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Kwasniak-Owczarek M, Janska H. Experimental approaches to studying translation in plant semi-autonomous organelles. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5175-5187. [PMID: 38592734 PMCID: PMC11389837 DOI: 10.1093/jxb/erae151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/08/2024] [Indexed: 04/10/2024]
Abstract
Plant mitochondria and chloroplasts are semi-autonomous organelles originated from free-living bacteria that have retained reduced genomes during evolution. As a consequence, relatively few of the mitochondrial and chloroplast proteins are encoded in the organellar genomes and synthesized by the organellar ribosomes. Since both organellar genomes encode mainly components of the energy transduction systems, oxidative phosphorylation in mitochondria and photosynthetic apparatus in chloroplasts, understanding organellar translation is critical for a thorough comprehension of key aspects of mitochondrial and chloroplast activity affecting plant growth and development. Recent studies have clearly shown that translation is a key regulatory node in the expression of plant organellar genes, underscoring the need for an adequate methodology to study this unique stage of gene expression. The organellar translatome can be analysed by studying newly synthesized proteins or the mRNA pool recruited to the organellar ribosomes. In this review, we present experimental approaches used for studying translation in plant bioenergetic organelles. Their benefits and limitations, as well as the critical steps, are discussed. Additionally, we briefly mention several recently developed strategies to study organellar translation that have not yet been applied to plants.
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Affiliation(s)
- Malgorzata Kwasniak-Owczarek
- Department of Cellular Molecular Biology, Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie 14A, Wroclaw, 50-383, Poland
| | - Hanna Janska
- Department of Cellular Molecular Biology, Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie 14A, Wroclaw, 50-383, Poland
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2
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Sun X, Lin R, Lu X, Wu Z, Qi X, Jiang T, Jiang J, Mu P, Chen Q, Wen J, Deng Y. UPF3B modulates endoplasmic reticulum stress through interaction with inositol-requiring enzyme-1α. Cell Death Dis 2024; 15:587. [PMID: 39138189 PMCID: PMC11322666 DOI: 10.1038/s41419-024-06973-3] [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: 11/14/2023] [Revised: 07/29/2024] [Accepted: 08/05/2024] [Indexed: 08/15/2024]
Abstract
The unfolded protein response (UPR) is a conserved and adaptive intracellular pathway that relieves the endoplasmic reticulum (ER) stress by activating ER transmembrane stress sensors. As a consequence of ER stress, the inhibition of nonsense-mediated mRNA decay (NMD) is due to an increase in the phosphorylation of eIF2α, which has the effect of inhibiting translation. However, the role of NMD in maintaining ER homeostasis remains unclear. In this study, we found that the three NMD factors, up-frameshift (UPF)1, UPF2, or UPF3B, were required to negate the UPR. Among these three NMD factors, only UPF3B interacted with inositol-requiring enzyme-1α (IRE1α). This interaction inhibited the kinase activity of IRE1α, abolished autophosphorylation, and reduced IRE1α clustering for ER stress. BiP and UPF3B jointly control the activation of IRE1α on both sides of the ER membrane. Under stress conditions, the phosphorylation of UPF3B was increased and the phosphorylated sites were identified. Both the UPF3BY160D genetic mutation and phosphorylation at Thr169 of UPF3B abolished its interaction with IRE1α and UPF2, respectively, leading to activation of ER stress and NMD dysfunction. Our study reveals a key physiological role for UPF3B in the reciprocal regulatory relationship between NMD and ER stress.
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Affiliation(s)
- XingSheng Sun
- State Key Laboratory of Swine and Poultry Breeding Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong provincial key laboratory for the development biology and environmental adaptation of agricultural organisms, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Ruqin Lin
- State Key Laboratory of Swine and Poultry Breeding Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong provincial key laboratory for the development biology and environmental adaptation of agricultural organisms, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Xinxia Lu
- State Key Laboratory of Swine and Poultry Breeding Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong provincial key laboratory for the development biology and environmental adaptation of agricultural organisms, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Zhikai Wu
- State Key Laboratory of Swine and Poultry Breeding Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong provincial key laboratory for the development biology and environmental adaptation of agricultural organisms, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Xueying Qi
- State Key Laboratory of Swine and Poultry Breeding Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong provincial key laboratory for the development biology and environmental adaptation of agricultural organisms, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Tianqing Jiang
- State Key Laboratory of Swine and Poultry Breeding Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong provincial key laboratory for the development biology and environmental adaptation of agricultural organisms, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Jun Jiang
- State Key Laboratory of Swine and Poultry Breeding Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong provincial key laboratory for the development biology and environmental adaptation of agricultural organisms, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Peiqiang Mu
- State Key Laboratory of Swine and Poultry Breeding Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong provincial key laboratory for the development biology and environmental adaptation of agricultural organisms, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Qingmei Chen
- State Key Laboratory of Swine and Poultry Breeding Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong provincial key laboratory for the development biology and environmental adaptation of agricultural organisms, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Jikai Wen
- State Key Laboratory of Swine and Poultry Breeding Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
- Guangdong provincial key laboratory for the development biology and environmental adaptation of agricultural organisms, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
| | - Yiqun Deng
- State Key Laboratory of Swine and Poultry Breeding Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
- Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China.
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Fåhraeus R. Has translation in the nucleus found its purpose? Nat Rev Mol Cell Biol 2024; 25:1-2. [PMID: 37592061 DOI: 10.1038/s41580-023-00651-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Affiliation(s)
- Robin Fåhraeus
- Department of Medical Biosciences, Umeå University, Umeå, Sweden.
- RECAMO, Masaryk Memorial Cancer Institute, Brno, Czech Republic.
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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: 4] [Impact Index Per Article: 4.0] [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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Zuniga G, Levy S, Ramirez P, Mange JD, Gonzalez E, Gamez M, Frost B. Tau-induced deficits in nonsense-mediated mRNA decay contribute to neurodegeneration. Alzheimers Dement 2023; 19:405-420. [PMID: 35416419 PMCID: PMC9673995 DOI: 10.1002/alz.12653] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 01/26/2022] [Accepted: 02/17/2022] [Indexed: 12/12/2022]
Abstract
INTRODUCTION While brains of patients with Alzheimer's disease and related tauopathies have evidence of altered RNA processing, we lack a mechanistic understanding of how altered RNA processing arises in these disorders and if such changes are causally linked to neurodegeneration. METHODS Using Drosophila melanogaster models of tauopathy, we find that overall activity of nonsense-mediated mRNA decay (NMD), a key RNA quality-control mechanism, is reduced. Genetic manipulation of NMD machinery significantly modifies tau-induced neurotoxicity, suggesting that deficits in NMD are causally linked to neurodegeneration. Mechanistically, we find that deficits in NMD are a consequence of aberrant RNA export and RNA accumulation within nuclear envelope invaginations in tauopathy. We identify a pharmacological activator of NMD that suppresses neurodegeneration in tau transgenic Drosophila, indicating that tau-induced deficits in RNA quality control are druggable. DISCUSSION Our studies suggest that NMD activators should be explored for their potential therapeutic value to patients with tauopathies.
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Affiliation(s)
- Gabrielle Zuniga
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Simon Levy
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Paulino Ramirez
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Jasmine De Mange
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Elias Gonzalez
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Maria Gamez
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Bess Frost
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
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mtIF3 is locally translated in axons and regulates mitochondrial translation for axonal growth. BMC Biol 2022; 20:12. [PMID: 34996455 PMCID: PMC8742369 DOI: 10.1186/s12915-021-01215-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
Background The establishment and maintenance of functional neural connections relies on appropriate distribution and localization of mitochondria in neurites, as these organelles provide essential energy and metabolites. In particular, mitochondria are transported to axons and support local energy production to maintain energy-demanding neuronal processes including axon branching, growth, and regeneration. Additionally, local protein synthesis is required for structural and functional changes in axons, with nuclear-encoded mitochondrial mRNAs having been found localized in axons. However, it remains unclear whether these mRNAs are locally translated and whether the potential translated mitochondrial proteins are involved in the regulation of mitochondrial functions in axons. Here, we aim to further understand the purpose of such compartmentalization by focusing on the role of mitochondrial initiation factor 3 (mtIF3), whose nuclear-encoded transcripts have been shown to be present in axonal growth cones. Results We demonstrate that brain-derived neurotrophic factor (BDNF) induces local translation of mtIF3 mRNA in axonal growth cones. Subsequently, mtIF3 protein is translocated into axonal mitochondria and promotes mitochondrial translation as assessed by our newly developed bimolecular fluorescence complementation sensor for the assembly of mitochondrial ribosomes. We further show that BDNF-induced axonal growth requires mtIF3-dependent mitochondrial translation in distal axons. Conclusion We describe a previously unknown function of mitochondrial initiation factor 3 (mtIF3) in axonal protein synthesis and development. These findings provide insight into the way neurons adaptively control mitochondrial physiology and axonal development via local mtIF3 translation. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01215-w.
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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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Abrahams L, Savisaar R, Mordstein C, Young B, Kudla G, Hurst LD. Evidence in disease and non-disease contexts that nonsense mutations cause altered splicing via motif disruption. Nucleic Acids Res 2021; 49:9665-9685. [PMID: 34469537 PMCID: PMC8464065 DOI: 10.1093/nar/gkab750] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 08/17/2021] [Accepted: 08/19/2021] [Indexed: 12/21/2022] Open
Abstract
Transcripts containing premature termination codons (PTCs) can be subject to nonsense-associated alternative splicing (NAS). Two models have been evoked to explain this, scanning and splice motif disruption. The latter postulates that exonic cis motifs, such as exonic splice enhancers (ESEs), are disrupted by nonsense mutations. We employ genome-wide transcriptomic and k-mer enrichment methods to scrutinize this model. First, we show that ESEs are prone to disruptive nonsense mutations owing to their purine richness and paucity of TGA, TAA and TAG. The motif model correctly predicts that NAS rates should be low (we estimate 5–30%) and approximately in line with estimates for the rate at which random point mutations disrupt splicing (8–20%). Further, we find that, as expected, NAS-associated PTCs are predictable from nucleotide-based machine learning approaches to predict splice disruption and, at least for pathogenic variants, are enriched in ESEs. Finally, we find that both in and out of frame mutations to TAA, TGA or TAG are associated with exon skipping. While a higher relative frequency of such skip-inducing mutations in-frame than out of frame lends some credence to the scanning model, these results reinforce the importance of considering splice motif modulation to understand the etiology of PTC-associated disease.
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Affiliation(s)
- Liam Abrahams
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Rosina Savisaar
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK.,Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Christine Mordstein
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK.,MRC Human Genetics Unit, The University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK.,Aarhus University, Department of Molecular Biology and Genetics, C F Møllers Allé 3, 8000 Aarhus, Denmark
| | - Bethan Young
- MRC Human Genetics Unit, The University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Grzegorz Kudla
- MRC Human Genetics Unit, The University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
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Abstract
Biomolecular condensates concentrate molecules to facilitate basic biochemical processes, including transcription and DNA replication. While liquid-like condensates have been ascribed various functions, solid-like condensates are generally thought of as amorphous sites of protein storage. Here, we show that solid-like amyloid bodies coordinate local nuclear protein synthesis (LNPS) during stress. On stimulus, translationally active ribosomes accumulate along fiber-like assemblies that characterize amyloid bodies. Mass spectrometry analysis identified regulatory ribosomal proteins and translation factors that relocalize from the cytoplasm to amyloid bodies to sustain LNPS. These amyloidogenic compartments are enriched in newly transcribed messenger RNA by Heat Shock Factor 1 (HSF1). Depletion of stress-induced ribosomal intergenic spacer noncoding RNA (rIGSRNA) that constructs amyloid bodies prevents recruitment of the nuclear protein synthesis machinery, abolishes LNPS, and impairs the nuclear HSF1 response. We propose that amyloid bodies support local nuclear translation during stress and that solid-like condensates can facilitate complex biochemical reactions as their liquid counterparts can.
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10
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Lashkevich KA, Dmitriev SE. mRNA Targeting, Transport and Local Translation in Eukaryotic Cells: From the Classical View to a Diversity of New Concepts. Mol Biol 2021; 55:507-537. [PMID: 34092811 PMCID: PMC8164833 DOI: 10.1134/s0026893321030080] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 02/26/2021] [Accepted: 03/12/2021] [Indexed: 12/28/2022]
Abstract
Spatial organization of protein biosynthesis in the eukaryotic cell has been studied for more than fifty years, thus many facts have already been included in textbooks. According to the classical view, mRNA transcripts encoding secreted and transmembrane proteins are translated by ribosomes associated with endoplasmic reticulum membranes, while soluble cytoplasmic proteins are synthesized on free polysomes. However, in the last few years, new data has emerged, revealing selective translation of mRNA on mitochondria and plastids, in proximity to peroxisomes and endosomes, in various granules and at the cytoskeleton (actin network, vimentin intermediate filaments, microtubules and centrosomes). There are also long-standing debates about the possibility of protein synthesis in the nucleus. Localized translation can be determined by targeting signals in the synthesized protein, nucleotide sequences in the mRNA itself, or both. With RNA-binding proteins, many transcripts can be assembled into specific RNA condensates and form RNP particles, which may be transported by molecular motors to the sites of active translation, form granules and provoke liquid-liquid phase separation in the cytoplasm, both under normal conditions and during cell stress. The translation of some mRNAs occurs in specialized "translation factories," assemblysomes, transperons and other structures necessary for the correct folding of proteins, interaction with functional partners and formation of oligomeric complexes. Intracellular localization of mRNA has a significant impact on the efficiency of its translation and presumably determines its response to cellular stress. Compartmentalization of mRNAs and the translation machinery also plays an important role in viral infections. Many viruses provoke the formation of specific intracellular structures, virus factories, for the production of their proteins. Here we review the current concepts of the molecular mechanisms of transport, selective localization and local translation of cellular and viral mRNAs, their effects on protein targeting and topogenesis, and on the regulation of protein biosynthesis in different compartments of the eukaryotic cell. Special attention is paid to new systems biology approaches, providing new cues to the study of localized translation.
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Affiliation(s)
- Kseniya A Lashkevich
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119234 Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Moscow State University, 119234 Moscow, Russia
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119234 Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Moscow State University, 119234 Moscow, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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11
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The science of puromycin: From studies of ribosome function to applications in biotechnology. Comput Struct Biotechnol J 2020; 18:1074-1083. [PMID: 32435426 PMCID: PMC7229235 DOI: 10.1016/j.csbj.2020.04.014] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 04/19/2020] [Accepted: 04/19/2020] [Indexed: 11/20/2022] Open
Abstract
Puromycin is a naturally occurring aminonucleoside antibiotic that inhibits protein synthesis by ribosome-catalyzed incorporation into the C-terminus of elongating nascent chains, blocking further extension and resulting in premature termination of translation. It is most commonly known as a selection marker for cell lines genetically engineered to express a resistance transgene, but its additional uses as a probe for protein synthesis have proven invaluable across a wide variety of model systems, ranging from purified ribosomes and cell-free translation to intact cultured cells and whole animals. Puromycin is comprised of a nucleoside covalently bound to an amino acid, mimicking the 3′ end of aminoacylated tRNAs that participate in delivery of amino acids to elongating ribosomes. Both moieties can tolerate some chemical substitutions and modifications without significant loss of activity, generating a diverse toolbox of puromycin-based reagents with added functionality, such as biotin for affinity purification or fluorophores for fluorescent microscopy detection. These reagents, as well as anti-puromycin antibodies, have played a pivotal role in advancing our understanding of the regulation and dysregulation of protein synthesis in normal and pathological processes, including immune response and neurological function. This manuscript reviews the current state of puromycin-based research, including structure and mechanism of action, relevant derivatives, use in advanced methodologies and some of the major insights generated using such techniques both in the lab and the clinic.
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12
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Singh AK, Abdullahi A, Soller M, David A, Brogna S. Visualisation of ribosomes in Drosophila axons using Ribo-BiFC. Biol Open 2020; 8:bio047233. [PMID: 31822474 PMCID: PMC6955225 DOI: 10.1242/bio.047233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/02/2019] [Indexed: 11/20/2022] Open
Abstract
The distribution of assembled, and potentially translating, ribosomes within cells can be visualised in Drosophila by using Bimolecular Fluorescence Complementation (BiFC) to monitor the interaction between tagged pairs of 40S and 60S ribosomal proteins (RPs) that are close neighbours across inter-subunit junctions in the assembled 80S ribosome. Here we describe transgenes expressing two novel RP pairs tagged with Venus-based BiFC fragments that considerably increase the sensitivity of this technique we termed Ribo-BiFC. This improved method should provide a convenient way of monitoring the local distribution of ribosomes in most Drosophila cells and we suggest that it could be implemented in other organisms. We visualised 80S ribosomes in different neurons, particularly photoreceptors in the larva, pupa and adult brain. Assembled ribosomes are most abundant in the various neuronal cell bodies, but they are also present along the full length of axons. They are concentrated in growth cones of developing photoreceptors and are apparent at the terminals of mature larval photoreceptors targeting the larval optical neuropil. Surprisingly, there is relatively less puromycin incorporation in the distal portion of axons in the larval optic stalk, suggesting that some of the ribosomes that have initiated translation may not be engaged in elongation in growing axons.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Anand K Singh
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Akilu Abdullahi
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Matthias Soller
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Alexandre David
- Oncology Department, Institut de Génomique Fonctionnelle, 141 rue de la Cardonille, 34094 Montpellier cedex 5, France
| | - Saverio Brogna
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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13
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Díaz-López I, Toribio R, Berlanga JJ, Ventoso I. An mRNA-binding channel in the ES6S region of the translation 48S-PIC promotes RNA unwinding and scanning. eLife 2019; 8:48246. [PMID: 31789591 PMCID: PMC6887119 DOI: 10.7554/elife.48246] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 11/16/2019] [Indexed: 11/30/2022] Open
Abstract
Loading of mRNA onto the ribosomal 43S pre-initiation complex (PIC) and its subsequent scanning require the removal of the secondary structure of the by RNA helicases such as eIF4A. However, the topology and mechanics of the scanning complex bound to mRNA (48S-PIC) and the influence of its solvent-side composition on the scanning process are poorly known. Here, we found that the ES6S region of the 48S-PIC constitutes an extended binding channel for eIF4A-mediated unwinding of mRNA and scanning. Blocking ES6S inhibited the cap-dependent translation of mRNAs that have structured 5′ UTRs (including G-quadruplexes), many of which are involved in signal transduction and growth, but it did not affect IRES-driven translation. Genome-wide analysis of mRNA translation revealed a great diversity in ES6S-mediated scanning dependency. Our data suggest that mRNA threading into the ES6S region makes scanning by 48S PIC slower but more processive. Hence, we propose a topological and functional model of the scanning 48S-PIC.
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Affiliation(s)
- Irene Díaz-López
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - René Toribio
- Centro de Biotecnología y Genómica de Plantas, Madrid, Spain
| | - Juan José Berlanga
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Iván Ventoso
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain
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14
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Manganese-induced cellular disturbance in the baker's yeast, Saccharomyces cerevisiae with putative implications in neuronal dysfunction. Sci Rep 2019; 9:6563. [PMID: 31024033 PMCID: PMC6484083 DOI: 10.1038/s41598-019-42907-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 04/09/2019] [Indexed: 12/24/2022] Open
Abstract
Manganese (Mn) is an essential element, but in humans, chronic and/or acute exposure to this metal can lead to neurotoxicity and neurodegenerative disorders including Parkinsonism and Parkinson’s Disease by unclear mechanisms. To better understand the effects that exposure to Mn2+ exert on eukaryotic cell biology, we exposed a non-essential deletion library of the yeast Saccharomyces cerevisiae to a sub-inhibitory concentration of Mn2+ followed by targeted functional analyses of the positive hits. This screen produced a set of 43 sensitive deletion mutants that were enriched for genes associated with protein biosynthesis. Our follow-up investigations demonstrated that Mn reduced total rRNA levels in a dose-dependent manner and decreased expression of a β-galactosidase reporter gene. This was subsequently supported by analysis of ribosome profiles that suggested Mn-induced toxicity was associated with a reduction in formation of active ribosomes on the mRNAs. Altogether, these findings contribute to the current understanding of the mechanism of Mn-triggered cytotoxicity. Lastly, using the Comparative Toxicogenomic Database, we revealed that Mn shared certain similarities in toxicological mechanisms with neurodegenerative disorders including amyotrophic lateral sclerosis, Alzheimer’s, Parkinson’s and Huntington’s diseases.
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15
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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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16
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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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17
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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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18
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Abstract
Since the publication of the DRiP (defective ribosomal product) hypothesis in 1996, numerous studies have addressed the contribution of DRiPs to generating viral antigenic peptides for CD8+ T cell immunosurveillance. Here, we review studies characterizing the generation of antigenic peptides from influenza A virus encoded DRiPs, discuss the many remaining mysteries regarding the nature of their co-translational generation, and speculate on where the future might lead.
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19
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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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20
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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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21
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Choudhury SR, Singh AK, McLeod T, Blanchette M, Jang B, Badenhorst P, Kanhere A, Brogna S. Exon junction complex proteins bind nascent transcripts independently of pre-mRNA splicing in Drosophila melanogaster. eLife 2016; 5:e19881. [PMID: 27879206 PMCID: PMC5158136 DOI: 10.7554/elife.19881] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/21/2016] [Indexed: 12/16/2022] Open
Abstract
Although it is currently understood that the exon junction complex (EJC) is recruited on spliced mRNA by a specific interaction between its central protein, eIF4AIII, and splicing factor CWC22, we found that eIF4AIII and the other EJC core proteins Y14 and MAGO bind the nascent transcripts of not only intron-containing but also intronless genes on Drosophila polytene chromosomes. Additionally, Y14 ChIP-seq demonstrates that association with transcribed genes is also splicing-independent in Drosophila S2 cells. The association of the EJC proteins with nascent transcripts does not require CWC22 and that of Y14 and MAGO is independent of eIF4AIII. We also show that eIF4AIII associates with both polysomal and monosomal RNA in S2 cell extracts, whereas Y14 and MAGO fractionate separately. Cumulatively, our data indicate a global role of eIF4AIII in gene expression, which would be independent of Y14 and MAGO, splicing, and of the EJC, as currently understood.
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Affiliation(s)
| | - Anand K Singh
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Tina McLeod
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Marco Blanchette
- Stowers Institute for Medical Research, Kansas city, United States
| | - Boyun Jang
- Institute of Biomedical Research, University of Birmingham, Birmingham, United Kingdom
| | - Paul Badenhorst
- Institute of Biomedical Research, University of Birmingham, Birmingham, United Kingdom
| | - Aditi Kanhere
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Saverio Brogna
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
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22
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Ahmad M, Xue Y, Lee SK, Martindale JL, Shen W, Li W, Zou S, Ciaramella M, Debat H, Nadal M, Leng F, Zhang H, Wang Q, Siaw GEL, Niu H, Pommier Y, Gorospe M, Hsieh TS, Tse-Dinh YC, Xu D, Wang W. RNA topoisomerase is prevalent in all domains of life and associates with polyribosomes in animals. Nucleic Acids Res 2016; 44:6335-49. [PMID: 27257063 PMCID: PMC4994864 DOI: 10.1093/nar/gkw508] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/25/2016] [Indexed: 12/14/2022] Open
Abstract
DNA Topoisomerases are essential to resolve topological problems during DNA metabolism in all species. However, the prevalence and function of RNA topoisomerases remain uncertain. Here, we show that RNA topoisomerase activity is prevalent in Type IA topoisomerases from bacteria, archaea, and eukarya. Moreover, this activity always requires the conserved Type IA core domains and the same catalytic residue used in DNA topoisomerase reaction; however, it does not absolutely require the non-conserved carboxyl-terminal domain (CTD), which is necessary for relaxation reactions of supercoiled DNA. The RNA topoisomerase activity of human Top3β differs from that of Escherichia coli topoisomerase I in that the former but not the latter requires the CTD, indicating that topoisomerases have developed distinct mechanisms during evolution to catalyze RNA topoisomerase reactions. Notably, Top3β proteins from several animals associate with polyribosomes, which are units of mRNA translation, whereas the Top3 homologs from E. coli and yeast lack the association. The Top3β-polyribosome association requires TDRD3, which directly interacts with Top3β and is present in animals but not bacteria or yeast. We propose that RNA topoisomerases arose in the early RNA world, and that they are retained through all domains of DNA-based life, where they mediate mRNA translation as part of polyribosomes in animals.
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Affiliation(s)
- Muzammil Ahmad
- Genome Instability and Chromatin Remodeling Section, Lab of Genetics, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Yutong Xue
- Genome Instability and Chromatin Remodeling Section, Lab of Genetics, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Seung Kyu Lee
- Genome Instability and Chromatin Remodeling Section, Lab of Genetics, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Jennifer L Martindale
- RNA Regulation Section, Lab of Genetics, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Weiping Shen
- Genome Instability and Chromatin Remodeling Section, Lab of Genetics, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Wen Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, PeKing University, Beijing 1000871, China
| | - Sige Zou
- Translational Gerontology Branch, National Institute on Aging, National Institute of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Maria Ciaramella
- Institute of Biosciences and Bioresources, National Research Council of Italy, Naples 80131, Italy
| | - Hélène Debat
- Institut Jacques Monod, CNRS-Université Paris Diderot-UMR7592, 15 rue Hélène Brion, 75205 Paris Cedex, France
| | - Marc Nadal
- Institut Jacques Monod, CNRS-Université Paris Diderot-UMR7592, 15 rue Hélène Brion, 75205 Paris Cedex, France
| | - Fenfei Leng
- Department of Chemistry & Biochemistry, Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Hongliang Zhang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Quan Wang
- Molecular and Cellular Biochemistry Department, Indiana University, 212 South Hawthorne Drive, Bloomington, IN 47405, USA
| | - Grace Ee-Lu Siaw
- Institute of Cellular Organistic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Hengyao Niu
- Molecular and Cellular Biochemistry Department, Indiana University, 212 South Hawthorne Drive, Bloomington, IN 47405, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Myriam Gorospe
- RNA Regulation Section, Lab of Genetics, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Tao-Shih Hsieh
- Institute of Cellular Organistic Biology, Academia Sinica, Taipei 11529, Taiwan Department of Biochemistry, Duke University Medical Center, Durham, NC 73532, USA
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry & Biochemistry, Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Dongyi Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, PeKing University, Beijing 1000871, China
| | - Weidong Wang
- Genome Instability and Chromatin Remodeling Section, Lab of Genetics, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
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23
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Brogna S, McLeod T, Petric M. The Meaning of NMD: Translate or Perish. Trends Genet 2016; 32:395-407. [PMID: 27185236 DOI: 10.1016/j.tig.2016.04.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 04/02/2016] [Accepted: 04/25/2016] [Indexed: 02/08/2023]
Abstract
Premature translation termination leads to a reduced mRNA level in all types of organisms. In eukaryotes, the phenomenon is known as nonsense-mediated mRNA decay (NMD). This is commonly regarded as the output of a specific surveillance and destruction mechanism that is activated by the presence of a premature translation termination codon (PTC) in an atypical sequence context. Despite two decades of research, it is still unclear how NMD discriminates between PTCs and normal stop codons. We suggest that cells do not possess any such mechanism and instead propose a new model in which this mRNA depletion is a consequence of the appearance of long tracts of mRNA that are unprotected by scanning ribosomes.
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Affiliation(s)
- Saverio Brogna
- University of Birmingham, School of Biosciences, Edgbaston, Birmingham, B15 2TT, UK.
| | - Tina McLeod
- University of Birmingham, School of Biosciences, Edgbaston, Birmingham, B15 2TT, UK
| | - Marija Petric
- University of Birmingham, School of Biosciences, Edgbaston, Birmingham, B15 2TT, UK
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24
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Waku T, Nakajima Y, Yokoyama W, Nomura N, Kako K, Kobayashi A, Shimizu T, Fukamizu A. NML-mediated rRNA base methylation links ribosomal subunit formation to cell proliferation in a p53-dependent manner. J Cell Sci 2016; 129:2382-93. [PMID: 27149924 DOI: 10.1242/jcs.183723] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 04/29/2016] [Indexed: 12/25/2022] Open
Abstract
Ribosomal RNAs (rRNAs) act as scaffolds and ribozymes in ribosomes, and these functions are modulated by post-transcriptional modifications. However, the biological role of base methylation, a well-conserved modification of rRNA, is poorly understood. Here, we demonstrate that a nucleolar factor, nucleomethylin (NML; also known as RRP8), is required for the N(1)-methyladenosine (m(1)A) modification in 28S rRNAs of human and mouse cells. NML also contributes to 60S ribosomal subunit formation. Intriguingly, NML depletion increases 60S ribosomal protein L11 (RPL11) levels in the ribosome-free fraction and protein levels of p53 through an RPL11-MDM2 complex, which activates the p53 pathway. Consequently, the growth of NML-depleted cells is suppressed in a p53-dependent manner. These observations reveal a new biological function of rRNA base methylation, which links ribosomal subunit formation to p53-dependent inhibition of cell proliferation in mammalian cells.
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Affiliation(s)
- Tsuyoshi Waku
- Graduate School of Pharmaceutical Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuka Nakajima
- Life Science Center, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Wataru Yokoyama
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Naoto Nomura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Koichiro Kako
- Life Science Center, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Akira Kobayashi
- Laboratory for Genetic Code, Graduate School of Life and Medical Sciences, Doshisha University, Kyotanabe, Kyoto 610-0394, Japan
| | - Toshiyuki Shimizu
- Graduate School of Pharmaceutical Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Akiyoshi Fukamizu
- Life Science Center, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
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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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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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Halstead JM, Lionnet T, Wilbertz JH, Wippich F, Ephrussi A, Singer RH, Chao JA. Translation. An RNA biosensor for imaging the first round of translation from single cells to living animals. Science 2015; 347:1367-671. [PMID: 25792328 DOI: 10.1126/science.aaa3380] [Citation(s) in RCA: 198] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Analysis of single molecules in living cells has provided quantitative insights into the kinetics of fundamental biological processes; however, the dynamics of messenger RNA (mRNA) translation have yet to be addressed. We have developed a fluorescence microscopy technique that reports on the first translation events of individual mRNA molecules. This allowed us to examine the spatiotemporal regulation of translation during normal growth and stress and during Drosophila oocyte development. We have shown that mRNAs are not translated in the nucleus but translate within minutes after export, that sequestration within P-bodies regulates translation, and that oskar mRNA is not translated until it reaches the posterior pole of the oocyte. This methodology provides a framework for studying initiation of protein synthesis on single mRNAs in living cells.
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Affiliation(s)
- James M Halstead
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Timothée Lionnet
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA. Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA. Transcription Imaging Consortium, Howard Hughes Medical Institute Janelia Farm Research Campus, Ashburn, VA 20147, USA
| | - Johannes H Wilbertz
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland. University of Basel, CH-4003 Basel, Switzerland
| | - Frank Wippich
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA. Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA. Transcription Imaging Consortium, Howard Hughes Medical Institute Janelia Farm Research Campus, Ashburn, VA 20147, USA.
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland. Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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28
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High capsid-genome correlation facilitates creation of AAV libraries for directed evolution. Mol Ther 2015; 23:675-82. [PMID: 25586687 DOI: 10.1038/mt.2015.3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 12/28/2014] [Indexed: 12/13/2022] Open
Abstract
Directed evolution of adeno-associated virus (AAV) through successive rounds of phenotypic selection is a powerful method to isolate variants with improved properties from large libraries of capsid mutants. Importantly, AAV libraries used for directed evolution are based on the "natural" AAV genome organization where the capsid proteins are encoded in cis from replicating genomes. This is necessary to allow the recovery of the capsid DNA after each step of phenotypic selection. For directed evolution to be used successfully, it is essential to minimize the random mixing of capsomers and the encapsidation of nonmatching viral genomes during the production of the viral libraries. Here, we demonstrate that multiple AAV capsid variants expressed from Rep/Cap containing viral genomes result in near-homogeneous capsids that display an unexpectedly high capsid-DNA correlation. Next-generation sequencing of AAV progeny generated by bulk transfection of a semi-random peptide library showed a strong counter-selection of capsid variants encoding premature stop codons, which further supports a strong capsid-genome identity correlation. Overall, our observations demonstrate that production of "natural" AAVs results in low capsid mosaicism and high capsid-genome correlation. These unique properties allow the production of highly diverse AAV libraries in a one-step procedure with a minimal loss in phenotype-genotype correlation.
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Argüello RJ, Rodriguez Rodrigues C, Gatti E, Pierre P. Protein synthesis regulation, a pillar of strength for innate immunity? Curr Opin Immunol 2014; 32:28-35. [PMID: 25553394 DOI: 10.1016/j.coi.2014.12.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 12/04/2014] [Accepted: 12/10/2014] [Indexed: 12/31/2022]
Abstract
Recognition of pathogen derived molecules by Pattern Recognition Receptors (PRR) induces the production of cytokines (i.e. type I interferons) that stimulate the surrounding cells to transcribe and translate hundreds of genes, in order to prevent further infection and organize the immune response. Here, we report on the rising matter that metabolism sensing and gene expression control at the level of mRNA translation, allow swift responses that mobilize host defenses and coordinate innate responses to infection.
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Affiliation(s)
- Rafael J Argüello
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université, U2M, 13288 Marseille, France; INSERM, U1104, 13288 Marseille, France; CNRS, UMR 7280, 13288 Marseille, France
| | - Christian Rodriguez Rodrigues
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université, U2M, 13288 Marseille, France; INSERM, U1104, 13288 Marseille, France; CNRS, UMR 7280, 13288 Marseille, France
| | - Evelina Gatti
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université, U2M, 13288 Marseille, France; INSERM, U1104, 13288 Marseille, France; CNRS, UMR 7280, 13288 Marseille, France; Institute for Research in Biomedicine - iBiMED and Aveiro Health Sciences Program, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Philippe Pierre
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université, U2M, 13288 Marseille, France; INSERM, U1104, 13288 Marseille, France; CNRS, UMR 7280, 13288 Marseille, France; Institute for Research in Biomedicine - iBiMED and Aveiro Health Sciences Program, University of Aveiro, 3810-193 Aveiro, Portugal.
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Maruyama Y, Miyazaki T, Ikeda K, Okumura T, Sato W, Horie-Inoue K, Okamoto K, Takeda S, Inoue S. Short hairpin RNA library-based functional screening identified ribosomal protein L31 that modulates prostate cancer cell growth via p53 pathway. PLoS One 2014; 9:e108743. [PMID: 25285958 PMCID: PMC4186824 DOI: 10.1371/journal.pone.0108743] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 08/25/2014] [Indexed: 11/22/2022] Open
Abstract
Androgen receptor is a primary transcription factor involved in the proliferation of prostate cancer cells. Thus, hormone therapy using antiandrogens, such as bicalutamide, is a first-line treatment for the disease. Although hormone therapy initially reduces the tumor burden, many patients eventually relapse, developing tumors with acquired endocrine resistance. Elucidation of the molecular mechanisms underlying endocrine resistance is therefore a fundamental issue for the understanding and development of alternative therapeutics for advanced prostate cancer. In the present study, we performed short hairpin RNA (shRNA)-mediated functional screening to identify genes involved in bicalutamide-mediated effects on LNCaP prostate cancer cells. Among such candidate genes selected by screening using volcano plot analysis, ribosomal protein L31 (RPL31) was found to be essential for cell proliferation and cell-cycle progression in bicalutamide-resistant LNCaP (BicR) cells, based on small interfering RNA (siRNA)-mediated knockdown experiments. Of note, RPL31 mRNA is more abundantly expressed in BicR cells than in parental LNCaP cells, and clinical data from ONCOMINE and The Cancer Genome Altas showed that RPL31 is overexpressed in prostate carcinomas compared with benign prostate tissues. Intriguingly, protein levels of the tumor suppressor p53 and its targets, p21 and MDM2, were increased in LNCaP and BicR cells treated with RPL31 siRNA. We observed decreased degradation of p53 protein after RPL31 knockdown. Moreover, the suppression of growth and cell cycle upon RPL31 knockdown was partially recovered with p53 siRNA treatment. These results suggest that RPL31 is involved in bicalutamide-resistant growth of prostate cancer cells. The shRNA-mediated functional screen in this study provides new insight into the molecular mechanisms and therapeutic targets of advanced prostate cancer.
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Affiliation(s)
- Yojiro Maruyama
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan
- Department of Obstetrics and Gynecology, Juntendo University School of Medicine, Tokyo, Japan
| | - Toshiaki Miyazaki
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan
| | - Kazuhiro Ikeda
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan
| | - Toshiyuki Okumura
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan
| | - Wataru Sato
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan
| | - Kuniko Horie-Inoue
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan
| | - Koji Okamoto
- Division of Cancer Differentiation, National Cancer Center Research Institute, Tokyo, Japan
| | - Satoru Takeda
- Department of Obstetrics and Gynecology, Juntendo University School of Medicine, Tokyo, Japan
| | - Satoshi Inoue
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan
- Departments of Geriatric Medicine and Anti-Aging Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- * E-mail:
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31
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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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Baboo S, Bhushan B, Jiang H, Grovenor CRM, Pierre P, Davis BG, Cook PR. Most human proteins made in both nucleus and cytoplasm turn over within minutes. PLoS One 2014; 9:e99346. [PMID: 24911415 PMCID: PMC4050049 DOI: 10.1371/journal.pone.0099346] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 05/13/2014] [Indexed: 12/25/2022] Open
Abstract
In bacteria, protein synthesis can be coupled to transcription, but in eukaryotes it is believed to occur solely in the cytoplasm. Using pulses as short as 5 s, we find that three analogues – L-azidohomoalanine, puromycin (detected after attaching fluors using ‘click’ chemistry or immuno-labeling), and amino acids tagged with ‘heavy’ 15N and 13C (detected using secondary ion mass spectrometry) – are incorporated into the nucleus and cytoplasm in a process sensitive to translational inhibitors. The nuclear incorporation represents a significant fraction of the total, and labels in both compartments have half-lives of less than a minute; results are consistent with most newly-made peptides being destroyed soon after they are made. As nascent RNA bearing a premature termination codon (detected by fluorescence in situ hybridization) is also eliminated by a mechanism sensitive to a translational inhibitor, the nuclear turnover of peptides is probably a by-product of proof-reading the RNA for stop codons (a process known as nonsense-mediated decay). We speculate that the apparently-wasteful turnover of this previously-hidden (‘dark-matter’) world of peptide is involved in regulating protein production.
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Affiliation(s)
- Sabyasachi Baboo
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Bhaskar Bhushan
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Haibo Jiang
- Department of Materials, University of Oxford, Oxford, United Kingdom
| | | | - Philippe Pierre
- Centre d′Immunologie de Marseille-Luminy, Aix-Marseille Université, Marseille, France
- Institut National de la Santé et de la Recherche Médicale, U1104, Marseille, France
- Centre National de la Recherche Scientifique, Unités Mixtes de Recherche 7280, Marseille, France
| | - Benjamin G. Davis
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Peter R. Cook
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
- * E-mail:
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Antón LC, Yewdell JW. Translating DRiPs: MHC class I immunosurveillance of pathogens and tumors. J Leukoc Biol 2014; 95:551-62. [PMID: 24532645 PMCID: PMC3958739 DOI: 10.1189/jlb.1113599] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 01/15/2014] [Accepted: 01/19/2014] [Indexed: 11/24/2022] Open
Abstract
MHC class I molecules display oligopeptides on the cell surface to enable T cell immunosurveillance of intracellular pathogens and tumors. Speed is of the essence in detecting viruses, which can complete a full replication cycle in just hours, whereas tumor detection is typically a finding-the-needle-in-the-haystack exercise. We review current evidence supporting a nonrandom, compartmentalized selection of peptidogenic substrates that focuses on rapidly degraded translation products as a main source of peptide precursors to optimize immunosurveillance of pathogens and tumors.
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Affiliation(s)
- Luis C Antón
- 1.NIAID, NIH, Bldg. 33, Bethesda, MD 20892, USA.
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