41467-019-12518-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 08/26/2019] [Indexed: 12/30/2022] Open
Abstract
Many of the regulatory features governing erythrocyte specification, maturation, and associated disorders remain enigmatic. To identify new regulators of erythropoiesis, we utilize a functional genomic screen for genes affecting expression of the erythroid marker CD235a/GYPA. Among validating hits are genes coding for the N6-methyladenosine (m6A) mRNA methyltransferase (MTase) complex, including, METTL14, METTL3, and WTAP. We demonstrate that m6A MTase activity promotes erythroid gene expression programs through selective translation of ~300 m6A marked mRNAs, including those coding for SETD histone methyltransferases, ribosomal components, and polyA RNA binding proteins. Remarkably, loss of m6A marks results in dramatic loss of H3K4me3 marks across key erythroid-specific KLF1 transcriptional targets (e.g., Heme biosynthesis genes). Further, each m6A MTase subunit and a subset of their mRNAs targets are required for human erythroid specification in primary bone-marrow derived progenitors. Thus, m6A mRNA marks promote the translation of a network of genes required for human erythropoiesis.
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Affiliation(s)
- Daniel A Kuppers
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Yiting Lim
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Andrea R Lim
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, 98195, USA
| | - Lucas M Carter
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Philip D Corrin
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Christopher L Plaisier
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, 85281, USA
| | - Ryan Basom
- Genomics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Jeffrey J Delrow
- Genomics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Shiyan Wang
- Princess Margaret Cancer Centre/University Health Network, Toronto, ON, Canada
| | - Housheng Hansen He
- Princess Margaret Cancer Centre/University Health Network, Toronto, ON, Canada
| | - Beverly Torok-Storb
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Andrew C Hsieh
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
- School of Medicine, University of Washington, Seattle, WA, 98195, USA.
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
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14
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Zhao J, Qin B, Nikolay R, Spahn CMT, Zhang G. Translatomics: The Global View of Translation. Int J Mol Sci 2019; 20:ijms20010212. [PMID: 30626072 PMCID: PMC6337585 DOI: 10.3390/ijms20010212] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/19/2018] [Accepted: 01/02/2019] [Indexed: 01/01/2023] Open
Abstract
In all kingdoms of life, proteins are synthesized by ribosomes in a process referred to as translation. The amplitude of translational regulation exceeds the sum of transcription, mRNA degradation and protein degradation. Therefore, it is essential to investigate translation in a global scale. Like the other “omics”-methods, translatomics investigates the totality of the components in the translation process, including but not limited to translating mRNAs, ribosomes, tRNAs, regulatory RNAs and nascent polypeptide chains. Technical advances in recent years have brought breakthroughs in the investigation of these components at global scale, both for their composition and dynamics. These methods have been applied in a rapidly increasing number of studies to reveal multifaceted aspects of translation control. The process of translation is not restricted to the conversion of mRNA coding sequences into polypeptide chains, it also controls the composition of the proteome in a delicate and responsive way. Therefore, translatomics has extended its unique and innovative power to many fields including proteomics, cancer research, bacterial stress response, biological rhythmicity and plant biology. Rational design in translation can enhance recombinant protein production for thousands of times. This brief review summarizes the main state-of-the-art methods of translatomics, highlights recent discoveries made in this field and introduces applications of translatomics on basic biological and biomedical research.
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Affiliation(s)
- Jing Zhao
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| | - Bo Qin
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Rainer Nikolay
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
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15
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Liu J, Li R, Liao X, Jiang W. Comprehensive Bioinformatic Analysis Genes Associated to the Prognosis of Liposarcoma. Med Sci Monit 2018; 24:7329-7339. [PMID: 30317246 PMCID: PMC6198710 DOI: 10.12659/msm.913043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Liposarcoma is the most common type of soft tissue sarcoma, but its molecular mechanism is poorly defined. This study aimed to identify genes crucial to the pathogenesis of liposarcoma and to explore their functions, related pathways, and prognostic value. MATERIAL AND METHODS Differentially expressed genes (DEGs) in the GSE59568 dataset were screened. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted to investigate the DEGs at the functional level. Protein-protein interaction (PPI) networks and module analysis were applied to identify hub genes from among the DEGs. The GSE30929 dataset was used to validate the relationship between hub genes and the distant recurrence-free survival (DRFS) of liposarcoma patients using Cox model analysis. RESULTS A total of 1111 DEGs were identified. GO and KEGG pathway analysis indicated that the DEGs were mainly associated with lipopolysaccharides and pathways in cancer. The PPI network and module analysis identified 10 hub genes from the DEG network. The Cox model identified 3 genes (NIP7, RPL10L, and MCM2) significantly associated with DRFS. The risk score calculated by the Cox model of the NIP7-RPL10L-MCM2 signature could largely predict the 1-, 3-, and 5-year DRFS of liposarcoma patients, and the prognostic value was even higher for subtypes of liposarcoma. CONCLUSIONS This study identified genes that might play critical roles in liposarcoma pathogenesis as well as a 3-gene-based signature that could be used as a candidate prognostic biomarker for patients with liposarcoma.
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Affiliation(s)
- Jianwei Liu
- Department of Osteology, The Third Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Rong Li
- Department of Osteology, The Third Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Xiwen Liao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Weiping Jiang
- Department of Osteology, The Third Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
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16
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Tomecki R, Sikorski PJ, Zakrzewska-Placzek M. Comparison of preribosomal RNA processing pathways in yeast, plant and human cells - focus on coordinated action of endo- and exoribonucleases. FEBS Lett 2017; 591:1801-1850. [PMID: 28524231 DOI: 10.1002/1873-3468.12682] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/14/2017] [Accepted: 05/15/2017] [Indexed: 12/17/2022]
Abstract
Proper regulation of ribosome biosynthesis is mandatory for cellular adaptation, growth and proliferation. Ribosome biogenesis is the most energetically demanding cellular process, which requires tight control. Abnormalities in ribosome production have severe consequences, including developmental defects in plants and genetic diseases (ribosomopathies) in humans. One of the processes occurring during eukaryotic ribosome biogenesis is processing of the ribosomal RNA precursor molecule (pre-rRNA), synthesized by RNA polymerase I, into mature rRNAs. It must not only be accurate but must also be precisely coordinated with other phenomena leading to the synthesis of functional ribosomes: RNA modification, RNA folding, assembly with ribosomal proteins and nucleocytoplasmic RNP export. A multitude of ribosome biogenesis factors ensure that these events take place in a correct temporal order. Among them are endo- and exoribonucleases involved in pre-rRNA processing. Here, we thoroughly present a wide spectrum of ribonucleases participating in rRNA maturation, focusing on their biochemical properties, regulatory mechanisms and substrate specificity. We also discuss cooperation between various ribonucleolytic activities in particular stages of pre-rRNA processing, delineating major similarities and differences between three representative groups of eukaryotes: yeast, plants and humans.
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Affiliation(s)
- Rafal Tomecki
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.,Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Poland
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17
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Tomecki R, Labno A, Drazkowska K, Cysewski D, Dziembowski A. hUTP24 is essential for processing of the human rRNA precursor at site A1, but not at site A0. RNA Biol 2016; 12:1010-29. [PMID: 26237581 DOI: 10.1080/15476286.2015.1073437] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Production of ribosomes relies on more than 200 accessory factors to ensure the proper sequence of steps and faultless assembly of ribonucleoprotein machinery. Among trans-acting factors are numerous enzymes, including ribonucleases responsible for processing the large rRNA precursor synthesized by RNA polymerase I that encompasses sequences corresponding to mature 18S, 5.8S, and 25/28S rRNA. In humans, the identity of most enzymes responsible for individual processing steps, including endoribonucleases that cleave pre-rRNA at specific sites within regions flanking and separating mature rRNA, remains largely unknown. Here, we investigated the role of hUTP24 in rRNA maturation in human cells. hUTP24 is a human homolog of the Saccharomyces cerevisiae putative PIN domain-containing endoribonuclease Utp24 (yUtp24), which was suggested to participate in the U3 snoRNA-dependent processing of yeast pre-rRNA at sites A0, A1, and A2. We demonstrate that hUTP24 interacts to some extent with proteins homologous to the components of the yeast small subunit (SSU) processome. Moreover, mutation in the putative catalytic site of hUTP24 results in slowed growth of cells and reduced metabolic activity. These effects are associated with a defect in biogenesis of the 40S ribosomal subunit, which results from decreased amounts of 18S rRNA as a consequence of inaccurate pre-rRNA processing at the 5'-end of the 18S rRNA segment (site A1). Interestingly, and in contrast to yeast, site A0 located upstream of A1 is efficiently processed upon UTP24 dysfunction. Finally, hUTP24 inactivation leads to aberrant processing of 18S rRNA 2 nucleotides downstream of the normal A1 cleavage site.
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Affiliation(s)
- Rafal Tomecki
- a Institute of Biochemistry and Biophysics; Polish Academy of Sciences ; Warsaw , Poland.,b Institute of Genetics and Biotechnology; Faculty of Biology; University of Warsaw ; Warsaw , Poland
| | - Anna Labno
- a Institute of Biochemistry and Biophysics; Polish Academy of Sciences ; Warsaw , Poland.,b Institute of Genetics and Biotechnology; Faculty of Biology; University of Warsaw ; Warsaw , Poland
| | - Karolina Drazkowska
- a Institute of Biochemistry and Biophysics; Polish Academy of Sciences ; Warsaw , Poland.,b Institute of Genetics and Biotechnology; Faculty of Biology; University of Warsaw ; Warsaw , Poland
| | - Dominik Cysewski
- a Institute of Biochemistry and Biophysics; Polish Academy of Sciences ; Warsaw , Poland.,b Institute of Genetics and Biotechnology; Faculty of Biology; University of Warsaw ; Warsaw , Poland
| | - Andrzej Dziembowski
- a Institute of Biochemistry and Biophysics; Polish Academy of Sciences ; Warsaw , Poland.,b Institute of Genetics and Biotechnology; Faculty of Biology; University of Warsaw ; Warsaw , Poland
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18
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Waku T, Nakajima Y, Yokoyama W, Nomura N, Kako K, Kobayashi A, Shimizu T, Fukamizu A. NML-mediated rRNA base methylation links ribosomal subunit formation to cell proliferation in a p53-dependent manner. J Cell Sci 2016; 129:2382-93. [PMID: 27149924 DOI: 10.1242/jcs.183723] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 04/29/2016] [Indexed: 12/25/2022] Open
Abstract
Ribosomal RNAs (rRNAs) act as scaffolds and ribozymes in ribosomes, and these functions are modulated by post-transcriptional modifications. However, the biological role of base methylation, a well-conserved modification of rRNA, is poorly understood. Here, we demonstrate that a nucleolar factor, nucleomethylin (NML; also known as RRP8), is required for the N(1)-methyladenosine (m(1)A) modification in 28S rRNAs of human and mouse cells. NML also contributes to 60S ribosomal subunit formation. Intriguingly, NML depletion increases 60S ribosomal protein L11 (RPL11) levels in the ribosome-free fraction and protein levels of p53 through an RPL11-MDM2 complex, which activates the p53 pathway. Consequently, the growth of NML-depleted cells is suppressed in a p53-dependent manner. These observations reveal a new biological function of rRNA base methylation, which links ribosomal subunit formation to p53-dependent inhibition of cell proliferation in mammalian cells.
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Affiliation(s)
- Tsuyoshi Waku
- Graduate School of Pharmaceutical Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuka Nakajima
- Life Science Center, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Wataru Yokoyama
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Naoto Nomura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Koichiro Kako
- Life Science Center, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Akira Kobayashi
- Laboratory for Genetic Code, Graduate School of Life and Medical Sciences, Doshisha University, Kyotanabe, Kyoto 610-0394, Japan
| | - Toshiyuki Shimizu
- Graduate School of Pharmaceutical Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Akiyoshi Fukamizu
- Life Science Center, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
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19
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Burroughs AM, Aravind L. Analysis of two domains with novel RNA-processing activities throws light on the complex evolution of ribosomal RNA biogenesis. Front Genet 2014; 5:424. [PMID: 25566315 PMCID: PMC4275035 DOI: 10.3389/fgene.2014.00424] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 11/19/2014] [Indexed: 11/13/2022] Open
Abstract
Ribosomal biogenesis has been extensively investigated, especially to identify the elusive nucleases and cofactors involved in the complex rRNA processing events in eukaryotes. Large-scale screens in yeast identified two biochemically uncharacterized proteins, TSR3 and TSR4, as being key players required for rRNA maturation. Using multiple computational approaches we identify the conserved domains comprising these proteins and establish sequence and structural features providing novel insights regarding their roles. TSR3 is unified with the DTW domain into a novel superfamily of predicted enzymatic domains, with the balance of the available evidence pointing toward an RNase role with the archaeo-eukaryotic TSR3 proteins processing rRNA and the bacterial versions potentially processing tRNA. TSR4, its other eukaryotic homologs PDCD2/rp-8, PDCD2L, Zfrp8, and trus, the predominantly bacterial DUF1963 proteins, and other uncharacterized proteins are unified into a new domain superfamily, which arose from an ancient duplication event of a strand-swapped, dimer-forming all-beta unit. We identify conserved features mediating protein-protein interactions (PPIs) and propose a potential chaperone-like function. While contextual evidence supports a conserved role in ribosome biogenesis for the eukaryotic TSR4-related proteins, there is no evidence for such a role for the bacterial versions. Whereas TSR3-related proteins can be traced to the last universal common ancestor (LUCA) with a well-supported archaeo-eukaryotic branch, TSR4-related proteins of eukaryotes are derived from within the bacterial radiation of this superfamily, with archaea entirely lacking them. This provides evidence for “systems admixture,” which followed the early endosymbiotic event, playing a key role in the emergence of the uniquely eukaryotic ribosome biogenesis process.
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Affiliation(s)
- A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD, USA
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20
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Welsby I, Hutin D, Gueydan C, Kruys V, Rongvaux A, Leo O. PARP12, an interferon-stimulated gene involved in the control of protein translation and inflammation. J Biol Chem 2014; 289:26642-26657. [PMID: 25086041 DOI: 10.1074/jbc.m114.589515] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Transcriptome analyses have recently identified PARP12, a member of a large family of ADP-ribosyl transferases, as an interferon-induced gene (ISG), whose function remains incompletely characterized. We demonstrate herein that PARP12 is a genuine ISG, whose expressed protein displays at least two distinct subcellular locations and related functions. Upon ectopic expression or exposure to oxidative stress, PARP12 is recruited to stress-granules (SGs), known sites of mRNA translational arrest. Accordingly, PARP12 was found to block mRNA translation, possibly upon association to the translational machinery. Both the N-terminal domain (containing an RNA-binding domain characterized by the presence of five CCCH-type Zn-fingers) and integrity of the catalytic domain are required for this suppressive function. In contrast, stimulation with LPS leads to the localization of PARP12 to p62/SQSTM1 (an adaptor protein involved in innate signaling and autophagy) containing structures, unrelated to SGs. Deletion of the N-terminal domain promotes the association of the protein to p62/SQSTM1, suggesting that the RNA-binding domain is responsible for the subcellular localization of PARP12. Association to p62/SQSTM1 was found to correlate with increased NF-κB signaling, suggesting a role for PARP12 in inflammation. Collectively, these observations suggest that PARP12 can alternate between two distinct subcellular compartments associated to two distinct cellular functions. The present work therefore identifies PARP12 as an ISG with a potential role in cellular defenses against viral infections.
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Affiliation(s)
- Iain Welsby
- Laboratoire d'Immunobiologie, Université Libre de Bruxelles, Gosselies, Belgium; Institute for Medical Immunology, Université Libre de Bruxelles, Gosselies, Belgium
| | - David Hutin
- Laboratoire d'Immunobiologie, Université Libre de Bruxelles, Gosselies, Belgium
| | - Cyril Gueydan
- Laboratoire de Biologie Moléculaire du Gène, Université Libre de Bruxelles, Gosselies, Belgium
| | - Veronique Kruys
- Laboratoire de Biologie Moléculaire du Gène, Université Libre de Bruxelles, Gosselies, Belgium; Center for Microscopy and Molecular Imaging (CMMI), Gosselies 6041, Belgium, and
| | - Anthony Rongvaux
- Department of Immunobiology, Yale University, New Haven, Connecticut 06520
| | - Oberdan Leo
- Laboratoire d'Immunobiologie, Université Libre de Bruxelles, Gosselies, Belgium; Institute for Medical Immunology, Université Libre de Bruxelles, Gosselies, Belgium,.
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21
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MDM2 mediates nonproteolytic polyubiquitylation of the DEAD-Box RNA helicase DDX24. Mol Cell Biol 2014; 34:3321-40. [PMID: 24980433 DOI: 10.1128/mcb.00320-14] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
MDM2 mediates the ubiquitylation and thereby triggers the proteasomal degradation of the tumor suppressor protein p53. However, genetic evidence suggests that MDM2 contributes to multiple regulatory networks independently of p53 degradation. We have now identified the DEAD-box RNA helicase DDX24 as a nucleolar protein that interacts with MDM2. DDX24 was found to bind to the central region of MDM2, resulting in the polyubiquitylation of DDX24 both in vitro and in vivo. Unexpectedly, however, the polyubiquitylation of DDX24 did not elicit its proteasomal degradation but rather promoted its association with preribosomal ribonucleoprotein (pre-rRNP) processing complexes that are required for the early steps of pre-rRNA processing. Consistently with these findings, depletion of DDX24 in cells impaired pre-rRNA processing and resulted both in abrogation of MDM2 function and in consequent p53 stabilization. Our results thus suggest an unexpected role of MDM2 in the nonproteolytic ubiquitylation of DDX24, which may contribute to the regulation of pre-rRNA processing.
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22
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Cava C, Bertoli G, Ripamonti M, Mauri G, Zoppis I, Rosa PAD, Gilardi MC, Castiglioni I. Integration of mRNA expression profile, copy number alterations, and microRNA expression levels in breast cancer to improve grade definition. PLoS One 2014; 9:e97681. [PMID: 24866763 PMCID: PMC4035288 DOI: 10.1371/journal.pone.0097681] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 04/23/2014] [Indexed: 12/20/2022] Open
Abstract
Defining the aggressiveness and growth rate of a malignant cell population is a key step in the clinical approach to treating tumor disease. The correct grading of breast cancer (BC) is a fundamental part in determining the appropriate treatment. Biological variables can make it difficult to elucidate the mechanisms underlying BC development. To identify potential markers that can be used for BC classification, we analyzed mRNAs expression profiles, gene copy numbers, microRNAs expression and their association with tumor grade in BC microarray-derived datasets. From mRNA expression results, we found that grade 2 BC is most likely a mixture of grade 1 and grade 3 that have been misclassified, being described by the gene signature of either grade 1 or grade 3. We assessed the potential of the new approach of integrating mRNA expression profile, copy number alterations, and microRNA expression levels to select a limited number of genomic BC biomarkers. The combination of mRNA profile analysis and copy number data with microRNA expression levels led to the identification of two gene signatures of 42 and 4 altered genes (FOXM1, KPNA4, H2AFV and DDX19A) respectively, the latter obtained through a meta-analytical procedure. The 42-based gene signature identifies 4 classes of up- or down-regulated microRNAs (17 microRNAs) and of their 17 target mRNA, and the 4-based genes signature identified 4 microRNAs (Hsa-miR-320d, Hsa-miR-139-5p, Hsa-miR-567 and Hsa-let-7c). These results are discussed from a biological point of view with respect to pathological features of BC. Our identified mRNAs and microRNAs were validated as prognostic factors of BC disease progression, and could potentially facilitate the implementation of assays for laboratory validation, due to their reduced number.
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Affiliation(s)
- Claudia Cava
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy
| | - Gloria Bertoli
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy
| | - Marilena Ripamonti
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy
| | - Giancarlo Mauri
- Department of Informatics, Systems and Communications, University of Milan–Bicocca, Milan, Italy
| | - Italo Zoppis
- Department of Informatics, Systems and Communications, University of Milan–Bicocca, Milan, Italy
| | | | - Maria Carla Gilardi
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy
| | - Isabella Castiglioni
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy
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23
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Mapping the cleavage sites on mammalian pre-rRNAs: Where do we stand? Biochimie 2012; 94:1521-32. [DOI: 10.1016/j.biochi.2012.02.001] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 02/01/2012] [Indexed: 11/23/2022]
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24
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Simabuco FM, Morello LG, Aragão AZB, Paes Leme AF, Zanchin NIT. Proteomic characterization of the human FTSJ3 preribosomal complexes. J Proteome Res 2012; 11:3112-26. [PMID: 22540864 DOI: 10.1021/pr201106n] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
In eukaryotes, ribosome biogenesis involves excision of transcribed spacer sequences from the preribosomal RNA, base and ribose covalent modification at specific sites, assembly of ribosomal proteins, and transport of subunits from the nucleolus to the cytoplasm where mature ribosomes engage in mRNA translation. The biochemical reactions throughout ribosome synthesis are mediated by factors that associate transiently to the preribosomal complexes. In this work, we describe the complexes containing the human protein FTSJ3. This protein functions in association with NIP7 in ribosome synthesis and contains a putative RNA-methyl-transferase domain (FtsJ) in the N-terminal region and two uncharacterized domains in the central (DUF3381) and C-terminal (Spb1_C) regions. FLAG-tagged FTSJ3 coimmunoprecipitates both RPS and RPL proteins, ribosome synthesis factors, and proteins whose function in ribosome synthesis has not been demonstrated yet. A similar set of proteins coimmunoprecipitates with the Spb1_C domain, suggesting that FTSJ3 interaction with the preribosome complexes is mediated by the Spb1_C domain. Approximately 50% of the components of FTSJ3 complexes are shared by complexes described for RPS19, Par14, nucleolin, and NOP56. A significant number of factors are also found in complexes described for nucleophosmin, SBDS, ISG20L2, and NIP7. These findings provide information on the dynamics of preribosome complexes in human cells.
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Affiliation(s)
- Fernando M Simabuco
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais , Rua Giuseppe Maximo Scolfaro 10000, P.O. Box 6192, CEP 13083-970, Campinas SP, Brazil
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25
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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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Vilotti S, Biagioli M, Foti R, Dal Ferro M, Lavina ZS, Collavin L, Del Sal G, Zucchelli S, Gustincich S. The PML nuclear bodies-associated protein TTRAP regulates ribosome biogenesis in nucleolar cavities upon proteasome inhibition. Cell Death Differ 2011; 19:488-500. [PMID: 21921940 DOI: 10.1038/cdd.2011.118] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
TRAF and TNF receptor-associated protein (TTRAP) is a multifunctional protein that can act in the nucleus as a 5'-tyrosyl DNA phosphodiesterase and in the cytoplasm as a regulator of cell signaling. In this paper we show that in response to proteasome inhibition TTRAP accumulates in nucleolar cavities in a promyelocytic leukemia protein-dependent manner. In the nucleolus, TTRAP contributes to control levels of ribosomal RNA precursor and processing intermediates, and this phenotype is independent from its 5'-tyrosyl DNA phosphodiesterase activity. Our findings suggest a previously unidentified function for TTRAP and nucleolar cavities in ribosome biogenesis under stress.
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Affiliation(s)
- S Vilotti
- Sector of Neurobiology, International School for Advanced Studies, Via Bonomea 265, Trieste, Italy
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27
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Gonçalves KDA, Bressan GC, Saito A, Morello LG, Zanchin NIT, Kobarg J. Evidence for the association of the human regulatory protein Ki-1/57 with the translational machinery. FEBS Lett 2011; 585:2556-60. [PMID: 21771594 DOI: 10.1016/j.febslet.2011.07.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2011] [Revised: 07/04/2011] [Accepted: 07/04/2011] [Indexed: 02/06/2023]
Abstract
Ki-1/57 is a cytoplasmic and nuclear protein of 57 kDa first identified in malignant cells from Hodgkin's lymphoma. Based on yeast-two hybrid protein interaction we found out that Ki-1/57 interacts with adaptor protein RACK1 (receptor of activated kinase 1), CIRP (cold-inducible RNA-binding protein), RPL38 (ribosomal protein L38) and FXR1 (fragile X mental retardation-related protein 1). Since these proteins are involved in the regulation of translation we suspected that Ki-1/57 may have a role in it. We show by immunoprecipitation the association of Ki-1/57 with FMRP. Confocal microscopy revealed that Ki-1/57 colocalizes with FMRP/FXR1/2 to stress granules. Furthermore Ki-1/57 cosediments with free ribosomal particles and enhances translation, when tethered to a reporter mRNA, suggesting that Ki-1/57 may be involved in translational regulation.
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Affiliation(s)
- Kaliandra de Almeida Gonçalves
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil
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