1
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Ng AYE, Chan SN, Pek JW. Genetic compensation between ribosomal protein paralogs mediated by a cognate circular RNA. Cell Rep 2024; 43:114228. [PMID: 38735045 DOI: 10.1016/j.celrep.2024.114228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/19/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024] Open
Abstract
Inter-regulation between related genes, such as ribosomal protein (RP) paralogs, has been observed to be important for genetic compensation and paralog-specific functions. However, how paralogs communicate to modulate their expression levels is unknown. Here, we report a circular RNA involved in the inter-regulation between RP paralogs RpL22 and RpL22-like during Drosophila spermatogenesis. Both paralogs are mutually regulated by the circular stable intronic sequence RNA (sisRNA) circRpL22(NE,3S) produced from the RpL22 locus. RpL22 represses itself and RpL22-like. Interestingly, circRpL22 binds to RpL22 to repress RpL22-like, but not RpL22, suggesting that circRpL22 modulates RpL22's function. circRpL22 is in turn controlled by RpL22-like, which regulates RpL22 binding to circRpL22 to indirectly modulate RpL22. This circRpL22-centric inter-regulatory circuit enables the loss of RpL22-like to be genetically compensated by RpL22 upregulation to ensure robust male germline development. Thus, our study identifies sisRNA as a possible mechanism of genetic crosstalk between paralogous genes.
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Affiliation(s)
- Amanda Yunn Ee Ng
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive Singapore 117543, Singapore
| | - Seow Neng Chan
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore 117604, Singapore
| | - Jun Wei Pek
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive Singapore 117543, Singapore.
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2
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Singh AK. Rules and impacts of nonsense-mediated mRNA decay in the degradation of long noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1853. [PMID: 38741356 DOI: 10.1002/wrna.1853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024]
Abstract
Nonsense-mediated mRNA decay (NMD) is a quality-control process that selectively degrades mRNAs having premature termination codon, upstream open reading frame, or unusually long 3'UTR. NMD detects such mRNAs and rapidly degrades them during initial rounds of translation in the eukaryotic cells. Since NMD is a translation-dependent cytoplasmic mRNA surveillance process, the noncoding RNAs were initially believed to be NMD-resistant. The sequence feature-based analysis has revealed that many putative long noncoding RNAs (lncRNAs) have short open reading frames, most of which have translation potential. Subsequent transcriptome-based molecular studies showed an association of a large set of such putative lncRNAs with translating ribosomes, and some of them produce stable and functionally active micropeptides. The translationally active lncRNAs typically have relatively longer and unprotected 3'UTR, which can induce their NMD-dependent degradation. This review defines the mechanism and regulation of NMD-dependent degradation of lncRNAs and its impact on biological processes related to the functions of lncRNAs or their encoded micropeptides. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Turnover and Surveillance > Regulation of RNA Stability RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Anand Kumar Singh
- Department of Biology, Indian Institute of Science Education and Research Tirupati, Tirupati, Andhra Pradesh, India
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3
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Janissen R, Barth R, Polinder M, van der Torre J, Dekker C. Single-molecule visualization of twin-supercoiled domains generated during transcription. Nucleic Acids Res 2024; 52:1677-1687. [PMID: 38084930 PMCID: PMC10899792 DOI: 10.1093/nar/gkad1181] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/13/2023] [Accepted: 11/30/2023] [Indexed: 02/29/2024] Open
Abstract
Transcription-coupled supercoiling of DNA is a key factor in chromosome compaction and the regulation of genetic processes in all domains of life. It has become common knowledge that, during transcription, the DNA-dependent RNA polymerase (RNAP) induces positive supercoiling ahead of it (downstream) and negative supercoils in its wake (upstream), as rotation of RNAP around the DNA axis upon tracking its helical groove gets constrained due to drag on its RNA transcript. Here, we experimentally validate this so-called twin-supercoiled-domain model with in vitro real-time visualization at the single-molecule scale. Upon binding to the promoter site on a supercoiled DNA molecule, RNAP merges all DNA supercoils into one large pinned plectoneme with RNAP residing at its apex. Transcription by RNAP in real time demonstrates that up- and downstream supercoils are generated simultaneously and in equal portions, in agreement with the twin-supercoiled-domain model. Experiments carried out in the presence of RNases A and H, revealed that an additional viscous drag of the RNA transcript is not necessary for the RNAP to induce supercoils. The latter results contrast the current consensus and simulations on the origin of the twin-supercoiled domains, pointing at an additional mechanistic cause underlying supercoil generation by RNAP in transcription.
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Affiliation(s)
- Richard Janissen
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, South-Holland 2629HZ, The Netherlands
| | - Roman Barth
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, South-Holland 2629HZ, The Netherlands
| | - Minco Polinder
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, South-Holland 2629HZ, The Netherlands
| | - Jaco van der Torre
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, South-Holland 2629HZ, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, South-Holland 2629HZ, The Netherlands
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4
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Zou S, Kim B, Tian Y, Liu G, Zhang J, Zerda R, Li Z, Zhang G, Du X, Lin W, Gao X, Huang W, Fu X. Enhanced nuclear translation is associated with proliferation and progression across multiple cancers. MedComm (Beijing) 2023; 4:e248. [PMID: 37063610 PMCID: PMC10104727 DOI: 10.1002/mco2.248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/16/2023] [Accepted: 03/03/2023] [Indexed: 04/18/2023] Open
Abstract
Recent technological advances have re-invigorated the interest in nuclear translation (NT), but the underlying mechanisms and functional implications of NT remain unknown. Here we show that NT is enhanced in malignant cancer cells and is associated with rapid cell growth. Nuclear ribopuromycylation analyses in a panel of diverse cell lines revealed that NT is scarce in normal immortalized cells, but is ubiquitous and robust in malignant cancer cells. Moreover, NT occurs in the nucleolus and requires normal nucleolar function. Intriguingly, NT is reduced by cellular stresses and anti-tumor agents and positively correlates with cancer cell proliferation and growth. By using a modified puromycin-associated nascent chain proteomics, we further identified numerous oncoproteins that are preferentially translated in the nucleus, such as transforming growth factor-beta 2 (TGFB2) and nucleophosmin 1 (NMP1). Specific overexpression of TGFB2 and NMP1 messenger RNAs in the nucleus can increase their protein levels and promote tumorigenesis. These findings establish a previously unknown link between NT and malignancy and suggest that cancer cells might have adapted a mechanism of NT to support their need for rapid growth, which highlight the potential of NT in tumorigenesis and might also open up new possibilities for therapeutic targeting of cancer-specific cellular functions.
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Affiliation(s)
- Sailan Zou
- Division of Endocrinology and MetabolismState Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center of BiotherapyChengduChina
| | - Byung‐Wook Kim
- Department of Diabetes Complications and MetabolismArthur Riggs Diabetes and Metabolism Research InstituteIrell & Manella Graduate School of Biological SciencesBeckman Research InstituteCity of Hope National Medical CenterDuarteUSA
| | - Yan Tian
- Division of Endocrinology and MetabolismState Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center of BiotherapyChengduChina
| | - Geng Liu
- Division of Endocrinology and MetabolismState Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center of BiotherapyChengduChina
| | - Jiawei Zhang
- Department of Diabetes Complications and MetabolismArthur Riggs Diabetes and Metabolism Research InstituteIrell & Manella Graduate School of Biological SciencesBeckman Research InstituteCity of Hope National Medical CenterDuarteUSA
- Cancer Institute (Key Laboratory of Cancer Prevention and InterventionChina National Ministry of Education)Second Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouChina
| | - Ricardo Zerda
- Electron Microscopy and Atomic Force Microscopy CoreCity of Hope National Medical CenterDuarteUSA
| | - Zhuo Li
- Electron Microscopy and Atomic Force Microscopy CoreCity of Hope National Medical CenterDuarteUSA
| | - Guixiang Zhang
- Division of Gastrointestinal SurgeryDepartment of General Surgery and Gastric Cancer CenterWest China HospitalSichuan UniversityChengduChina
| | - Xiao Du
- Division of Gastrointestinal SurgeryDepartment of General Surgery and Gastric Cancer CenterWest China HospitalSichuan UniversityChengduChina
- Department of General SurgeryYaan People's HospitalYaanChina
| | - Weiqiang Lin
- Department of NephrologyThe Fourth Affiliated HospitalInternational Institutes of MedicineSchool of MedicineZhejiang UniversityZhejiangChina
| | - Xiang Gao
- Department of Neurosurgery and Institute of NeurosurgeryState Key Laboratory of Biotherapy and Cancer CenterWest China HospitalWest China Medical SchoolSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Wendong Huang
- Department of Diabetes Complications and MetabolismArthur Riggs Diabetes and Metabolism Research InstituteIrell & Manella Graduate School of Biological SciencesBeckman Research InstituteCity of Hope National Medical CenterDuarteUSA
| | - Xianghui Fu
- Division of Endocrinology and MetabolismState Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center of BiotherapyChengduChina
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5
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Grunchec H, Deraze J, Dardalhon-Cuménal D, Ribeiro V, Coléno-Costes A, Dias K, Bloyer S, Mouchel-Vielh E, Peronnet F, Thomassin H. Single amino-acid mutation in a Drosoph ila melanogaster ribosomal protein: An insight in uL11 transcriptional activity. PLoS One 2022; 17:e0273198. [PMID: 35981051 PMCID: PMC9387862 DOI: 10.1371/journal.pone.0273198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 08/04/2022] [Indexed: 11/26/2022] Open
Abstract
The ribosomal protein uL11 is located at the basis of the ribosome P-stalk and plays a paramount role in translational efficiency. In addition, no mutant for uL11 is available suggesting that this gene is haplo-insufficient as many other Ribosomal Protein Genes (RPGs). We have previously shown that overexpression of Drosophila melanogaster uL11 enhances the transcription of many RPGs and Ribosomal Biogenesis genes (RiBis) suggesting that uL11 might globally regulate the level of translation through its transcriptional activity. Moreover, uL11 trimethylated on lysine 3 (uL11K3me3) interacts with the chromodomain of the Enhancer of Polycomb and Trithorax Corto, and both proteins co-localize with RNA Polymerase II at many sites on polytene chromosomes. These data have led to the hypothesis that the N-terminal end of uL11, and more particularly the trimethylation of lysine 3, supports the extra-ribosomal activity of uL11 in transcription. To address this question, we mutated the lysine 3 codon using a CRISPR/Cas9 strategy and obtained several lysine 3 mutants. We describe here the first mutants of D. melanogaster uL11. Unexpectedly, the uL11K3A mutant, in which the lysine 3 codon is replaced by an alanine, displays a genuine Minute phenotype known to be characteristic of RPG deletions (longer development, low fertility, high lethality, thin and short bristles) whereas the uL11K3Y mutant, in which the lysine 3 codon is replaced by a tyrosine, is unaffected. In agreement, the rate of translation decreases in uL11K3A but not in uL11K3Y. Co-immunoprecipitation experiments show that the interaction between uL11 and the Corto chromodomain is impaired by both mutations. However, Histone Association Assays indicate that the mutant proteins still bind chromatin. RNA-seq analyses from wing imaginal discs show that Corto represses RPG expression whereas very few genes are deregulated in uL11 mutants. We propose that Corto, by repressing RPG expression, ensures that all ribosomal proteins are present at the correct stoichiometry, and that uL11 fine-tunes its transcriptional regulation of RPGs.
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Affiliation(s)
- Héloïse Grunchec
- Laboratoire de Biologie du développement (LBD), Institut de Biologie Paris Seine (IBPS), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Paris, France
| | - Jérôme Deraze
- Laboratoire de Biologie du développement (LBD), Institut de Biologie Paris Seine (IBPS), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Paris, France
| | - Delphine Dardalhon-Cuménal
- Laboratoire de Biologie du développement (LBD), Institut de Biologie Paris Seine (IBPS), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Paris, France
| | - Valérie Ribeiro
- Laboratoire de Biologie du développement (LBD), Institut de Biologie Paris Seine (IBPS), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Paris, France
| | - Anne Coléno-Costes
- Laboratoire de Biologie du développement (LBD), Institut de Biologie Paris Seine (IBPS), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Paris, France
| | - Karine Dias
- Genomics Core Facility, Institut de Biologie de l’ENS (IBENS), Département de biologie, École normale supérieure, CNRS, Inserm, Université PSL, Paris, France
| | - Sébastien Bloyer
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Emmanuèle Mouchel-Vielh
- Laboratoire de Biologie du développement (LBD), Institut de Biologie Paris Seine (IBPS), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Paris, France
| | - Frédérique Peronnet
- Laboratoire de Biologie du développement (LBD), Institut de Biologie Paris Seine (IBPS), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Paris, France
| | - Hélène Thomassin
- Laboratoire de Biologie du développement (LBD), Institut de Biologie Paris Seine (IBPS), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Paris, France
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6
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Berloco MF, Minervini CF, Moschetti R, Palazzo A, Viggiano L, Marsano RM. Evidence of the Physical Interaction between Rpl22 and the Transposable Element Doc5, a Heterochromatic Transposon of Drosophila melanogaster. Genes (Basel) 2021; 12:genes12121997. [PMID: 34946947 PMCID: PMC8701128 DOI: 10.3390/genes12121997] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/06/2021] [Accepted: 12/12/2021] [Indexed: 11/16/2022] Open
Abstract
Chromatin is a highly dynamic biological entity that allows for both the control of gene expression and the stabilization of chromosomal domains. Given the high degree of plasticity observed in model and non-model organisms, it is not surprising that new chromatin components are frequently described. In this work, we tested the hypothesis that the remnants of the Doc5 transposable element, which retains a heterochromatin insertion pattern in the melanogaster species complex, can be bound by chromatin proteins, and thus be involved in the organization of heterochromatic domains. Using the Yeast One Hybrid approach, we found Rpl22 as a potential interacting protein of Doc5. We further tested in vitro the observed interaction through Electrophoretic Mobility Shift Assay, uncovering that the N-terminal portion of the protein is sufficient to interact with Doc5. However, in situ localization of the native protein failed to detect Rpl22 association with chromatin. The results obtained are discussed in the light of the current knowledge on the extra-ribosomal role of ribosomal protein in eukaryotes, which suggests a possible role of Rpl22 in the determination of the heterochromatin in Drosophila.
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Affiliation(s)
- Maria Francesca Berloco
- Department of Biology, University of Bari “Aldo Moro”, 70126 Bari, Italy; (M.F.B.); (R.M.); (A.P.)
| | - Crescenzio Francesco Minervini
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology and Stem Cell Transplantation Unit, University of Bari “Aldo Moro”, 70124 Bari, Italy;
| | - Roberta Moschetti
- Department of Biology, University of Bari “Aldo Moro”, 70126 Bari, Italy; (M.F.B.); (R.M.); (A.P.)
| | - Antonio Palazzo
- Department of Biology, University of Bari “Aldo Moro”, 70126 Bari, Italy; (M.F.B.); (R.M.); (A.P.)
| | - Luigi Viggiano
- Department of Biology, University of Bari “Aldo Moro”, 70126 Bari, Italy; (M.F.B.); (R.M.); (A.P.)
- Correspondence: (L.V.); (R.M.M.)
| | - René Massimiliano Marsano
- Department of Biology, University of Bari “Aldo Moro”, 70126 Bari, Italy; (M.F.B.); (R.M.); (A.P.)
- Correspondence: (L.V.); (R.M.M.)
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7
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Kachaev ZM, Ivashchenko SD, Kozlov EN, Lebedeva LA, Shidlovskii YV. Localization and Functional Roles of Components of the Translation Apparatus in the Eukaryotic Cell Nucleus. Cells 2021; 10:3239. [PMID: 34831461 PMCID: PMC8623629 DOI: 10.3390/cells10113239] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 12/15/2022] Open
Abstract
Components of the translation apparatus, including ribosomal proteins, have been found in cell nuclei in various organisms. Components of the translation apparatus are involved in various nuclear processes, particularly those associated with genome integrity control and the nuclear stages of gene expression, such as transcription, mRNA processing, and mRNA export. Components of the translation apparatus control intranuclear trafficking; the nuclear import and export of RNA and proteins; and regulate the activity, stability, and functional recruitment of nuclear proteins. The nuclear translocation of these components is often involved in the cell response to stimulation and stress, in addition to playing critical roles in oncogenesis and viral infection. Many components of the translation apparatus are moonlighting proteins, involved in integral cell stress response and coupling of gene expression subprocesses. Thus, this phenomenon represents a significant interest for both basic and applied molecular biology. Here, we provide an overview of the current data regarding the molecular functions of translation factors and ribosomal proteins in the cell nucleus.
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Affiliation(s)
- Zaur M. Kachaev
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
- Center for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Sergey D. Ivashchenko
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
| | - Eugene N. Kozlov
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
| | - Lyubov A. Lebedeva
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
| | - Yulii V. Shidlovskii
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
- Center for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sochi, Russia
- Department of Biology and General Genetics, Sechenov First Moscow State Medical University (Sechenov University), 119992 Moscow, Russia
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8
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Fujimura A, Yasui S, Igawa K, Ueda A, Watanabe K, Hanafusa T, Ichikawa Y, Yoshihashi S, Tsuchida K, Kamiya A, Furuya S. In Vitro Studies to Define the Cell-Surface and Intracellular Targets of Polyarginine-Conjugated Sodium Borocaptate as a Potential Delivery Agent for Boron Neutron Capture Therapy. Cells 2020; 9:E2149. [PMID: 32977522 PMCID: PMC7598271 DOI: 10.3390/cells9102149] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 12/16/2022] Open
Abstract
Boron neutron capture therapy (BNCT) requires pharmaceutical innovations and molecular-based evidence of effectiveness to become a standard cancer therapeutic in the future. Recently, in Japan, 4-borono-L-phenylalanine (BPA) was approved as a boron agent for BNCT against head and neck (H&N) cancers. H&N cancer appears to be a suitable target for BPA-BNCT, because the expression levels of L-type amino acid transporter 1 (LAT1), one of the amino acid transporters responsible for BPA uptake, are elevated in most cases of H&N cancer. However, in other types of cancer including malignant brain tumors, LAT1 is not always highly expressed. To expand the possibility of BNCT for these cases, we previously developed poly-arginine peptide (polyR)-conjugated mercaptoundecahydrododecaborate (BSH). PolyR confers the cell membrane permeability and tumor selectivity of BSH. However, the molecular determinants for the properties are not fully understood. In this present study, we have identified the cluster of differentiation 44 (CD44) protein and translational machinery proteins as a major cell surface target and intracellular targets of BSH-polyR, respectively. CD44, also known as a stem cell-associated maker in various types of cancer, is required for the cellular uptake of polyR-conjugated molecules. We showed that BSH-polyR was predominantly delivered to a CD44High cell population of cancer cells. Once delivered, BSH-polyR interacted with the translational machinery components, including the initiation factors, termination factors, and poly(A)-biding protein (PABP). As a proof of principle, we performed BSH-polyR-based BNCT against glioma stem-like cells and revealed that BSH-polyR successfully induced BNCT-dependent cell death specifically in CD44High cells. Bioinformatics analysis indicated that BSH-polyR would be suitable for certain types of malignant tumors. Our results shed light on the biochemical properties of BSH-polyR, which may further contribute to the therapeutic optimization of BSH-BNCT in the future.
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Affiliation(s)
- Atsushi Fujimura
- Department of Physiology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan;
- Neutron Therapy Research Center, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan; (S.Y.); (K.I.); (A.U.); (K.W.); (T.H.); (Y.I.); (S.F.)
| | - Seiji Yasui
- Neutron Therapy Research Center, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan; (S.Y.); (K.I.); (A.U.); (K.W.); (T.H.); (Y.I.); (S.F.)
| | - Kazuyo Igawa
- Neutron Therapy Research Center, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan; (S.Y.); (K.I.); (A.U.); (K.W.); (T.H.); (Y.I.); (S.F.)
| | - Ai Ueda
- Neutron Therapy Research Center, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan; (S.Y.); (K.I.); (A.U.); (K.W.); (T.H.); (Y.I.); (S.F.)
| | - Kaori Watanabe
- Neutron Therapy Research Center, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan; (S.Y.); (K.I.); (A.U.); (K.W.); (T.H.); (Y.I.); (S.F.)
| | - Tadashi Hanafusa
- Neutron Therapy Research Center, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan; (S.Y.); (K.I.); (A.U.); (K.W.); (T.H.); (Y.I.); (S.F.)
| | - Yasuaki Ichikawa
- Neutron Therapy Research Center, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan; (S.Y.); (K.I.); (A.U.); (K.W.); (T.H.); (Y.I.); (S.F.)
| | - Sachiko Yoshihashi
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan; (S.Y.); (K.T.)
| | - Kazuki Tsuchida
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan; (S.Y.); (K.T.)
| | - Atsunori Kamiya
- Department of Physiology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan;
| | - Shuichi Furuya
- Neutron Therapy Research Center, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan; (S.Y.); (K.I.); (A.U.); (K.W.); (T.H.); (Y.I.); (S.F.)
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9
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Davuluri G, Giusto M, Chandel R, Welch N, Alsabbagh K, Kant S, Kumar A, Kim A, Gangadhariah M, Ghosh PK, Tran U, Krajcik DM, Vasu K, DiDonato AJ, DiDonato JA, Willard B, Monga SP, Wang Y, Fox PL, Stark GR, Wessely O, Esser KA, Dasarathy S. Impaired Ribosomal Biogenesis by Noncanonical Degradation of β-Catenin during Hyperammonemia. Mol Cell Biol 2019; 39:e00451-18. [PMID: 31138664 PMCID: PMC6664607 DOI: 10.1128/mcb.00451-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/19/2018] [Accepted: 05/18/2019] [Indexed: 12/21/2022] Open
Abstract
Increased ribosomal biogenesis occurs during tissue hypertrophy, but whether ribosomal biogenesis is impaired during atrophy is not known. We show that hyperammonemia, which occurs in diverse chronic disorders, impairs protein synthesis as a result of decreased ribosomal content and translational capacity. Transcriptome analyses, real-time PCR, and immunoblotting showed consistent reductions in the expression of the large and small ribosomal protein subunits (RPL and RPS, respectively) in hyperammonemic murine skeletal myotubes, HEK cells, and skeletal muscle from hyperammonemic rats and human cirrhotics. Decreased ribosomal content was accompanied by decreased expression of cMYC, a positive regulator of ribosomal biogenesis, as well as reduced expression and activity of β-catenin, a transcriptional activator of cMYC. However, unlike the canonical regulation of β-catenin via glycogen synthase kinase 3β (GSK3β)-dependent degradation, GSK3β expression and phosphorylation were unaltered during hyperammonemia, and depletion of GSK3β did not prevent ammonia-induced degradation of β-catenin. Overexpression of GSK3β-resistant variants, genetic depletion of IκB kinase β (IKKβ) (activated during hyperammonemia), protein interactions, and in vitro kinase assays showed that IKKβ phosphorylated β-catenin directly. Overexpressing β-catenin restored hyperammonemia-induced perturbations in signaling responses that regulate ribosomal biogenesis. Our data show that decreased protein synthesis during hyperammonemia is mediated via a novel GSK3β-independent, IKKβ-dependent impairment of the β-catenin-cMYC axis.
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Affiliation(s)
- Gangarao Davuluri
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, Ohio, USA
| | - Michela Giusto
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, Ohio, USA
| | - Rajeev Chandel
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, Ohio, USA
| | - Nicole Welch
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, Ohio, USA
| | - Khaled Alsabbagh
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, Ohio, USA
| | - Sashi Kant
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, Ohio, USA
| | - Avinash Kumar
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, Ohio, USA
| | - Adam Kim
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, Ohio, USA
| | | | - Prabar K Ghosh
- Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, Ohio, USA
| | - Uyen Tran
- Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, Ohio, USA
| | - Daniel M Krajcik
- Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, Ohio, USA
| | - Kommireddy Vasu
- Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, Ohio, USA
| | - Anthony J DiDonato
- Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, Ohio, USA
| | - Joseph A DiDonato
- Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, Ohio, USA
| | - Belinda Willard
- Proteomics Research Core Services, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Satdarshan P Monga
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yuxin Wang
- Department of Cancer Biology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Paul L Fox
- Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, Ohio, USA
| | - George R Stark
- Department of Cancer Biology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Oliver Wessely
- Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, Ohio, USA
| | - Karyn A Esser
- Department of Physiology and Functional Genomics, Institute of Myology, University of Florida, Gainesville, Florida, USA
| | - Srinivasan Dasarathy
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, Ohio, USA
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10
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Martins RP, Malbert-Colas L, Lista MJ, Daskalogianni C, Apcher S, Pla M, Findakly S, Blondel M, Fåhraeus R. Nuclear processing of nascent transcripts determines synthesis of full-length proteins and antigenic peptides. Nucleic Acids Res 2019; 47:3086-3100. [PMID: 30624716 PMCID: PMC6451098 DOI: 10.1093/nar/gky1296] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 11/23/2018] [Accepted: 12/18/2018] [Indexed: 01/19/2023] Open
Abstract
Peptides presented on major histocompatibility (MHC) class I molecules form an essential part of the immune system's capacity to detect virus-infected or transformed cells. Earlier works have shown that pioneer translation peptides (PTPs) for the MHC class I pathway are as efficiently produced from introns as from exons, or from mRNAs targeted for the nonsense-mediated decay pathway. The production of PTPs is a target for viral immune evasion but the underlying molecular mechanisms that govern this non-canonical translation are unknown. Here, we have used different approaches to show how events taking place on the nascent transcript control the synthesis of PTPs and full-length proteins. By controlling the subcellular interaction between the G-quadruplex structure (G4) of a gly-ala encoding mRNA and nucleolin (NCL) and by interfering with mRNA maturation using multiple approaches, we demonstrate that antigenic peptides derive from a nuclear non-canonical translation event that is independently regulated from the synthesis of full-length proteins. Moreover, we show that G4 are exploited to control mRNA localization and translation by distinguishable mechanisms that are targets for viral immune evasion.
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Affiliation(s)
| | | | - María José Lista
- Université de Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France
| | - Chrysoula Daskalogianni
- Université Paris 7, Inserm, UMR 1162, Paris, France
- ICCVS, University of Gdańsk, Science, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Sebastien Apcher
- Institut Gustave Roussy, Université Paris Sud, UMR 1015, Villejuif, France
| | - Marika Pla
- Université Paris 7, IUH, Inserm, UMR-S-1131, Paris, France
| | | | - Marc Blondel
- Université de Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France
| | - Robin Fåhraeus
- Université Paris 7, Inserm, UMR 1162, Paris, France
- ICCVS, University of Gdańsk, Science, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic
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11
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Singh AK, Choudhury SR, De S, Zhang J, Kissane S, Dwivedi V, Ramanathan P, Petric M, Orsini L, Hebenstreit D, Brogna S. The RNA helicase UPF1 associates with mRNAs co-transcriptionally and is required for the release of mRNAs from gene loci. eLife 2019; 8:e41444. [PMID: 30907728 PMCID: PMC6447362 DOI: 10.7554/elife.41444] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 03/22/2019] [Indexed: 12/21/2022] Open
Abstract
UPF1 is an RNA helicase that is required for nonsense-mediated mRNA decay (NMD) in eukaryotes, and the predominant view is that UPF1 mainly operates on the 3'UTRs of mRNAs that are directed for NMD in the cytoplasm. Here we offer evidence, obtained from Drosophila, that UPF1 constantly moves between the nucleus and cytoplasm by a mechanism that requires its RNA helicase activity. UPF1 is associated, genome-wide, with nascent RNAs at most of the active Pol II transcription sites and at some Pol III-transcribed genes, as demonstrated microscopically on the polytene chromosomes of salivary glands and by ChIP-seq analysis in S2 cells. Intron recognition seems to interfere with association and translocation of UPF1 on nascent pre-mRNAs, and cells depleted of UPF1 show defects in the release of mRNAs from transcription sites and their export from the nucleus.
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Affiliation(s)
- Anand K Singh
- School of BiosciencesUniversity of BirminghamBirminghamUnited Kingdom
| | | | - Sandip De
- School of BiosciencesUniversity of BirminghamBirminghamUnited Kingdom
| | - Jie Zhang
- Life SciencesUniversity of WarwickCoventryUnited Kingdom
| | - Stephen Kissane
- School of BiosciencesUniversity of BirminghamBirminghamUnited Kingdom
| | - Vibha Dwivedi
- School of BiosciencesUniversity of BirminghamBirminghamUnited Kingdom
| | | | - Marija Petric
- School of BiosciencesUniversity of BirminghamBirminghamUnited Kingdom
| | - Luisa Orsini
- School of BiosciencesUniversity of BirminghamBirminghamUnited Kingdom
| | | | - Saverio Brogna
- School of BiosciencesUniversity of BirminghamBirminghamUnited Kingdom
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12
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Aranda S, Alcaine-Colet A, Blanco E, Borràs E, Caillot C, Sabidó E, Di Croce L. Chromatin capture links the metabolic enzyme AHCY to stem cell proliferation. SCIENCE ADVANCES 2019; 5:eaav2448. [PMID: 30854431 PMCID: PMC6402848 DOI: 10.1126/sciadv.aav2448] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 01/28/2019] [Indexed: 05/19/2023]
Abstract
Profiling the chromatin-bound proteome (chromatome) in a simple, direct, and reliable manner might be key to uncovering the role of yet uncharacterized chromatin factors in physiology and disease. Here, we have designed an experimental strategy to survey the chromatome of proliferating cells by using the DNA-mediated chromatin pull-down (Dm-ChP) technology. Our approach provides a global view of cellular chromatome under normal physiological conditions and enables the identification of chromatin-bound proteins de novo. Integrating Dm-ChP with genomic and functional data, we have discovered an unexpected chromatin function for adenosylhomocysteinase, a major one-carbon pathway metabolic enzyme, in gene activation. Our study reveals a new regulatory axis between the metabolic state of pluripotent cells, ribosomal protein production, and cell division during the early phase of embryo development, in which the metabolic flux of methylation reactions is favored in a local milieu.
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Affiliation(s)
- Sergi Aranda
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Anna Alcaine-Colet
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Eva Borràs
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Claire Caillot
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, Barcelona 08010, Spain
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13
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Liu XM, Yan MQ, Ji SY, Sha QQ, Huang T, Zhao H, Liu HB, Fan HY, Chen ZJ. Loss of oocyte Rps26 in mice arrests oocyte growth and causes premature ovarian failure. Cell Death Dis 2018; 9:1144. [PMID: 30451825 PMCID: PMC6242890 DOI: 10.1038/s41419-018-1196-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/09/2018] [Accepted: 10/15/2018] [Indexed: 11/08/2022]
Abstract
Global transcriptional activity increases as oocytes grow and is silenced in fully grown oocytes. Thus, the chromatin configuration varies during oocyte growth, but the molecular mechanisms regulating these changes remain to be clarified. Here, we studied a susceptibility gene of polycystic ovary syndrome (PCOS), RPS26, which is a ribosomal protein-encoding gene that is highly expressed in the ovary, but the functions of which remain unknown. Specific knockout of Rps26 in mouse oocytes resulted in retarded follicle development from pre-antral follicles to antral follicles, while the chromatin configurations of the oocytes were arrested at the transition from the non-surrounded nucleolus (NSN) to surrounded nucleolus (SN)-type. As a consequence, all oocytes died by postnatal day 84 resulting in premature ovarian failure (POF). Loss of Rps26 in oocytes led to decreased mRNA transcription and low levels of histone trimethylation on H3K4/H3K9 and DNA methylation at 5-cytosine, high levels of which are required for oocytes to transform from NSN to SN-type. Low protein levels of oocyte-derived growth differentiation factor 9, bone morphogenetic protein 15, and the oocyte-granulosa cell gap junction protein connexin 37 inhibited oocyte growth and retarded follicle development. The disruption of the phosphoinositide 3-kinase/protein kinase B/Forkhead box O-3a pathway contributed to oocyte death and follicle atresia. These results provide genetic clues for the clinical diagnosis of POF, especially in PCOS patients without treatment.
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Affiliation(s)
- Xiao-Man Liu
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, 250001, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, 250001, China
- The Key Laboratory for Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, 250001, China
| | - Ming-Qi Yan
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, 250001, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, 250001, China
- The Key Laboratory for Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, 250001, China
| | - Shu-Yan Ji
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, 310058, China
| | - Qian-Qian Sha
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, 310058, China
| | - Tao Huang
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, 250001, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, 250001, China
- The Key Laboratory for Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, 250001, China
| | - Han Zhao
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, 250001, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, 250001, China
- The Key Laboratory for Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, 250001, China
| | - Hong-Bin Liu
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, 250001, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, 250001, China
- The Key Laboratory for Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, 250001, China
| | - Heng-Yu Fan
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, 310058, China
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, 250001, China.
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, 250001, China.
- The Key Laboratory for Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, 250001, China.
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200135, China.
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, 200135, China.
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14
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Lin WH, He M, Fan YN, Baines RA. An RNAi-mediated screen identifies novel targets for next-generation antiepileptic drugs based on increased expression of the homeostatic regulator pumilio. J Neurogenet 2018; 32:106-117. [PMID: 29718742 PMCID: PMC5989157 DOI: 10.1080/01677063.2018.1465570] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Despite availability of a diverse range of anti-epileptic drugs (AEDs), only about two-thirds of epilepsy patients respond well to drug treatment. Thus, novel targets are required to catalyse the design of next-generation AEDs. Manipulation of neuron firing-rate homoeostasis, through enhancing Pumilio (Pum) activity, has been shown to be potently anticonvulsant in Drosophila. In this study, we performed a genome-wide RNAi screen in S2R + cells, using a luciferase-based dPum activity reporter and identified 1166 genes involved in dPum regulation. Of these genes, we focused on 699 genes that, on knock-down, potentiate dPum activity/expression. Of this subgroup, 101 genes are activity-dependent based on comparison with genes previously identified as activity-dependent by RNA-sequencing. Functional cluster analysis shows these genes are enriched in pathways involved in DNA damage, regulation of cell cycle and proteasomal protein catabolism. To test for anticonvulsant activity, we utilised an RNA-interference approach in vivo. RNAi-mediated knockdown showed that 57/101 genes (61%) are sufficient to significantly reduce seizure duration in the characterized seizure mutant, parabss. We further show that chemical inhibitors of protein products of some of the genes targeted are similarly anticonvulsant. Finally, to establish whether the anticonvulsant activity of identified compounds results from increased dpum transcription, we performed a luciferase-based assay to monitor dpum promoter activity. Third instar larvae exposed to sodium fluoride, gemcitabine, metformin, bestatin, WP1066 or valproic acid all showed increased dpum promoter activity. Thus, this study validates Pum as a favourable target for AED design and, moreover, identifies a number of lead compounds capable of increasing the expression of this homeostatic regulator.
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Affiliation(s)
- Wei-Hsiang Lin
- a Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health , University of Manchester, Manchester Academic Health Science Centre , Manchester , UK
| | - Miaomiao He
- a Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health , University of Manchester, Manchester Academic Health Science Centre , Manchester , UK
| | - Yuen Ngan Fan
- a Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health , University of Manchester, Manchester Academic Health Science Centre , Manchester , UK
| | - Richard A Baines
- a Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health , University of Manchester, Manchester Academic Health Science Centre , Manchester , UK
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15
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Immunoribosomes: Where's there's fire, there's fire. Mol Immunol 2018; 113:38-42. [PMID: 29361306 DOI: 10.1016/j.molimm.2017.12.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 12/31/2017] [Indexed: 01/13/2023]
Abstract
The MHC class I antigen presentation pathway enables T cell immunosurveillance of cancer cells, viruses and other intracellular pathogens. Rapidly degraded newly synthesized proteins (DRiPs) are a major source of self-, and particularly, viral antigenic peptides. A number of findings support the idea that a substantial fraction of antigenic peptides are synthesized by "immunoribosomes", a subset of translating ribosomes that generate class I peptides with enhanced efficiency. Here, we review the evidence for the immunoribosome hypothesis.
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16
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Martins RP, Fåhraeus R. A matter of maturity: The impact of pre-mRNA processing in gene expression and antigen presentation. Int J Biochem Cell Biol 2017; 91:203-211. [PMID: 28549625 DOI: 10.1016/j.biocel.2017.05.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/15/2017] [Accepted: 05/18/2017] [Indexed: 12/28/2022]
Abstract
RNA processing plays a pivotal role in the diversification of high eukaryotes transcriptome and proteome. The expression of gene products controlling a variety of cellular and physiological processes depends largely on a complex maturation process undergone by pre-mRNAs to become translation-competent mRNAs. Here we review the different mechanisms involved in the pre-mRNA processing and disclose their impact in the gene regulation process in eukaryotic cells. We describe some viral strategies targeting pre-mRNA processing to control gene expression and host immune response and discuss their relevance as tools for a better understanding of cell biology. Finally, we highlight accumulating evidences toward the occurrence of a translation event coupled to mRNA biogenesis in the nuclear compartment and argue how this is relevant for the production of antigenic peptide substrates for the major histocompatibility complex class I pathway.
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Affiliation(s)
- Rodrigo Prado Martins
- Équipe Labellisée Ligue Contre le Cancer, Université Paris 7, INSERM UMR 1162, 27 rue Juliette Dodu, 75010 Paris, France.
| | - Robin Fåhraeus
- Équipe Labellisée Ligue Contre le Cancer, Université Paris 7, INSERM UMR 1162, 27 rue Juliette Dodu, 75010 Paris, France; Department of Medical Biosciences, Umeå University, Umeå, Sweden; RECAMO, Masaryk Memorial Cancer Institute, Brno, Czech Republic
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17
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Das S, Das B. eIF4G—an integrator of mRNA metabolism? FEMS Yeast Res 2016; 16:fow087. [DOI: 10.1093/femsyr/fow087] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2016] [Indexed: 11/14/2022] Open
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18
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Minakhina S, Naryshkina T, Changela N, Tan W, Steward R. Zfrp8/PDCD2 Interacts with RpS2 Connecting Ribosome Maturation and Gene-Specific Translation. PLoS One 2016; 11:e0147631. [PMID: 26807849 PMCID: PMC4726551 DOI: 10.1371/journal.pone.0147631] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 11/25/2015] [Indexed: 11/28/2022] Open
Abstract
Zfrp8/PDCD2 is a highly conserved protein essential for stem cell maintenance in both flies and mammals. It is also required in fast proliferating cells such as cancer cells. Our previous studies suggested that Zfrp8 functions in the formation of mRNP (mRNA ribonucleoprotein) complexes and also controls RNA of select Transposable Elements (TEs). Here we show that in Zfrp8/PDCD2 knock down (KD) ovaries, specific mRNAs and TE transcripts show increased nuclear accumulation. We also show that Zfrp8/PDCD2 interacts with the (40S) small ribosomal subunit through direct interaction with RpS2 (uS5). By studying the distribution of endogenous and transgenic fluorescently tagged ribosomal proteins we demonstrate that Zfrp8/PDCD2 regulates the cytoplasmic levels of components of the small (40S) ribosomal subunit, but does not control nuclear/nucleolar localization of ribosomal proteins. Our results suggest that Zfrp8/PDCD2 functions at late stages of ribosome assembly and may regulate the binding of specific mRNA-RNPs to the small ribosomal subunit ultimately controlling their cytoplasmic localization and translation.
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Affiliation(s)
- Svetlana Minakhina
- Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
- * E-mail: (SM); (RS)
| | - Tatyana Naryshkina
- Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Neha Changela
- Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - William Tan
- Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Ruth Steward
- Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
- * E-mail: (SM); (RS)
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19
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Xu J, Zhang P, Kusakabe T, Mon H, Li Z, Zhu L, Iiyama K, Banno Y, Morokuma D, Lee JM. Comparative proteomic analysis of hemolymph proteins from Autographa californica multiple nucleopolyhedrovirus (AcMNPV)-sensitive or -resistant silkworm strains during infections. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2015; 16:36-47. [DOI: 10.1016/j.cbd.2015.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 07/21/2015] [Accepted: 07/26/2015] [Indexed: 01/07/2023]
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20
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RPS12 increases the invasiveness in cervical cancer activated by c-Myc and inhibited by the dietary flavonoids luteolin and quercetin. J Funct Foods 2015. [DOI: 10.1016/j.jff.2015.09.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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21
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Rasheedi S, Suragani M, Raviprasad P, Ghosh S, Suragani RNVS, Ramaiah KVA, Ehtesham NZ. Functional characterization of PeIF5B as eIF5B homologue from Pisum sativum. Biochimie 2015; 118:36-43. [PMID: 26215376 DOI: 10.1016/j.biochi.2015.07.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 07/21/2015] [Indexed: 10/23/2022]
Abstract
We earlier reported 'PeIF5B' as a novel factor from Pisum sativum that has sequence similarity to eIF5B (S. Rasheedi, S. Ghosh, M. Suragani et al., P. sativum contains a factor with strong homology to eIF5B, Gene 399 (2007) 144-151). The main aim of the present study was to perform functional characterization of PeIF5B as an eIF5B homologue from plant system. PeIF5B shows binding to Met - tRNA(f)(Met), hydrolyses GTP and interacts with ribosomes. In vivo growth complementation analysis shows that PeIF5B partially complements its yeast homologue. Interestingly, PeIF5B mainly localizes in the nucleus as confirmed by nuclear localization signal (NLS) prediction, confocal imaging and immunoblots of cellular fractions. Similar to the yeast eIF5B but unlike the human orthologue, PeIF5B is an intron-less gene. This study highlights PeIF5B's role as a functional eIF5B homologue possibly participating in nuclear translation in plant system.
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Affiliation(s)
- Sheeba Rasheedi
- Laboratory of Molecular and Cellular Biology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500 001, India
| | - Madhuri Suragani
- Molecular Biology Unit, National Institute of Nutrition, Hyderabad 500 007, India
| | - Podili Raviprasad
- Molecular Biology Unit, National Institute of Nutrition, Hyderabad 500 007, India
| | - Sudip Ghosh
- Molecular Biology Unit, National Institute of Nutrition, Hyderabad 500 007, India
| | | | - Kolluru V A Ramaiah
- Department of Biochemistry, University of Hyderabad, Prof. C. R. Rao Road, Hyderabad 500 046, India
| | - Nasreen Z Ehtesham
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology, Safdarjung Hospital, New Delhi 110029, India.
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22
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Perina D, Korolija M, Hadžija MP, Grbeša I, Belužić R, Imešek M, Morrow C, Marjanović MP, Bakran-Petricioli T, Mikoč A, Ćetković H. Functional and Structural Characterization of FAU Gene/Protein from Marine Sponge Suberites domuncula. Mar Drugs 2015. [PMID: 26198235 PMCID: PMC4515611 DOI: 10.3390/md13074179] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed (FAU) gene is down-regulated in human prostate, breast and ovarian cancers. Moreover, its dysregulation is associated with poor prognosis in breast cancer. Sponges (Porifera) are animals without tissues which branched off first from the common ancestor of all metazoans. A large majority of genes implicated in human cancers have their homologues in the sponge genome. Our study suggests that FAU gene from the sponge Suberites domuncula reflects characteristics of the FAU gene from the metazoan ancestor, which have changed only slightly during the course of animal evolution. We found pro-apoptotic activity of sponge FAU protein. The same as its human homologue, sponge FAU increases apoptosis in human HEK293T cells. This indicates that the biological functions of FAU, usually associated with "higher" metazoans, particularly in cancer etiology, possess a biochemical background established early in metazoan evolution. The ancestor of all animals possibly possessed FAU protein with the structure and function similar to evolutionarily more recent versions of the protein, even before the appearance of true tissues and the origin of tumors and metastasis. It provides an opportunity to use pre-bilaterian animals as a simpler model for studying complex interactions in human cancerogenesis.
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Affiliation(s)
- Dragutin Perina
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb 10000, Croatia.
| | - Marina Korolija
- Forensic Science Centre "Ivan Vučetić", Zagreb 10000, Croatia.
| | | | - Ivana Grbeša
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramaty-Gan 5290002, Israel.
| | - Robert Belužić
- Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb 10000, Croatia.
| | - Mirna Imešek
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb 10000, Croatia.
| | - Christine Morrow
- Queen's University Belfast, Marine Laboratory, Portaferry BT22 1PF, Northern Ireland, UK.
| | | | | | - Andreja Mikoč
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb 10000, Croatia.
| | - Helena Ćetković
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb 10000, Croatia.
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23
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Recent studies implicate the nucleolus as the major site of nuclear translation. Biochem Soc Trans 2015; 42:1224-8. [PMID: 25110029 DOI: 10.1042/bst20140062] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The nucleolus is the most prominent morphological feature within the nucleus of eukaryotic cells and is best known for its role in ribosome biogenesis. It forms around highly transcribed ribosomal RNA gene repeats which yield precursor rRNAs that are co-transcriptionally processed, folded and, while still within the nucleolus, associate with most of the ribosomal proteins. The nucleolus is therefore often thought of as a factory for making ribosomal subunits, which are exported as inactive precursors to the cytoplasm where late maturation makes them capable of mRNA binding and translation initiation. However, recent studies have shown substantial evidence for the presence of functional, translation competent ribosomal subunits within the nucleus, particularly in the nucleolus. These observations raise the intriguing possibility that the nucleolus, as well as being a ribosome factory, is also an important nuclear protein-synthesis plant.
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24
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Mondal BC, Shim J, Evans CJ, Banerjee U. Pvr expression regulators in equilibrium signal control and maintenance of Drosophila blood progenitors. eLife 2014; 3:e03626. [PMID: 25201876 PMCID: PMC4185420 DOI: 10.7554/elife.03626] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 09/05/2014] [Indexed: 12/18/2022] Open
Abstract
Blood progenitors within the lymph gland, a larval organ that supports hematopoiesis in Drosophila melanogaster, are maintained by integrating signals emanating from niche-like cells and those from differentiating blood cells. We term the signal from differentiating cells the 'equilibrium signal' in order to distinguish it from the 'niche signal'. Earlier we showed that equilibrium signaling utilizes Pvr (the Drosophila PDGF/VEGF receptor), STAT92E, and adenosine deaminase-related growth factor A (ADGF-A) (Mondal et al., 2011). Little is known about how this signal initiates during hematopoietic development. To identify new genes involved in lymph gland blood progenitor maintenance, particularly those involved in equilibrium signaling, we performed a genetic screen that identified bip1 (bric à brac interacting protein 1) and Nucleoporin 98 (Nup98) as additional regulators of the equilibrium signal. We show that the products of these genes along with the Bip1-interacting protein RpS8 (Ribosomal protein S8) are required for the proper expression of Pvr.
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Affiliation(s)
- Bama Charan Mondal
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
| | - Jiwon Shim
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
- Department of Life Science, Hanyang University, Seoul, Republic of Korea
| | - Cory J Evans
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
| | - Utpal Banerjee
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, United States
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, United States
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25
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Baboo S, Cook PR. "Dark matter" worlds of unstable RNA and protein. Nucleus 2014; 5:281-6. [PMID: 25482115 PMCID: PMC4152340 DOI: 10.4161/nucl.29577] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 06/10/2014] [Accepted: 06/13/2014] [Indexed: 12/11/2022] Open
Abstract
Astrophysicists use the term "dark matter" to describe the majority of the matter and/or energy in the universe that is hidden from view, and biologists now apply it to the new families of RNA they are uncovering. We review evidence for an analogous hidden world containing peptides. The critical experiments involved pulse-labeling human cells with tagged amino acids for periods as short as five seconds. Results are extraordinary in two respects: both nucleus and cytoplasm become labeled, and most signals disappear with a half-life of less than one minute. Just as the synthesis of each mature mRNA is regulated by the abortive production of hundreds of shorter transcripts that are quickly degraded, it seems that the synthesis of each full-length protein in the stable proteome is regulated by an apparently wasteful production and degradation of shorter peptides. Some of the nuclear synthesis is probably a byproduct of nuclear ribosomes proofreading newly-made RNA for inappropriately-placed termination codons (a process that triggers "nonsense-mediated decay"). We speculate that some "dark-matter" peptides will play other important roles in the cell.
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Affiliation(s)
- Sabyasachi Baboo
- Sir William Dunn School of Pathology; University of Oxford; Oxford, UK
| | - Peter R Cook
- Sir William Dunn School of Pathology; University of Oxford; Oxford, UK
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26
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Al-Jubran K, Wen J, Abdullahi A, Roy Chaudhury S, Li M, Ramanathan P, Matina A, De S, Piechocki K, Rugjee KN, Brogna S. Visualization of the joining of ribosomal subunits reveals the presence of 80S ribosomes in the nucleus. RNA (NEW YORK, N.Y.) 2013; 19:1669-83. [PMID: 24129492 PMCID: PMC3884666 DOI: 10.1261/rna.038356.113] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 08/13/2013] [Indexed: 05/29/2023]
Abstract
In eukaryotes the 40S and 60S ribosomal subunits are assembled in the nucleolus, but there appear to be mechanisms preventing mRNA binding, 80S formation, and initiation of translation in the nucleus. To visualize association between ribosomal subunits, we tagged pairs of Drosophila ribosomal proteins (RPs) located in different subunits with mutually complementing halves of fluorescent proteins. Pairs of tagged RPs expected to interact, or be adjacent in the 80S structure, showed strong fluorescence, while pairs that were not in close proximity did not. Moreover, the complementation signal is found in ribosomal fractions and it was enhanced by translation elongation inhibitors and reduced by initiation inhibitors. Our technique achieved 80S visualization both in cultured cells and in fly tissues in vivo. Notably, while the main 80S signal was in the cytoplasm, clear signals were also seen in the nucleolus and at other nuclear sites. Furthermore, we detected rapid puromycin incorporation in the nucleolus and at transcription sites, providing an independent indication of functional 80S in the nucleolus and 80S association with nascent transcripts.
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Affiliation(s)
- Khalid Al-Jubran
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Jikai Wen
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Akilu Abdullahi
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Subhendu Roy Chaudhury
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Min Li
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Preethi Ramanathan
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Annunziata Matina
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Sandip De
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Kim Piechocki
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Kushal Nivriti Rugjee
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Saverio Brogna
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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27
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Abstract
Adaptive mutations that accumulate during species divergence are likely to contribute to reproductive incompatibilities and hinder gene flow; however, there may also be a class of mutations that are generally advantageous and can spread across species boundaries. In this study, we characterize a 15 kb region on chromosome 3R that has introgressed from the cosmopolitan generalist species Drosophila simulans into the island endemic D. sechellia, which is an ecological specialist. The introgressed haplotype is fixed in D. sechellia over almost the entirety of the resequenced region, whereas a core region of the introgressed haplotype occurs at high frequency in D. simulans. The observed patterns of nucleotide variation and linkage disequilibrium are consistent with a recently completed selective sweep in D. sechellia and an incomplete sweep in D. simulans. Independent estimates of both the time to the introgression and sweep events are all close to 10,000 years before the present. Interestingly, the most likely target of selection is a highly occupied transcription factor binding region. This work confirms that it is possible for mutations to be globally advantageous, despite their occurrence in divergent genomic and ecological backgrounds.
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Affiliation(s)
| | | | - Longjun Wu
- Department of Biology, University of Rochester
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28
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Papantonis A, Cook PR. Transcription factories: genome organization and gene regulation. Chem Rev 2013; 113:8683-705. [PMID: 23597155 DOI: 10.1021/cr300513p] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Argyris Papantonis
- Sir William Dunn School of Pathology, University of Oxford , South Parks Road, Oxford OX1 3RE, United Kingdom
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29
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Trcek T, Sato H, Singer RH, Maquat LE. Temporal and spatial characterization of nonsense-mediated mRNA decay. Genes Dev 2013; 27:541-51. [PMID: 23431032 PMCID: PMC3605467 DOI: 10.1101/gad.209635.112] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 01/29/2013] [Indexed: 12/11/2022]
Abstract
Nonsense-mediated mRNA decay (NMD) is a quality control mechanism responsible for "surveying" mRNAs during translation and degrading those that harbor a premature termination codon (PTC). Currently the intracellular spatial location of NMD and the kinetics of its decay step in mammalian cells are under debate. To address these issues, we used single-RNA fluorescent in situ hybridization (FISH) and measured the NMD of PTC-containing β-globin mRNA in intact single cells after the induction of β-globin gene transcription. This approach preserves temporal and spatial information of the NMD process, both of which would be lost in an ensemble study. We determined that decay of the majority of PTC-containing β-globin mRNA occurs soon after its export into the cytoplasm, with a half-life of <1 min; the remainder is degraded with a half-life of >12 h, similar to the half-life of normal PTC-free β-globin mRNA, indicating that it had evaded NMD. Importantly, NMD does not occur within the nucleoplasm, thus countering the long-debated idea of nuclear degradation of PTC-containing transcripts. We provide a spatial and temporal model for the biphasic decay of NMD targets.
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Affiliation(s)
- Tatjana Trcek
- Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Hanae Sato
- Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Robert H. Singer
- Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Lynne E. Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
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30
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Rugjee KN, Roy Chaudhury S, Al-Jubran K, Ramanathan P, Matina T, Wen J, Brogna S. Fluorescent protein tagging confirms the presence of ribosomal proteins at Drosophila polytene chromosomes. PeerJ 2013; 1:e15. [PMID: 23638349 PMCID: PMC3629075 DOI: 10.7717/peerj.15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 01/03/2013] [Indexed: 11/20/2022] Open
Abstract
Most ribosomal proteins (RPs) are stoichiometrically incorporated into ribosomal subunits and play essential roles in ribosome biogenesis and function. However, a number of RPs appear to have non-ribosomal functions, which involve direct association with pre-mRNA and transcription factors at transcription sites. The consensus is that the RPs found at these sites are off ribosomal subunits, but observation that different RPs are usually found together suggests that ribosomal or ribosomal-like subunits might be present. Notably, it has previously been reported that antibodies against 20 different RPs stain the same Pol II transcription sites in Drosophila polytene chromosomes. Some concerns, however, were raised about the specificity of the antibodies. To investigate further whether RPs are present at transcription sites in Drosophila, we have generated several transgenic flies expressing RPs (RpS2, RpS5a, RpS9, RpS11, RpS13, RpS18, RpL8, RpL11, RpL32, and RpL36) tagged with either green or red fluorescent protein. Imaging of salivary gland cells showed that these proteins are, as expected, abundant in the cytoplasm as well as in the nucleolus. However, these RPs are also apparent in the nucleus in the region occupied by the chromosomes. Indeed, polytene chromosome immunostaining of a representative subset of tagged RPs confirms the association with transcribed loci. Furthermore, characterization of a strain expressing RpL41 functionally tagged at its native genomic locus with YFP, also showed apparent nuclear accumulation and chromosomal association, suggesting that such a nuclear localization pattern might be a shared feature of RPs and is biologically important. We anticipate that the transgenes described here should provide a useful research tool to visualize ribosomal subunits in Drosophila tissues and to study the non-ribosomal functions of RPs.
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Affiliation(s)
| | | | | | | | - Tina Matina
- University of Birmingham, School of Biosciences, UK
| | - Jikai Wen
- University of Birmingham, School of Biosciences, UK
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31
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Möller A, Xie SQ, Hosp F, Lang B, Phatnani HP, James S, Ramirez F, Collin GB, Naggert JK, Babu MM, Greenleaf AL, Selbach M, Pombo A. Proteomic analysis of mitotic RNA polymerase II reveals novel interactors and association with proteins dysfunctional in disease. Mol Cell Proteomics 2012; 11:M111.011767. [PMID: 22199231 PMCID: PMC3433901 DOI: 10.1074/mcp.m111.011767] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Revised: 11/19/2011] [Indexed: 11/06/2022] Open
Abstract
RNA polymerase II (RNAPII) transcribes protein-coding genes in eukaryotes and interacts with factors involved in chromatin remodeling, transcriptional activation, elongation, and RNA processing. Here, we present the isolation of native RNAPII complexes using mild extraction conditions and immunoaffinity purification. RNAPII complexes were extracted from mitotic cells, where they exist dissociated from chromatin. The proteomic content of native complexes in total and size-fractionated extracts was determined using highly sensitive LC-MS/MS. Protein associations with RNAPII were validated by high-resolution immunolocalization experiments in both mitotic cells and in interphase nuclei. Functional assays of transcriptional activity were performed after siRNA-mediated knockdown. We identify >400 RNAPII associated proteins in mitosis, among these previously uncharacterized proteins for which we show roles in transcriptional elongation. We also identify, as novel functional RNAPII interactors, two proteins involved in human disease, ALMS1 and TFG, emphasizing the importance of gene regulation for normal development and physiology.
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Affiliation(s)
- André Möller
- From the ‡MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, London W12 0NN, United Kingdom
| | - Sheila Q. Xie
- From the ‡MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, London W12 0NN, United Kingdom
| | - Fabian Hosp
- §Max-Delbrück Center for Molecular Medicine, 13092 Berlin, Germany
| | - Benjamin Lang
- ¶MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Hemali P. Phatnani
- ‖Department of Biochemistry, Duke University, Medical Center, Durham, North Carolina 27710
| | - Sonya James
- From the ‡MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, London W12 0NN, United Kingdom
| | | | | | | | - M. Madan Babu
- ¶MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Arno L. Greenleaf
- ‖Department of Biochemistry, Duke University, Medical Center, Durham, North Carolina 27710
| | - Matthias Selbach
- §Max-Delbrück Center for Molecular Medicine, 13092 Berlin, Germany
| | - Ana Pombo
- From the ‡MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, London W12 0NN, United Kingdom
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32
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Reid DW, Nicchitta CV. The enduring enigma of nuclear translation. J Cell Biol 2012; 197:7-9. [PMID: 22472436 PMCID: PMC3317809 DOI: 10.1083/jcb.201202140] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 03/05/2012] [Indexed: 11/22/2022] Open
Abstract
Although the physical separation of transcription in the nucleus and translation in the cytoplasm has presided as a fundamental tenet of cell biology for decades, it has not done so without recurring challenges and contentious debate. In this issue, David et al. (2012. J. Cell Biol. http://dx.doi.org/10.1083/jcb.201112145) rekindle the controversy by providing convincing experimental evidence for nuclear translation.
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Affiliation(s)
- David W. Reid
- Department of Biochemistry and Department of Cell Biology, Duke University Medical Center, Durham, NC 27710
| | - Christopher V. Nicchitta
- Department of Biochemistry and Department of Cell Biology, Duke University Medical Center, Durham, NC 27710
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33
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de Turris V, Nicholson P, Orozco RZ, Singer RH, Mühlemann O. Cotranscriptional effect of a premature termination codon revealed by live-cell imaging. RNA (NEW YORK, N.Y.) 2011; 17:2094-107. [PMID: 22028363 PMCID: PMC3222123 DOI: 10.1261/rna.02918111] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 08/30/2011] [Indexed: 05/29/2023]
Abstract
Aberrant mRNAs with premature translation termination codons (PTCs) are recognized and eliminated by the nonsense-mediated mRNA decay (NMD) pathway in eukaryotes. We employed a novel live-cell imaging approach to investigate the kinetics of mRNA synthesis and release at the transcription site of PTC-containing (PTC+) and PTC-free (PTC-) immunoglobulin-μ reporter genes. Fluorescence recovery after photobleaching (FRAP) and photoconversion analyses revealed that PTC+ transcripts are specifically retained at the transcription site. Remarkably, the retained PTC+ transcripts are mainly unspliced, and this RNA retention is dependent upon two important NMD factors, UPF1 and SMG6, since their depletion led to the release of the PTC+ transcripts. Finally, ChIP analysis showed a physical association of UPF1 and SMG6 with both the PTC+ and the PTC- reporter genes in vivo. Collectively, our data support a mechanism for regulation of PTC+ transcripts at the transcription site.
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Affiliation(s)
| | - Pamela Nicholson
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
| | | | | | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
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34
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De S, Varsally W, Falciani F, Brogna S. Ribosomal proteins' association with transcription sites peaks at tRNA genes in Schizosaccharomyces pombe. RNA (NEW YORK, N.Y.) 2011; 17:1713-26. [PMID: 21757508 PMCID: PMC3162336 DOI: 10.1261/rna.2808411] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2011] [Accepted: 06/13/2011] [Indexed: 05/05/2023]
Abstract
Ribosomal proteins (RPs) are essential components of ribosomes, but several RPs are also present at transcription sites of eukaryotic chromosomes. Here, we report a genome-wide ChIP-on-chip analysis of the association of three representative 60S RPs with sites in the Schizosaccharomyces pombe chromosomes. All three proteins tend to bind at the same subset of coding and noncoding loci. The data demonstrate selective RNA-dependent interactions between RPs and many transcription sites and suggest that the RPs bind as components of a preassembled multiprotein complex, perhaps 60S or pre-60S subunits. These findings further indicate that the presence of RPs complexes at transcription sites might be a general feature of eukaryotic cells and functionally important. Unexpectedly, the RPs' chromosomal association is highest at centromeres and tRNA genes-the RPs were found at 167 of the 171 tRNA genes assayed. These findings raise the intriguing possibility that RP complexes are involved in tRNA biogenesis and possibly centromere functions.
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Affiliation(s)
- Sandip De
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Wazeer Varsally
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Francesco Falciani
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Saverio Brogna
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
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35
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Are ribosomal proteins present at transcription sites on or off ribosomal subunits? Biochem Soc Trans 2011; 38:1543-7. [PMID: 21118123 DOI: 10.1042/bst0381543] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
RPs (ribosomal proteins) are main components of the ribosome having essential functions in its biogenesis, function and structural integrity. Although most of the RP molecules are in the cytoplasm, being incorporated into translating ribosomes, some RPs have non-ribosomal functions when they are off ribosomal subunits. Notably, in eukaryotes, RPs are also present at transcription sites and some of these proteins have a function in transcription and pre-mRNA processing of specific genes. Although the consensus is that the proteins found at these sites are isolated RPs not assembled into ribosomal subunits, it has been proposed that ribosomal subunits might also be present. In the present paper, we review the available evidence for RPs at transcription sites and conclude that ribosomal subunits might be present, but additional studies will be required to solve this important issue.
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36
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Tarallo R, Bamundo A, Nassa G, Nola E, Paris O, Ambrosino C, Facchiano A, Baumann M, Nyman TA, Weisz A. Identification of proteins associated with ligand-activated estrogen receptor α in human breast cancer cell nuclei by tandem affinity purification and nano LC-MS/MS. Proteomics 2010; 11:172-9. [PMID: 21182205 DOI: 10.1002/pmic.201000217] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Revised: 08/03/2010] [Accepted: 10/04/2010] [Indexed: 01/14/2023]
Abstract
Estrogen receptor α (ER-α) is a key mediator of estrogen actions in breast cancer (BC) cells. Understanding the effects of ligand-activated ER-α in target cells requires identification of the molecular partners acting in concert with this nuclear receptor to transduce the hormonal signal. We applied tandem affinity purification (TAP), glycerol gradient centrifugation and MS analysis to isolate and identify proteins interacting with ligand-activated ER-α in MCF-7 cell nuclei. This led to the identification of 264 ER-associated proteins, whose functions highlight the hinge role of ER-α in the coordination of multiple hormone-regulated nuclear processes in BC cells.
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Affiliation(s)
- Roberta Tarallo
- Department of General Pathology, Second University of Naples, Napoli, Italy
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37
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Nassa G, Tarallo R, Ambrosino C, Bamundo A, Ferraro L, Paris O, Ravo M, Guzzi PH, Cannataro M, Baumann M, Nyman TA, Nola E, Weisz A. A large set of estrogen receptor β-interacting proteins identified by tandem affinity purification in hormone-responsive human breast cancer cell nuclei. Proteomics 2010; 11:159-65. [DOI: 10.1002/pmic.201000344] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 08/04/2010] [Accepted: 09/27/2010] [Indexed: 12/17/2022]
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38
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Ambrosino C, Tarallo R, Bamundo A, Cuomo D, Franci G, Nassa G, Paris O, Ravo M, Giovane A, Zambrano N, Lepikhova T, Jänne OA, Baumann M, Nyman TA, Cicatiello L, Weisz A. Identification of a hormone-regulated dynamic nuclear actin network associated with estrogen receptor alpha in human breast cancer cell nuclei. Mol Cell Proteomics 2010; 9:1352-67. [PMID: 20308691 PMCID: PMC2877992 DOI: 10.1074/mcp.m900519-mcp200] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Revised: 02/22/2010] [Indexed: 11/06/2022] Open
Abstract
Estrogen receptor alpha (ERalpha) is a modular protein of the steroid/nuclear receptor family of transcriptional regulators that upon binding to the hormone undergoes structural changes, resulting in its nuclear translocation and docking to specific chromatin sites. In the nucleus, ERalpha assembles in multiprotein complexes that act as final effectors of estrogen signaling to the genome through chromatin remodeling and epigenetic modifications, leading to dynamic and coordinated regulation of hormone-responsive genes. Identification of the molecular partners of ERalpha and understanding their combinatory interactions within functional complexes is a prerequisite to define the molecular basis of estrogen control of cell functions. To this end, affinity purification was applied to map and characterize the ERalpha interactome in hormone-responsive human breast cancer cell nuclei. MCF-7 cell clones expressing human ERalpha fused to a tandem affinity purification tag were generated and used to purify native nuclear ER-containing complexes by IgG-Sepharose affinity chromatography and glycerol gradient centrifugation. Purified complexes were analyzed by two-dimensional DIGE and mass spectrometry, leading to the identification of a ligand-dependent multiprotein complex comprising beta-actin, myosins, and several proteins involved in actin filament organization and dynamics and/or known to participate in actin-mediated regulation of gene transcription, chromatin dynamics, and ribosome biogenesis. Time course analyses indicated that complexes containing ERalpha and actin are assembled in the nucleus early after receptor activation by ligands, and gene knockdown experiments showed that gelsolin and the nuclear isoform of myosin 1c are key determinants for assembly and/or stability of these complexes. Based on these results, we propose that the actin network plays a role in nuclear ERalpha actions in breast cancer cells, including coordinated regulation of target gene activity, spatial and functional reorganization of chromatin, and ribosome biogenesis.
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Affiliation(s)
- Concetta Ambrosino
- From the Departments of General Pathology and
- Department of Biological and Environmental Sciences, University of Sannio, 82100 Benevento, Italy
| | | | | | | | | | | | - Ornella Paris
- From the Departments of General Pathology and
- Associazione Italiana per la Ricerca sul Cancro (AIRC) Naples Oncogenomics Center, 80145 Naples, Italy
| | - Maria Ravo
- From the Departments of General Pathology and
| | - Alfonso Giovane
- Biochemistry and Biophysics “F. Cedrangolo,” Second University of Naples, 80138 Naples, Italy
| | - Nicola Zambrano
- CEINGE Biotecnologie Avanzate and Department of Biochemistry and Medical Biotechnologies, University of Naples Federico II, 80145 Naples, Italy
| | | | | | - Marc Baumann
- Protein Chemistry Unit, Biomedicum Helsinki, University of Helsinki, 00290 Helsinki, Finland
| | - Tuula A. Nyman
- Protein Chemistry Research Group, Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland, and
| | - Luigi Cicatiello
- From the Departments of General Pathology and
- Associazione Italiana per la Ricerca sul Cancro (AIRC) Naples Oncogenomics Center, 80145 Naples, Italy
| | - Alessandro Weisz
- From the Departments of General Pathology and
- Associazione Italiana per la Ricerca sul Cancro (AIRC) Naples Oncogenomics Center, 80145 Naples, Italy
- Molecular Medicine Laboratory, Faculty of Medicine and Surgery, University of Salerno, 84081 Baronissi, Italy
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Sha Z, Brill LM, Cabrera R, Kleifeld O, Scheliga JS, Glickman MH, Chang EC, Wolf DA. The eIF3 interactome reveals the translasome, a supercomplex linking protein synthesis and degradation machineries. Mol Cell 2009; 36:141-52. [PMID: 19818717 PMCID: PMC2789680 DOI: 10.1016/j.molcel.2009.09.026] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Revised: 06/23/2009] [Accepted: 09/11/2009] [Indexed: 01/18/2023]
Abstract
eIF3 promotes translation initiation, but relatively little is known about its full range of activities in the cell. Here, we employed affinity purification and highly sensitive LC-MS/MS to decipher the fission yeast eIF3 interactome, which was found to contain 230 proteins. eIF3 assembles into a large supercomplex, the translasome, which contains elongation factors, tRNA synthetases, 40S and 60S ribosomal proteins, chaperones, and the proteasome. eIF3 also associates with ribosome biogenesis factors and the importins-beta Kap123p and Sal3p. Our genetic data indicated that the binding to both importins-beta is essential for cell growth, and photobleaching experiments revealed a critical role for Sal3p in the nuclear import of one of the translasome constituents, the proteasome. Our data reveal the breadth of the eIF3 interactome and suggest that factors involved in translation initiation, ribosome biogenesis, translation elongation, quality control, and transport are physically linked to facilitate efficient protein synthesis.
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Affiliation(s)
- Zhe Sha
- 1 Baylor Plaza, Molecular and Cellular Biology Department, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030
| | - Laurence M. Brill
- Burnham Institute for Medical Research, Signal Transduction Program, NCI Cancer Center Proteomics Facility, 10901 North Torrey Pines Road, La Jolla, CA 92037
| | - Rodrigo Cabrera
- 1 Baylor Plaza, Molecular and Cellular Biology Department, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030
| | - Oded Kleifeld
- Department of Biology, Technion - Israel Institute of Technology, 32000 Haifa Israel
| | - Judith S. Scheliga
- Burnham Institute for Medical Research, Signal Transduction Program, NCI Cancer Center Proteomics Facility, 10901 North Torrey Pines Road, La Jolla, CA 92037
| | - Michael H. Glickman
- Department of Biology, Technion - Israel Institute of Technology, 32000 Haifa Israel
| | - Eric C. Chang
- 1 Baylor Plaza, Molecular and Cellular Biology Department, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030
| | - Dieter A. Wolf
- Burnham Institute for Medical Research, Signal Transduction Program, NCI Cancer Center Proteomics Facility, 10901 North Torrey Pines Road, La Jolla, CA 92037
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Abstract
Nonsense-mediated mRNA decay (NMD) is a translation-coupled mechanism that eliminates mRNAs containing premature translation-termination codons (PTCs). In mammalian cells, NMD is also linked to pre-mRNA splicing, as in many instances strong mRNA reduction occurs only when the PTC is located upstream of an intron. It is proposed that in these systems, the exon junction complex (EJC) mediates the link between splicing and NMD. Recent studies have questioned the role of splicing and the EJC in initiating NMD. Instead, they put forward a general and evolutionarily conserved mechanism in which the main regulator of NMD is the distance between a PTC and the poly(A) tail of an mRNA. Here we discuss the limitations of the new NMD model and the EJC concept; we argue that neither satisfactorily accounts for all of the available data and offer a new model to test in future studies.
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Affiliation(s)
- Saverio Brogna
- University of Birmingham, School of Biosciences, Edgbaston, Birmingham B15 2TT, UK.
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41
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Bhalla AD, Gudikote JP, Wang J, Chan WK, Chang YF, Olivas OR, Wilkinson MF. Nonsense codons trigger an RNA partitioning shift. J Biol Chem 2009; 284:4062-72. [PMID: 19091751 PMCID: PMC2640978 DOI: 10.1074/jbc.m805193200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2008] [Revised: 11/24/2008] [Indexed: 11/06/2022] Open
Abstract
T-cell receptor-beta (TCRbeta) genes naturally acquire premature termination codons (PTCs) as a result of programmed gene rearrangements. PTC-bearing TCRbeta transcripts are dramatically down-regulated to protect T-cells from the deleterious effects of the truncated proteins that would otherwise be produced. Here we provide evidence that two responses collaborate to elicit this dramatic down-regulation. One is rapid mRNA decay triggered by the nonsense-mediated decay (NMD) RNA surveillance pathway. We demonstrate that this occurs in highly purified nuclei lacking detectable levels of three different cytoplasmic markers, but containing an outer nuclear membrane marker, suggesting that decay occurs either in the nucleoplasm or at the outer nuclear membrane. The second response is a dramatic partitioning shift in the nuclear fraction-to-cytoplasmic fraction mRNA ratio that results in few TCRbeta transcripts escaping to the cytoplasmic fraction of cells. Analysis of TCRbeta mRNA kinetics after either transcriptional repression or induction suggested that this nonsense codon-induced partitioning shift (NIPS) response is not the result of cytoplasmic NMD but instead reflects retention of PTC(+) TCRbeta mRNA in the nuclear fraction of cells. We identified TCRbeta sequences crucial for NIPS but found that NIPS is not exclusively a property of TCRbeta transcripts, and we identified non-TCRbeta sequences that elicit NIPS. RNA interference experiments indicated that NIPS depends on the NMD factors UPF1 and eIF4AIII but not the NMD factor UPF3B. We propose that NIPS collaborates with NMD to retain and degrade a subset of PTC(+) transcripts at the outer nuclear membrane and/or within the nucleoplasm.
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MESH Headings
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- Codon, Nonsense/genetics
- Codon, Nonsense/metabolism
- DEAD-box RNA Helicases/genetics
- DEAD-box RNA Helicases/metabolism
- Down-Regulation/physiology
- Eukaryotic Initiation Factor-4A
- Gene Rearrangement, beta-Chain T-Cell Antigen Receptor/physiology
- HeLa Cells
- Humans
- Kinetics
- Pol1 Transcription Initiation Complex Proteins/genetics
- Pol1 Transcription Initiation Complex Proteins/metabolism
- RNA Interference
- RNA Stability/physiology
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Receptors, Antigen, T-Cell, alpha-beta/biosynthesis
- Receptors, Antigen, T-Cell, alpha-beta/genetics
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Affiliation(s)
- Angela D Bhalla
- Department of Biochemistry and Molecular Biology, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030-4009, USA
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42
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Abstract
Translation and mRNA decay are coupled processes; the link is most obvious in the case of NMD (nonsense-mediated mRNA decay). NMD is a mechanism that drastically reduces the level of mRNA harbouring PTCs (premature translation termination codons). The defining event in NMD is premature translation termination and the key question is: what distinguishes premature from normal translation termination? Surprisingly, in mammalian cells, PTC recognition is linked to pre-mRNA splicing. Here, we review the current understanding in view of recent developments.
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Abstract
Most eukaryotic genes are interrupted by non-coding introns that must be accurately removed from pre-messenger RNAs to produce translatable mRNAs. Splicing is guided locally by short conserved sequences, but genes typically contain many potential splice sites, and the mechanisms specifying the correct sites remain poorly understood. In most organisms, short introns recognized by the intron definition mechanism cannot be efficiently predicted solely on the basis of sequence motifs. In multicellular eukaryotes, long introns are recognized through exon definition and most genes produce multiple mRNA variants through alternative splicing. The nonsense-mediated mRNA decay (NMD) pathway may further shape the observed sets of variants by selectively degrading those containing premature termination codons, which are frequently produced in mammals. Here we show that the tiny introns of the ciliate Paramecium tetraurelia are under strong selective pressure to cause premature termination of mRNA translation in the event of intron retention, and that the same bias is observed among the short introns of plants, fungi and animals. By knocking down the two P. tetraurelia genes encoding UPF1, a protein that is crucial in NMD, we show that the intrinsic efficiency of splicing varies widely among introns and that NMD activity can significantly reduce the fraction of unspliced mRNAs. The results suggest that, independently of alternative splicing, species with large intron numbers universally rely on NMD to compensate for suboptimal splicing efficiency and accuracy.
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Cammas A, Pileur F, Bonnal S, Lewis SM, Lévêque N, Holcik M, Vagner S. Cytoplasmic relocalization of heterogeneous nuclear ribonucleoprotein A1 controls translation initiation of specific mRNAs. Mol Biol Cell 2007; 18:5048-59. [PMID: 17898077 PMCID: PMC2096577 DOI: 10.1091/mbc.e07-06-0603] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2007] [Revised: 09/07/2007] [Accepted: 09/14/2007] [Indexed: 01/30/2023] Open
Abstract
Heterogeneous nuclear ribonucleoprotein (hnRNP) A1 is a nucleocytoplasmic shuttling protein that regulates gene expression through its action on mRNA metabolism and translation. The cytoplasmic redistribution of hnRNP A1 is a regulated process during viral infection and cellular stress. Here, we show that hnRNP A1 is an internal ribosome entry site (IRES) trans-acting factor that binds specifically to the 5' untranslated region of both the human rhinovirus-2 and the human apoptotic peptidase activating factor 1 (apaf-1) mRNAs, thereby regulating their translation. Furthermore, the cytoplasmic redistribution of hnRNP A1 after rhinovirus infection leads to enhanced rhinovirus IRES-mediated translation, whereas the cytoplasmic relocalization of hnRNP A1 after UVC irradiation limits the UVC-triggered translational activation of the apaf-1 IRES. Therefore, this study provides a direct demonstration that IRESs behave as translational enhancer elements regulated by specific trans-acting mRNA binding proteins in given physiological conditions. Our data highlight a new way to regulate protein synthesis in eukaryotes through the subcellular relocalization of a nuclear mRNA-binding protein.
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Affiliation(s)
- Anne Cammas
- *Institut National de la Santé et de la Recherche Médicale U563, Toulouse, F-31000, France
- Institut Claudius Regaud, Toulouse, F-31052, France
- Université Toulouse III Paul Sabatier, Toulouse, F-31000, France
| | - Frédéric Pileur
- *Institut National de la Santé et de la Recherche Médicale U563, Toulouse, F-31000, France
- Institut Claudius Regaud, Toulouse, F-31052, France
- Université Toulouse III Paul Sabatier, Toulouse, F-31000, France
| | - Sophie Bonnal
- *Institut National de la Santé et de la Recherche Médicale U563, Toulouse, F-31000, France
- Institut Claudius Regaud, Toulouse, F-31052, France
- Université Toulouse III Paul Sabatier, Toulouse, F-31000, France
| | - Stephen M. Lewis
- Apoptosis Research Centre, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, K1H 8L1, Canada; and
| | - Nicolas Lévêque
- Laboratoire de Virologie et Pathologie Humaine, Centre National de la Recherche Scientifique FRE 3011, Université Claude Bernard Lyon 1, Faculté de Médecine RTH Laënnec, F-69372 Lyon, France
| | - Martin Holcik
- Apoptosis Research Centre, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, K1H 8L1, Canada; and
| | - Stéphan Vagner
- *Institut National de la Santé et de la Recherche Médicale U563, Toulouse, F-31000, France
- Institut Claudius Regaud, Toulouse, F-31052, France
- Université Toulouse III Paul Sabatier, Toulouse, F-31000, France
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45
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Singh G, Jakob S, Kleedehn MG, Lykke-Andersen J. Communication with the exon-junction complex and activation of nonsense-mediated decay by human Upf proteins occur in the cytoplasm. Mol Cell 2007; 27:780-92. [PMID: 17803942 DOI: 10.1016/j.molcel.2007.06.030] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Revised: 05/16/2007] [Accepted: 06/21/2007] [Indexed: 10/22/2022]
Abstract
The nonsense-mediated mRNA decay (NMD) pathway rids eukaryotic cells of mRNAs with premature termination codons. There is contradictory evidence as to whether mammalian NMD is a nuclear or a cytoplasmic process. Here, we show evidence that NMD in human cells occurs primarily, if not entirely, in the cytoplasm. Polypeptides designed to inhibit interactions between NMD factors specifically impede NMD when exogenously expressed in the cytoplasm. However, restricting the polypeptides to the nucleus strongly impairs their NMD-inhibitory function, even for those intended to inhibit interactions between the exon-junction complex (EJC) and hUpf3 proteins, which localize primarily in the nucleus. NMD substrates classified based on cell fractionation assays as "nucleus associated" or "cytoplasmic" are all inhibited in the same manner. Furthermore, retention of the NMD factor hUpf1 in the nucleus strongly impairs NMD. These observations suggest that the hUpf complex communicates with the EJC and triggers NMD in the cytoplasm.
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Affiliation(s)
- Guramrit Singh
- Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
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46
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Chang YF, Chan WK, Imam JS, Wilkinson MF. Alternatively Spliced T-cell Receptor Transcripts Are Up-regulated in Response to Disruption of Either Splicing Elements or Reading Frame. J Biol Chem 2007; 282:29738-47. [PMID: 17693403 DOI: 10.1074/jbc.m704372200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Nonsense mutations create premature termination codons (PTCs), leading to the generation of truncated proteins, some of which have deleterious gain-of-function or dominant-negative activity. Protecting cells from such aberrant proteins is non-sense-mediated decay (NMD), an RNA surveillance pathway that degrades transcripts harboring PTCs. A second response to nonsense mutations is the up-regulation of alternatively spliced transcripts that skip the PTC. This nonsense-associated altered splicing (NAS) response has the potential to rescue protein function, but the mechanism by which it is triggered has been controversial. Some studies suggest that, like NMD, NAS is triggered as a result of nonsense mutations disrupting reading frame, whereas other studies suggest that NAS is triggered when nonsense mutations disrupt exonic splicing enhancers (ESEs). Using T-cell receptor-beta (TCRbeta), which naturally acquires PTCs at high frequency, we provide evidence that both mechanisms act on a single type of mRNA. Mutations that disrupt consensus ESE sites up-regulated an alternatively spliced TCRbeta transcript that skipped the mutations independently of reading frame disruption and the NMD factor UPF1. In contrast, reading frame-disrupting mutations that did not disrupt consensus ESE sites elicited UPF1-dependent up-regulation of the alternatively spliced TCRbeta transcript. Restoration of reading frame prevented this up-regulation. Our results suggest that the response of an mRNA to a nonsense mutation depends on its context.
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Affiliation(s)
- Yao-Fu Chang
- Department of Biochemistry and Molecular Biology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, USA
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47
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Dynamic Chromatin Loops and the Regulation of Gene Expression. NUCLEAR DYNAMICS 2007. [PMCID: PMC7120644 DOI: 10.1007/978-4-431-30130-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Although we have a draft sequence of the human genome, little is known about how the chromatin fiber is packed in three-dimensional (3D) space, or how packing affects function (Jackson 2003). We know packing plays a major role; the rate of transcription of a typical gene can vary over eight orders of magnitude (Ivarie et al. 1983), but deleting local elements like promoters and enhancers reduces expression by less than 5000-fold in transient transfection assays where the 3D “context” is missing. Common sense suggests the fiber cannot be packed randomly, but elucidating what any underlying order might be has proved difficult. First, the foldings of the chromatin fiber have dimensions below the resolution (≈200 nm) of the light microscope (LM) and so can only be seen by electron microscopy (EM), but then the fixation required can distort structure. Second, DNA is so long and packed so tightly it breaks and/or aggregates easily on isolation. Third, chromatin is poised in a metastable state so small charge alterations trigger changes in structure and function, and replacing the natural environment with our buffers often promotes aggregation.
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48
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Abstract
The C-terminal repeat domain (CTD), an unusual extension appended to the C terminus of the largest subunit of RNA polymerase II, serves as a flexible binding scaffold for numerous nuclear factors; which factors bind is determined by the phosphorylation patterns on the CTD repeats. Changes in phosphorylation patterns, as polymerase transcribes a gene, are thought to orchestrate the association of different sets of factors with the transcriptase and strongly influence functional organization of the nucleus. In this review we appraise what is known, and what is not known, about patterns of phosphorylation on the CTD of RNA polymerases II at the beginning, the middle, and the end of genes; the proposal that doubly phosphorylated repeats are present on elongating polymerase is explored. We discuss briefly proteins known to associate with the phosphorylated CTD at the beginning and ends of genes; we explore in more detail proteins that are recruited to the body of genes, the diversity of their functions, and the potential consequences of tethering these functions to elongating RNA polymerase II. We also discuss accumulating structural information on phosphoCTD-binding proteins and how it illustrates the variety of binding domains and interaction modes, emphasizing the structural flexibility of the CTD. We end with a number of open questions that highlight the extent of what remains to be learned about the phosphorylation and functions of the CTD.
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Affiliation(s)
- Hemali P Phatnani
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
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49
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Ni JQ, Liu LP, Hess D, Rietdorf J, Sun FL. Drosophila ribosomal proteins are associated with linker histone H1 and suppress gene transcription. Genes Dev 2006; 20:1959-73. [PMID: 16816001 PMCID: PMC1522087 DOI: 10.1101/gad.390106] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2005] [Accepted: 05/08/2006] [Indexed: 11/24/2022]
Abstract
The dynamics and function of ribosomal proteins in the cell nucleus remain enigmatic. Here we provide evidence that specific components of Drosophila melanogaster ribosomes copurify with linker histone H1. Using various experimental approaches, we demonstrate that this association of nuclear ribosomal proteins with histone H1 is specific, and that colocalization occurs on condensed chromatin in vivo. Chromatin immunoprecipitation analysis confirmed that specific ribosomal proteins are associated with chromatin in a histone H1-dependent manner. Overexpression of either histone H1 or ribosomal protein L22 in Drosophila cells resulted in global suppression of the same set of genes, while depletion of H1 and L22 caused up-regulation of tested genes, suggesting that H1 and ribosomal proteins are essential for transcriptional gene repression. Overall, this study provides evidence for a previously undefined link between ribosomal proteins and chromatin, and suggests a role for this association in transcriptional regulation in higher eukaryotes.
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Affiliation(s)
- Jian-Quan Ni
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
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50
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Couté Y, Burgess JA, Diaz JJ, Chichester C, Lisacek F, Greco A, Sanchez JC. Deciphering the human nucleolar proteome. MASS SPECTROMETRY REVIEWS 2006; 25:215-34. [PMID: 16211575 DOI: 10.1002/mas.20067] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Nucleoli are plurifunctional nuclear domains involved in the regulation of several major cellular processes such as ribosome biogenesis, the biogenesis of non-ribosomal ribonucleoprotein complexes, cell cycle, and cellular aging. Until recently, the protein content of nucleoli was poorly described. Several proteomic analyses have been undertaken to discover the molecular bases of the biological roles fulfilled by nucleoli. These studies have led to the identification of more than 700 proteins. Extensive bibliographic and bioinformatic analyses allowed the classification of the identified proteins into functional groups and suggested potential functions of 150 human proteins previously uncharacterized. The combination of improvements in mass spectrometry technologies, the characterization of protein complexes, and data mining will assist in furthering our understanding of the role of nucleoli in different physiological and pathological cell states.
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Affiliation(s)
- Yohann Couté
- Biomedical Proteomics Research Group, Département de Biologie Structurale et Bioinformatique, Centre Médical Universitaire, 1 Rue Michel Servet, 1211 Geneva 14, Switzerland.
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