1
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Potrich C, Pedrotti A, Pederzolli C, Lunelli L. Functional surfaces for exosomes capturing and exosomal microRNAs analysis. Colloids Surf B Biointerfaces 2024; 233:113627. [PMID: 37948834 DOI: 10.1016/j.colsurfb.2023.113627] [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: 09/07/2023] [Revised: 10/19/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
Exosomes are small extracellular vesicles well-studied both as cell signaling elements and as source of highly informative biomarkers, in particular microRNAs. Standard techniques for exosome isolation are in general scarcely efficient and give low purity vesicles. New techniques combining microfluidics with suitable functionalized surfaces could overcome these disadvantages. Here, different functional surfaces aimed at exosomes capture are developed thank to the functionalization of silicon oxide substrates. Charged surfaces, both positive and negative, neutral and immunoaffinity surfaces are characterized and tested in functional assays with both exosome mimicking vesicles and exosomes purified from cell supernatants. The different surfaces showed promising properties, in particular the negatively-charged surface could capture more than 4 × 108 exosomes per square centimeter. The captured exosomes could be recovered and their biomarker cargo analyzed. Exosomal microRNAs were successfully analyzed with RT-PCR, confirming the good performances of the negatively-charged surface. The best-performing functionalization could be easily moved to microdevice surfaces for developing modular microfluidic systems for on-chip isolation of exosomes, to be integrated in simple and fast biosensors aimed at biomarker analysis both in clinical settings and in research.
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Affiliation(s)
- Cristina Potrich
- FBK-Fondazione Bruno Kessler, Center for Sensors and Devices, via Sommarive, 18, I-38123, Trento, Italy; Consiglio Nazionale delle Ricerche, Istituto di Biofisica, via alla Cascata 56/C, I-38123, Trento, Italy.
| | - Anna Pedrotti
- FBK-Fondazione Bruno Kessler, Center for Sensors and Devices, via Sommarive, 18, I-38123, Trento, Italy
| | - Cecilia Pederzolli
- FBK-Fondazione Bruno Kessler, Center for Sensors and Devices, via Sommarive, 18, I-38123, Trento, Italy
| | - Lorenzo Lunelli
- FBK-Fondazione Bruno Kessler, Center for Sensors and Devices, via Sommarive, 18, I-38123, Trento, Italy; Consiglio Nazionale delle Ricerche, Istituto di Biofisica, via alla Cascata 56/C, I-38123, Trento, Italy
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2
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Gasperini C, Tuntevski K, Beatini S, Pelizzoli R, Lo Van A, Mangoni D, Cossu RM, Pascarella G, Bianchini P, Bielefeld P, Scarpato M, Pons‐Espinal M, Sanges R, Diaspro A, Fitzsimons CP, Carninci P, Gustincich S, De Pietri Tonelli D. Piwil2 (Mili) sustains neurogenesis and prevents cellular senescence in the postnatal hippocampus. EMBO Rep 2023; 24:e53801. [PMID: 36472244 PMCID: PMC9900342 DOI: 10.15252/embr.202153801] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/25/2022] [Accepted: 11/10/2022] [Indexed: 12/12/2022] Open
Abstract
Adult neural progenitor cells (aNPCs) ensure lifelong neurogenesis in the mammalian hippocampus. Proper regulation of aNPC fate has thus important implications for brain plasticity and healthy aging. Piwi proteins and the small noncoding RNAs interacting with them (piRNAs) have been proposed to control memory and anxiety, but the mechanism remains elusive. Here, we show that Piwil2 (Mili) is essential for proper neurogenesis in the postnatal mouse hippocampus. RNA sequencing of aNPCs and their differentiated progeny reveal that Mili and piRNAs are dynamically expressed in neurogenesis. Depletion of Mili and piRNAs in the adult hippocampus impairs aNPC differentiation toward a neural fate, induces senescence, and generates reactive glia. Transcripts modulated upon Mili depletion bear sequences complementary or homologous to piRNAs and include repetitive elements and mRNAs encoding essential proteins for proper neurogenesis. Our results provide evidence of a critical role for Mili in maintaining fitness and proper fate of aNPCs, underpinning a possible involvement of the piRNA pathway in brain plasticity and successful aging.
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Affiliation(s)
- Caterina Gasperini
- Neurobiology of miRNA LaboratoryIstituto Italiano di TecnologiaGenoaItaly
| | - Kiril Tuntevski
- Neurobiology of miRNA LaboratoryIstituto Italiano di TecnologiaGenoaItaly
- The Open University Affiliated Research Centre at Istituto Italiano di Tecnologia (ARC@IIT)GenoaItaly
| | - Silvia Beatini
- Neurobiology of miRNA LaboratoryIstituto Italiano di TecnologiaGenoaItaly
| | - Roberta Pelizzoli
- Neurobiology of miRNA LaboratoryIstituto Italiano di TecnologiaGenoaItaly
| | - Amanda Lo Van
- Neurobiology of miRNA LaboratoryIstituto Italiano di TecnologiaGenoaItaly
| | - Damiano Mangoni
- Central RNA LaboratoryIstituto Italiano di TecnologiaGenoaItaly
| | - Rosa M Cossu
- Central RNA LaboratoryIstituto Italiano di TecnologiaGenoaItaly
| | - Giovanni Pascarella
- Division of Genomic TechnologiesRIKEN Center for Life Science TechnologiesYokohamaJapan
| | - Paolo Bianchini
- Nanoscopy, CHT ErzelliIstituto Italiano di TecnologiaGenoaItaly
| | - Pascal Bielefeld
- Swammerdam Institute for Life Sciences, Faculty of ScienceUniversity of AmsterdamAmsterdamThe Netherlands
| | | | | | - Remo Sanges
- Central RNA LaboratoryIstituto Italiano di TecnologiaGenoaItaly
- Area of NeuroscienceSISSATriesteItaly
| | - Alberto Diaspro
- Nanoscopy, CHT ErzelliIstituto Italiano di TecnologiaGenoaItaly
| | - Carlos P Fitzsimons
- Swammerdam Institute for Life Sciences, Faculty of ScienceUniversity of AmsterdamAmsterdamThe Netherlands
| | - Piero Carninci
- Division of Genomic TechnologiesRIKEN Center for Life Science TechnologiesYokohamaJapan
- Human TechnopoleMilanItaly
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3
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Jiang W, Wagner J, Du W, Plitzko J, Baumeister W, Beck F, Guo Q. A transformation clustering algorithm and its application in polyribosomes structural profiling. Nucleic Acids Res 2022; 50:9001-9011. [PMID: 35811088 PMCID: PMC9458451 DOI: 10.1093/nar/gkac547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/01/2022] [Accepted: 06/10/2022] [Indexed: 12/26/2022] Open
Abstract
Improvements in cryo-electron tomography sample preparation, electron-microscopy instrumentations, and image processing algorithms have advanced the structural analysis of macromolecules in situ. Beyond such analyses of individual macromolecules, the study of their interactions with functionally related neighbors in crowded cellular habitats, i.e. ‘molecular sociology’, is of fundamental importance in biology. Here we present a NEighboring Molecule TOpology Clustering (NEMO-TOC) algorithm. We optimized this algorithm for the detection and profiling of polyribosomes, which play both constitutive and regulatory roles in gene expression. Our results suggest a model where polysomes are formed by connecting multiple nonstochastic blocks, in which translation is likely synchronized.
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Affiliation(s)
- Wenhong Jiang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University , Beijing 100871, China
| | - Jonathan Wagner
- Department of Structural Molecular Biology, Max Planck Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Wenjing Du
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University , Beijing 100871, China
| | - Juergen Plitzko
- CryoEM Technology, Max Planck Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Structural Molecular Biology, Max Planck Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Florian Beck
- CryoEM Technology, Max Planck Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Qiang Guo
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University , Beijing 100871, China
- Changping Laboratory , Beijing, China
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4
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Deng C, Reinhard S, Hennlein L, Eilts J, Sachs S, Doose S, Jablonka S, Sauer M, Moradi M, Sendtner M. Impaired dynamic interaction of axonal endoplasmic reticulum and ribosomes contributes to defective stimulus-response in spinal muscular atrophy. Transl Neurodegener 2022; 11:31. [PMID: 35650592 PMCID: PMC9161492 DOI: 10.1186/s40035-022-00304-2] [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: 10/15/2021] [Accepted: 04/28/2022] [Indexed: 11/19/2022] Open
Abstract
Background Axonal degeneration and defects in neuromuscular neurotransmission represent a pathological hallmark in spinal muscular atrophy (SMA) and other forms of motoneuron disease. These pathological changes do not only base on altered axonal and presynaptic architecture, but also on alterations in dynamic movements of organelles and subcellular structures that are not necessarily reflected by static histopathological changes. The dynamic interplay between the axonal endoplasmic reticulum (ER) and ribosomes is essential for stimulus-induced local translation in motor axons and presynaptic terminals. However, it remains enigmatic whether the ER and ribosome crosstalk is impaired in the presynaptic compartment of motoneurons with Smn (survival of motor neuron) deficiency that could contribute to axonopathy and presynaptic dysfunction in SMA. Methods Using super-resolution microscopy, proximity ligation assay (PLA) and live imaging of cultured motoneurons from a mouse model of SMA, we investigated the dynamics of the axonal ER and ribosome distribution and activation. Results We observed that the dynamic remodeling of ER was impaired in axon terminals of Smn-deficient motoneurons. In addition, in axon terminals of Smn-deficient motoneurons, ribosomes failed to respond to the brain-derived neurotrophic factor stimulation, and did not undergo rapid association with the axonal ER in response to extracellular stimuli. Conclusions These findings implicate impaired dynamic interplay between the ribosomes and ER in axon terminals of motoneurons as a contributor to the pathophysiology of SMA and possibly also other motoneuron diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s40035-022-00304-2.
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Affiliation(s)
- Chunchu Deng
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, 97078, Würzburg, Germany
| | - Sebastian Reinhard
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians-University Wuerzburg, 97074, Würzburg, Germany
| | - Luisa Hennlein
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, 97078, Würzburg, Germany
| | - Janna Eilts
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians-University Wuerzburg, 97074, Würzburg, Germany
| | - Stefan Sachs
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians-University Wuerzburg, 97074, Würzburg, Germany
| | - Sören Doose
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians-University Wuerzburg, 97074, Würzburg, Germany
| | - Sibylle Jablonka
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, 97078, Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians-University Wuerzburg, 97074, Würzburg, Germany
| | - Mehri Moradi
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, 97078, Würzburg, Germany.
| | - Michael Sendtner
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, 97078, Würzburg, Germany.
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5
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Liedmann S, Liu X, Guy CS, Crawford JC, Rodriguez DA, Kuzuoğlu-Öztürk D, Guo A, Verbist KC, Temirov J, Chen MJ, Ruggero D, Zhang H, Thomas PG, Green DR. Localization of a TORC1-eIF4F translation complex during CD8 + T cell activation drives divergent cell fate. Mol Cell 2022; 82:2401-2414.e9. [PMID: 35597236 DOI: 10.1016/j.molcel.2022.04.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 02/22/2022] [Accepted: 04/12/2022] [Indexed: 11/30/2022]
Abstract
Activated CD8+ T lymphocytes differentiate into heterogeneous subsets. Using super-resolution imaging, we found that prior to the first division, dynein-dependent vesicular transport polarized active TORC1 toward the microtubule-organizing center (MTOC) at the proximal pole. This active TORC1 was physically associated with active eIF4F, required for the translation of c-myc mRNA. As a consequence, c-myc-translating polysomes polarized toward the cellular pole proximal to the immune synapse, resulting in localized c-myc translation. Upon division, the TORC1-eIF4A complex preferentially sorted to the proximal daughter cell, facilitating asymmetric c-Myc synthesis. Transient disruption of eIF4A activity at first division skewed long-term cell fate trajectories to memory-like function. Using a genetic barcoding approach, we found that first-division sister cells often displayed differences in transcriptional profiles that largely correlated with c-Myc and TORC1 target genes. Our findings provide mechanistic insights as to how distinct T cell fate trajectories can be established during the first division.
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Affiliation(s)
- Swantje Liedmann
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Xueyan Liu
- Department of Mathematics, University of New Orleans, New Orleans, LA 70148, USA
| | - Clifford S Guy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jeremy Chase Crawford
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Diego A Rodriguez
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Duygu Kuzuoğlu-Öztürk
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ao Guo
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Katherine C Verbist
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jamshid Temirov
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mark J Chen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Davide Ruggero
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hui Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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6
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Incoming new IUPAB Councilor 2021-Gabriella Viero. Biophys Rev 2022; 13:845-847. [PMID: 35059004 DOI: 10.1007/s12551-021-00861-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 10/19/2021] [Indexed: 10/20/2022] Open
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7
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Arora V, Sanguinetti G. Challenges for machine learning in RNA-protein interaction prediction. Stat Appl Genet Mol Biol 2022; 21:sagmb-2021-0087. [PMID: 35073469 DOI: 10.1515/sagmb-2021-0087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/02/2022] [Indexed: 11/15/2022]
Abstract
RNA-protein interactions have long being recognised as crucial regulators of gene expression. Recently, the development of scalable experimental techniques to measure these interactions has revolutionised the field, leading to the production of large-scale datasets which offer both opportunities and challenges for machine learning techniques. In this brief note, we will discuss some of the major stumbling blocks towards the use of machine learning in computational RNA biology, focusing specifically on the problem of predicting RNA-protein interactions from next-generation sequencing data.
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Affiliation(s)
- Viplove Arora
- Data Science, Department of Physics, International School for Advanced Studies (SISSA), Trieste 34136, Italy
| | - Guido Sanguinetti
- Data Science, Department of Physics, International School for Advanced Studies (SISSA), Trieste 34136, Italy
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8
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Shirokikh NE. Translation complex stabilization on messenger RNA and footprint profiling to study the RNA responses and dynamics of protein biosynthesis in the cells. Crit Rev Biochem Mol Biol 2021; 57:261-304. [PMID: 34852690 DOI: 10.1080/10409238.2021.2006599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
During protein biosynthesis, ribosomes bind to messenger (m)RNA, locate its protein-coding information, and translate the nucleotide triplets sequentially as codons into the corresponding sequence of amino acids, forming proteins. Non-coding mRNA features, such as 5' and 3' untranslated regions (UTRs), start sites or stop codons of different efficiency, stretches of slower or faster code and nascent polypeptide interactions can alter the translation rates transcript-wise. Most of the homeostatic and signal response pathways of the cells converge on individual mRNA control, as well as alter the global translation output. Among the multitude of approaches to study translational control, one of the most powerful is to infer the locations of translational complexes on mRNA based on the mRNA fragments protected by these complexes from endonucleolytic hydrolysis, or footprints. Translation complex profiling by high-throughput sequencing of the footprints allows to quantify the transcript-wise, as well as global, alterations of translation, and uncover the underlying control mechanisms by attributing footprint locations and sizes to different configurations of the translational complexes. The accuracy of all footprint profiling approaches critically depends on the fidelity of footprint generation and many methods have emerged to preserve certain or multiple configurations of the translational complexes, often in challenging biological material. In this review, a systematic summary of approaches to stabilize translational complexes on mRNA for footprinting is presented and major findings are discussed. Future directions of translation footprint profiling are outlined, focusing on the fidelity and accuracy of inference of the native in vivo translation complex distribution on mRNA.
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Affiliation(s)
- Nikolay E Shirokikh
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
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9
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Bosco B, Rossi A, Rizzotto D, Hamadou MH, Bisio A, Giorgetta S, Perzolli A, Bonollo F, Gaucherot A, Catez F, Diaz JJ, Dassi E, Inga A. DHX30 Coordinates Cytoplasmic Translation and Mitochondrial Function Contributing to Cancer Cell Survival. Cancers (Basel) 2021; 13:4412. [PMID: 34503222 PMCID: PMC8430983 DOI: 10.3390/cancers13174412] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/27/2021] [Accepted: 08/27/2021] [Indexed: 02/06/2023] Open
Abstract
DHX30 was recently implicated in the translation control of mRNAs involved in p53-dependent apoptosis. Here, we show that DHX30 exhibits a more general function by integrating the activities of its cytoplasmic isoform and of the more abundant mitochondrial one. The depletion of both DHX30 isoforms in HCT116 cells leads to constitutive changes in polysome-associated mRNAs, enhancing the translation of mRNAs coding for cytoplasmic ribosomal proteins while reducing the translational efficiency of the nuclear-encoded mitoribosome mRNAs. Furthermore, the depletion of both DHX30 isoforms leads to higher global translation but slower proliferation and lower mitochondrial energy metabolism. Isoform-specific silencing supports a role for cytoplasmic DHX30 in modulating global translation. The impact on translation and proliferation was confirmed in U2OS and MCF7 cells. Exploiting RIP, eCLIP, and gene expression data, we identified fourteen mitoribosome transcripts we propose as direct DHX30 targets that can be used to explore the prognostic value of this mechanism in cancer. We propose that DHX30 contributes to cell homeostasis by coordinating ribosome biogenesis, global translation, and mitochondrial metabolism. Targeting DHX30 could, thus, expose a vulnerability in cancer cells.
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Affiliation(s)
- Bartolomeo Bosco
- Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy; (B.B.); (A.R.); (D.R.); (M.H.H.); (A.B.); (S.G.); (A.P.); (F.B.)
| | - Annalisa Rossi
- Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy; (B.B.); (A.R.); (D.R.); (M.H.H.); (A.B.); (S.G.); (A.P.); (F.B.)
| | - Dario Rizzotto
- Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy; (B.B.); (A.R.); (D.R.); (M.H.H.); (A.B.); (S.G.); (A.P.); (F.B.)
| | - Meriem Hadjer Hamadou
- Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy; (B.B.); (A.R.); (D.R.); (M.H.H.); (A.B.); (S.G.); (A.P.); (F.B.)
| | - Alessandra Bisio
- Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy; (B.B.); (A.R.); (D.R.); (M.H.H.); (A.B.); (S.G.); (A.P.); (F.B.)
| | - Sebastiano Giorgetta
- Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy; (B.B.); (A.R.); (D.R.); (M.H.H.); (A.B.); (S.G.); (A.P.); (F.B.)
| | - Alicia Perzolli
- Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy; (B.B.); (A.R.); (D.R.); (M.H.H.); (A.B.); (S.G.); (A.P.); (F.B.)
| | - Francesco Bonollo
- Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy; (B.B.); (A.R.); (D.R.); (M.H.H.); (A.B.); (S.G.); (A.P.); (F.B.)
| | - Angeline Gaucherot
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Centre Léon Bérard, F-69008 Lyon, France; (A.G.); (F.C.); (J.-J.D.)
| | - Frédéric Catez
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Centre Léon Bérard, F-69008 Lyon, France; (A.G.); (F.C.); (J.-J.D.)
| | - Jean-Jacques Diaz
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Centre Léon Bérard, F-69008 Lyon, France; (A.G.); (F.C.); (J.-J.D.)
| | - Erik Dassi
- Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy; (B.B.); (A.R.); (D.R.); (M.H.H.); (A.B.); (S.G.); (A.P.); (F.B.)
| | - Alberto Inga
- Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy; (B.B.); (A.R.); (D.R.); (M.H.H.); (A.B.); (S.G.); (A.P.); (F.B.)
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Morphological Heterogeneity of the Endoplasmic Reticulum within Neurons and Its Implications in Neurodegeneration. Cells 2021; 10:cells10050970. [PMID: 33919188 PMCID: PMC8143122 DOI: 10.3390/cells10050970] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/13/2021] [Accepted: 04/19/2021] [Indexed: 12/19/2022] Open
Abstract
The endoplasmic reticulum (ER) is a multipurpose organelle comprising dynamic structural subdomains, such as ER sheets and tubules, serving to maintain protein, calcium, and lipid homeostasis. In neurons, the single ER is compartmentalized with a careful segregation of the structural subdomains in somatic and neurite (axodendritic) regions. The distribution and arrangement of these ER subdomains varies between different neuronal types. Mutations in ER membrane shaping proteins and morphological changes in the ER are associated with various neurodegenerative diseases implying significance of ER morphology in maintaining neuronal integrity. Specific neurons, such as the highly arborized dopaminergic neurons, are prone to stress and neurodegeneration. Differences in morphology and functionality of ER between the neurons may account for their varied sensitivity to stress and neurodegenerative changes. In this review, we explore the neuronal ER and discuss its distinct morphological attributes and specific functions. We hypothesize that morphological heterogeneity of the ER in neurons is an important factor that accounts for their selective susceptibility to neurodegeneration.
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11
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González García JS, Delgado J. Stochastic microswimming model of ribosome motion on the polysome. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2021; 44:9. [PMID: 33683520 DOI: 10.1140/epje/s10189-021-00011-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/24/2020] [Indexed: 06/12/2023]
Abstract
In this work we assume that the ribosome propels itself during the translocation step of the translation process of protein synthesis by running a cycle of stochastically generated conformational changes involving its two subunits. This cycle includes only two experimentally found ribosome shape changes. The main result is an analytic expression for ribosome's average swimming speed on a polysome, where the ribosome is in the presence of other ribosomes. Relevant geometric parameters of ribosome deformations are calculated first by solving a deterministic problem where the ribosome runs a cycle of prescribed conformational changes. The method of reflections and pairwise additivity are used to obtain the stresses and forces needed to apply the multiparticle reciprocal theorem. Ribosome's average velocity when it runs the corresponding stochastic cycle of deformations is calculated assuming independence among the conformational cycles of different ribosomes on the polysome. The results obtained show that swimming in tandem on the polysome allows the ribosome to reach any typical subcellular speed with deformations whose amplitude is of a smaller size than when it swims alone in the fluid. Also, the flow organized by its swimming stroke becomes more determinant for its motion than random diffusion, compared to the solitary ribosome.
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Affiliation(s)
- José Santiago González García
- Seminario de Bifurcaciones y Singularidades, Departamento de Matemáticas, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186 Col. Vicentina, Iztapalapa, Ciudad de México, 09340, Mexico.
| | - Joaquín Delgado
- Departamento de Matemáticas, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186 Col. Vicentina, Iztapalapa, Ciudad de México, 09340, Mexico
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12
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Neelagandan N, Lamberti I, Carvalho HJF, Gobet C, Naef F. What determines eukaryotic translation elongation: recent molecular and quantitative analyses of protein synthesis. Open Biol 2020; 10:200292. [PMID: 33292102 PMCID: PMC7776565 DOI: 10.1098/rsob.200292] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/10/2020] [Indexed: 12/14/2022] Open
Abstract
Protein synthesis from mRNA is an energy-intensive and tightly controlled cellular process. Translation elongation is a well-coordinated, multifactorial step in translation that undergoes dynamic regulation owing to cellular state and environmental determinants. Recent studies involving genome-wide approaches have uncovered some crucial aspects of translation elongation including the mRNA itself and the nascent polypeptide chain. Additionally, these studies have fuelled quantitative and mathematical modelling of translation elongation. In this review, we provide a comprehensive overview of the key determinants of translation elongation. We discuss consequences of ribosome stalling or collision, and how the cells regulate translation in case of such events. Next, we review theoretical approaches and widely used mathematical models that have become an essential ingredient to interpret complex molecular datasets and study translation dynamics quantitatively. Finally, we review recent advances in live-cell reporter and related analysis techniques, to monitor the translation dynamics of single cells and single-mRNA molecules in real time.
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Affiliation(s)
| | | | | | | | - Felix Naef
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
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13
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Lauria F, Bernabò P, Tebaldi T, Groen EJN, Perenthaler E, Maniscalco F, Rossi A, Donzel D, Clamer M, Marchioretto M, Omersa N, Orri J, Dalla Serra M, Anderluh G, Quattrone A, Inga A, Gillingwater TH, Viero G. SMN-primed ribosomes modulate the translation of transcripts related to spinal muscular atrophy. Nat Cell Biol 2020; 22:1239-1251. [PMID: 32958857 PMCID: PMC7610479 DOI: 10.1038/s41556-020-00577-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 08/13/2020] [Indexed: 12/20/2022]
Abstract
The contribution of ribosome heterogeneity and ribosome-associated proteins to the molecular control of proteomes in health and disease remains unclear. Here, we demonstrate that survival motor neuron (SMN) protein-the loss of which causes the neuromuscular disease spinal muscular atrophy (SMA)-binds to ribosomes and that this interaction is tissue-dependent. SMN-primed ribosomes are preferentially positioned within the first five codons of a set of mRNAs that are enriched for translational enhancer sequences in the 5' untranslated region (UTR) and rare codons at the beginning of their coding sequence. These SMN-specific mRNAs are associated with neurogenesis, lipid metabolism, ubiquitination, chromatin regulation and translation. Loss of SMN induces ribosome depletion, especially at the beginning of the coding sequence of SMN-specific mRNAs, leading to impairment of proteins that are involved in motor neuron function and stability, including acetylcholinesterase. Thus, SMN plays a crucial role in the regulation of ribosome fluxes along mRNAs encoding proteins that are relevant to SMA pathogenesis.
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Affiliation(s)
- Fabio Lauria
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
| | - Paola Bernabò
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
| | - Toma Tebaldi
- Department CIBIO, University of Trento, Trento, Italy
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Ewout Joan Nicolaas Groen
- Edinburgh Medical School, Biomedical Sciences & Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, UK
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, Utrecht, the Netherlands
| | - Elena Perenthaler
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Federica Maniscalco
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
- Department CIBIO, University of Trento, Trento, Italy
| | | | - Deborah Donzel
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
| | | | | | - Neža Omersa
- National Institute of Chemistry, Ljubljana, Slovenia
| | - Julia Orri
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
- La Fundació Jesuïtes Educació, Barcelona, Spain
| | | | | | | | - Alberto Inga
- Department CIBIO, University of Trento, Trento, Italy
| | - Thomas Henry Gillingwater
- Edinburgh Medical School, Biomedical Sciences & Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, UK
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14
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Carter SD, Hampton CM, Langlois R, Melero R, Farino ZJ, Calderon MJ, Li W, Wallace CT, Tran NH, Grassucci RA, Siegmund SE, Pemberton J, Morgenstern TJ, Eisenman L, Aguilar JI, Greenberg NL, Levy ES, Yi E, Mitchell WG, Rice WJ, Wigge C, Pilli J, George EW, Aslanoglou D, Courel M, Freyberg RJ, Javitch JA, Wills ZP, Area-Gomez E, Shiva S, Bartolini F, Volchuk A, Murray SA, Aridor M, Fish KN, Walter P, Balla T, Fass D, Wolf SG, Watkins SC, Carazo JM, Jensen GJ, Frank J, Freyberg Z. Ribosome-associated vesicles: A dynamic subcompartment of the endoplasmic reticulum in secretory cells. SCIENCE ADVANCES 2020; 6:eaay9572. [PMID: 32270040 PMCID: PMC7112762 DOI: 10.1126/sciadv.aay9572] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 01/13/2020] [Indexed: 05/21/2023]
Abstract
The endoplasmic reticulum (ER) is a highly dynamic network of membranes. Here, we combine live-cell microscopy with in situ cryo-electron tomography to directly visualize ER dynamics in several secretory cell types including pancreatic β-cells and neurons under near-native conditions. Using these imaging approaches, we identify a novel, mobile form of ER, ribosome-associated vesicles (RAVs), found primarily in the cell periphery, which is conserved across different cell types and species. We show that RAVs exist as distinct, highly dynamic structures separate from the intact ER reticular architecture that interact with mitochondria via direct intermembrane contacts. These findings describe a new ER subcompartment within cells.
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Affiliation(s)
- Stephen D. Carter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Cheri M. Hampton
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Robert Langlois
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Roberto Melero
- Biocomputing Unit, Centro Nacional de Biotecnología–CSIC, Darwin 3, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Zachary J. Farino
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Michael J. Calderon
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Wen Li
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Callen T. Wallace
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Ngoc Han Tran
- HHMI, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Robert A. Grassucci
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Stephanie E. Siegmund
- Department of Cellular, Molecular and Biophysical Studies, Columbia University Medical Center, New York, NY 10032, USA
- Department of Neurology, Columbia University, New York, NY 10032, USA
| | - Joshua Pemberton
- Section on Molecular Signal Transduction, Program for Developmental Neuroscience, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Travis J. Morgenstern
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Leanna Eisenman
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jenny I. Aguilar
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Nili L. Greenberg
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Elana S. Levy
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Edward Yi
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - William G. Mitchell
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | | | | | - Jyotsna Pilli
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Emily W. George
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Despoina Aslanoglou
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Maïté Courel
- CNRS-UMR7622, Institut de Biologie Paris-Seine, Université Pierre & Marie Curie, 75252 Paris, France
| | - Robin J. Freyberg
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jonathan A. Javitch
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Zachary P. Wills
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Estela Area-Gomez
- Department of Neurology, Columbia University, New York, NY 10032, USA
| | - Sruti Shiva
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Center for Metabolism and Mitochondrial Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Francesca Bartolini
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Allen Volchuk
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sandra A. Murray
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Meir Aridor
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Kenneth N. Fish
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Peter Walter
- HHMI, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tamas Balla
- Section on Molecular Signal Transduction, Program for Developmental Neuroscience, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sharon G. Wolf
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Simon C. Watkins
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - José María Carazo
- Biocomputing Unit, Centro Nacional de Biotecnología–CSIC, Darwin 3, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Grant J. Jensen
- HHMI, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Zachary Freyberg
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
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15
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Kandala D, Del Piano A, Minati L, Clamer M. Targeting Translation Activity at the Ribosome Interface with UV-Active Small Molecules. ACS OMEGA 2019; 4:10336-10345. [PMID: 31460127 PMCID: PMC6648492 DOI: 10.1021/acsomega.9b00366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 06/03/2019] [Indexed: 06/10/2023]
Abstract
Puromycin is a well-known antibiotic that is used to study the mechanism of protein synthesis and to monitor ribosome activity due to its incorporation into nascent peptide chains. However, puromycin effects outside the ribosome catalytic core remain unexplored. Here, we developed two analogues (3PB and 3PC) of the 3'-end of tyrosylated-tRNA that can efficiently interact with several proteins associated with ribosomes. We biochemically characterized the binding of these analogues and globally mapped the direct small molecule-protein interactions in living cells using clickable and photoreactive puromycin-like probes in combination with in-depth mass spectrometry. We identified a list of proteins targeted by the molecules during ribosome activity (e.g., GRP78), and we addressed possible uses of the probes to sense the activity of protein synthesis and to capture associated RNA. By coupling genome-wide RNA sequencing methods with these molecules, the characterization of unexplored translational control mechanisms will be feasible.
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16
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Fernandes LD, Ciandrini L. Driven transport on a flexible polymer with particle recycling: A model inspired by transcription and translation. Phys Rev E 2019; 99:052409. [PMID: 31212546 DOI: 10.1103/physreve.99.052409] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Indexed: 11/07/2022]
Abstract
Many theoretical works have attempted to coarse grain gene expression at the level of transcription and translation via frameworks based on exclusion processes. Usually in these models the three-dimensional conformation of the substrates (DNA and mRNA) is neglected, and particles move on a static unidimensional lattice in contact to an infinite reservoir. In this work we generalize the paradigmatic exclusion process and study the transport of particles along a unidimensional polymerlike flexible lattice immersed in a three-dimensional particle reservoir. We study the recycling of particles in the reservoir, how the transport is influenced by the global conformation of the lattice, and, in turn, how particle density dictates the structure of the polymer.
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Affiliation(s)
- Lucas D Fernandes
- Departamento de Entomologia e Acarologia, Escola Superior de Agricultura Luiz de Queiroz-Universidade de São Paulo (USP), 13418-900, Piracicaba/SP, Brazil and Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire, SL5 7PY, United Kingdom
| | - Luca Ciandrini
- Laboratoire Charles Coulomb (L2C), Université de Montpellier and CNRS, F-34095 Montpellier, France; CBS, Université de Montpellier, CNRS and INSERM, 34090 Montpellier, France; and DIMNP, Université de Montpellier and CNRS, Montpellier, France
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17
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Koley S, Rozenbaum M, Fainzilber M, Terenzio M. Translating regeneration: Local protein synthesis in the neuronal injury response. Neurosci Res 2019; 139:26-36. [DOI: 10.1016/j.neures.2018.10.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/13/2018] [Accepted: 10/02/2018] [Indexed: 12/21/2022]
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18
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Adivarahan S, Livingston N, Nicholson B, Rahman S, Wu B, Rissland OS, Zenklusen D. Spatial Organization of Single mRNPs at Different Stages of the Gene Expression Pathway. Mol Cell 2018; 72:727-738.e5. [PMID: 30415950 PMCID: PMC6592633 DOI: 10.1016/j.molcel.2018.10.010] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/24/2018] [Accepted: 10/04/2018] [Indexed: 12/21/2022]
Abstract
mRNAs form ribonucleoprotein complexes (mRNPs) by association with proteins that are crucial for mRNA metabolism. While the mRNP proteome has been well characterized, little is known about mRNP organization. Using a single-molecule approach, we show that mRNA conformation changes depending on its cellular localization and translational state. Compared to nuclear mRNPs and lncRNPs, association with ribosomes decompacts individual mRNAs, while pharmacologically dissociating ribosomes or sequestering them into stress granules leads to increased compaction. Moreover, translating mRNAs rarely show co-localized 5' and 3' ends, indicating either that mRNAs are not translated in a closed-loop configuration, or that mRNA circularization is transient, suggesting that a stable closed-loop conformation is not a universal state for all translating mRNAs.
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Affiliation(s)
- Srivathsan Adivarahan
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Nathan Livingston
- The Department of Biophysics and Biophysical Chemistry, the Solomon Snyder Department of Neuroscience, Center for Cell Dynamics, Johns Hopkins School of Medicine, Baltimore, MD 21224, USA
| | - Beth Nicholson
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Samir Rahman
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Bin Wu
- The Department of Biophysics and Biophysical Chemistry, the Solomon Snyder Department of Neuroscience, Center for Cell Dynamics, Johns Hopkins School of Medicine, Baltimore, MD 21224, USA
| | - Olivia S Rissland
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Daniel Zenklusen
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3T 1J4, Canada.
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19
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The Structural and Functional Organization of Ribosomal Compartment in the Cell: A Mystery or a Reality? Trends Biochem Sci 2018; 43:938-950. [PMID: 30337135 DOI: 10.1016/j.tibs.2018.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 09/21/2018] [Accepted: 09/21/2018] [Indexed: 11/23/2022]
Abstract
Great progress has been made toward solving the atomic structure of the ribosome, which is the main biosynthetic machine in cells, but we still do not have a full picture of exactly how cellular ribosomes function. Based on the analysis of crystallographic and electron microscopy data, we propose a basic model of the structural organization of ribosomes into a compartment. This compartment is regularly formed by arrays of ribosomal tetramers made up of two dimers that are actually facing in opposite directions. The compartment functions as the main 'factory' for the production of cellular proteins. The model is consistent with the existing biochemical and genetic data. We also consider the functional connections of such a compartment with cellular transcription and ribosomal biogenesis.
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20
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Khong A, Parker R. mRNP architecture in translating and stress conditions reveals an ordered pathway of mRNP compaction. J Cell Biol 2018; 217:4124-4140. [PMID: 30322972 PMCID: PMC6279387 DOI: 10.1083/jcb.201806183] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 09/05/2018] [Accepted: 10/04/2018] [Indexed: 12/31/2022] Open
Abstract
Khong and Parker use single-molecule FISH to examine the timing of mRNA entry to stress granule as well as mRNA protein complex (mRNP) architecture. mRNA compaction increases after ribosome runoff, suggesting that mRNPs preferentially adopt a closed-loop structure in nontranslating conditions. Stress granules (SGs) are transient membraneless organelles of nontranslating mRNA–protein complexes (mRNPs) that form during stress. In this study, we used multiple single-molecule FISH probes for particular mRNAs to examine their SG recruitment and spatial organization. Ribosome runoff is required for SG entry, as long open reading frame (ORF) mRNAs are delayed in SG accumulation, indicating that the SG transcriptome changes over time. Moreover, mRNAs are ∼20× compacted from an expected linear length when translating and compact ∼2-fold further in a stepwise manner beginning at the 5′ end during ribosome runoff. Surprisingly, the 5′ and 3′ ends of the examined mRNAs were separated when translating, but in nontranslating conditions the ends of long ORF mRNAs become close, suggesting that the closed-loop model of mRNPs preferentially forms on nontranslating mRNAs. Compaction of ribosome-free mRNAs is ATP independent, consistent with compaction occurring through RNA structure formation. These results suggest that translation inhibition triggers an mRNP reorganization that brings ends closer, which has implications for the regulation of mRNA stability and translation by 3′ UTR elements and the poly(A) tail.
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Affiliation(s)
- Anthony Khong
- Howard Hughes Medical Institute, University of Colorado, Boulder, CO.,Department of Biochemistry, University of Colorado, Boulder, CO
| | - Roy Parker
- Howard Hughes Medical Institute, University of Colorado, Boulder, CO .,Department of Biochemistry, University of Colorado, Boulder, CO
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21
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Active Ribosome Profiling with RiboLace. Cell Rep 2018; 25:1097-1108.e5. [DOI: 10.1016/j.celrep.2018.09.084] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 04/20/2018] [Accepted: 09/25/2018] [Indexed: 12/22/2022] Open
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22
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Yoshikawa H, Larance M, Harney DJ, Sundaramoorthy R, Ly T, Owen-Hughes T, Lamond AI. Efficient analysis of mammalian polysomes in cells and tissues using Ribo Mega-SEC. eLife 2018; 7:36530. [PMID: 30095066 PMCID: PMC6086667 DOI: 10.7554/elife.36530] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 07/28/2018] [Indexed: 12/14/2022] Open
Abstract
We describe Ribo Mega-SEC, a powerful approach for the separation and biochemical analysis of mammalian polysomes and ribosomal subunits using Size Exclusion Chromatography and uHPLC. Using extracts from either cells, or tissues, polysomes can be separated within 15 min from sample injection to fraction collection. Ribo Mega-SEC shows translating ribosomes exist predominantly in polysome complexes in human cell lines and mouse liver tissue. Changes in polysomes are easily quantified between treatments, such as the cellular response to amino acid starvation. Ribo Mega-SEC is shown to provide an efficient, convenient and highly reproducible method for studying functional translation complexes. We show that Ribo Mega-SEC is readily combined with high-throughput MS-based proteomics to characterize proteins associated with polysomes and ribosomal subunits. It also facilitates isolation of complexes for electron microscopy and structural studies.
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Affiliation(s)
- Harunori Yoshikawa
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Mark Larance
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom.,Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Dylan J Harney
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | | | - Tony Ly
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom.,Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Tom Owen-Hughes
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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23
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Negro S, Stazi M, Marchioretto M, Tebaldi T, Rodella U, Duregotti E, Gerke V, Quattrone A, Montecucco C, Rigoni M, Viero G. Hydrogen peroxide is a neuronal alarmin that triggers specific RNAs, local translation of Annexin A2, and cytoskeletal remodeling in Schwann cells. RNA (NEW YORK, N.Y.) 2018; 24:915-925. [PMID: 29643068 PMCID: PMC6004060 DOI: 10.1261/rna.064816.117] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/26/2018] [Indexed: 06/08/2023]
Abstract
Schwann cells are key players in neuro-regeneration: They sense "alarm" signals released by degenerating nerve terminals and differentiate toward a proregenerative phenotype, with phagocytosis of nerve debris and nerve guidance. At the murine neuromuscular junction, hydrogen peroxide (H2O2) is a key signal of Schwann cells' activation in response to a variety of nerve injuries. Here we report that Schwann cells exposed to low doses of H2O2 rewire the expression of several RNAs at both transcriptional and translational levels. Among the genes positively regulated at both levels, we identified an enriched cluster involved in cytoskeleton remodeling and cell migration, with the Annexin (Anxa) proteins being the most represented family. We show that both Annexin A2 (Anxa2) transcript and protein accumulate at the tips of long pseudopods that Schwann cells extend upon H2O2 exposure. Interestingly, Schwann cells reply to this signal and to nerve injury by locally translating Anxa2 in pseudopods, and undergo an extensive cytoskeleton remodeling. Our results show that, similarly to neurons, Schwann cells take advantage of local protein synthesis to change shape and move toward damaged axonal terminals to facilitate axonal regeneration.
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Affiliation(s)
- Samuele Negro
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
| | - Marco Stazi
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
| | | | - Toma Tebaldi
- Centre for Integrative Biology, University of Trento, 38123 Povo, Italy
| | - Umberto Rodella
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
| | - Elisa Duregotti
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
| | - Volker Gerke
- Institute of Medical Biochemistry, University of Münster, 48149 Münster, Germany
| | | | - Cesare Montecucco
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
- CNR Institute of Neuroscience, 35131 Padua, Italy
| | - Michela Rigoni
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
| | - Gabriella Viero
- Institute of Biophysics, CNR Unit at Trento, 38123 Povo, Italy
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24
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Wojcikiewicz RJH. The Making and Breaking of Inositol 1,4,5-Trisphosphate Receptor Tetramers. ACTA ACUST UNITED AC 2018; 6:45-49. [PMID: 30581688 DOI: 10.1166/msr.2018.1073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mammalian cells express three highly conserved inositol 1,4,5-trisphosphate (IP3) receptor types (IP3R1, IP3R2 and IP3R3), which have broadly similar characteristics, but markedly different distributions, and form homo- or heterotetrameric Ca2+ channels in endoplasmic reticulum (ER) membranes. A vast array of published work details how mature, ER membrane-located IP3 receptor tetramers are regulated, but much less attention has been paid to the intriguing questions of how the tetramers are assembled and destroyed as part of their natural life cycle. Are they assembled at the ER membrane from nascent, or completely translated polypeptides? How are they disassembled and degraded? These questions and other recently defined modes of IP3 receptor processing will be briefly reviewed.
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Afonina ZA, Shirokov VA. Three-Dimensional Organization of Polyribosomes–A Modern Approach. BIOCHEMISTRY (MOSCOW) 2018; 83:S48-S55. [DOI: 10.1134/s0006297918140055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Rossi A, Moro A, Tebaldi T, Cornella N, Gasperini L, Lunelli L, Quattrone A, Viero G, Macchi P. Identification and dynamic changes of RNAs isolated from RALY-containing ribonucleoprotein complexes. Nucleic Acids Res 2017; 45:6775-6792. [PMID: 28379492 PMCID: PMC5499869 DOI: 10.1093/nar/gkx235] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 03/30/2017] [Indexed: 12/13/2022] Open
Abstract
RALY is a member of the heterogeneous nuclear ribonucleoprotein family (hnRNP), a large family of RNA-binding proteins involved in many aspects of RNA metabolism. Although RALY interactome has been recently characterized, a comprehensive global analysis of RALY-associated RNAs is lacking and the biological function of RALY remains elusive. Here, we performed RIP-seq analysis to identify RALY interacting RNAs and assessed the role of RALY in gene expression. We demonstrate that RALY binds specific coding and non-coding RNAs and associates with translating mRNAs of mammalian cells. Among the identified transcripts, we focused on ANXA1 and H1FX mRNAs, encoding for Annexin A1 and for the linker variant of the histone H1X, respectively. Both proteins are differentially expressed by proliferating cells and are considered as markers for tumorigenesis. We demonstrate that cells lacking RALY expression exhibit changes in the levels of H1FX and ANXA1 mRNAs and proteins in an opposite manner. We also provide evidence for a direct binding of RALY to the U-rich elements present within the 3΄UTR of both transcripts. Thus, our results identify RALY as a poly-U binding protein and as a regulator of H1FX and ANXA1 in mammalian cells.
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Affiliation(s)
- Annalisa Rossi
- Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento (TN), Italy
| | - Albertomaria Moro
- Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento (TN), Italy
| | - Toma Tebaldi
- Laboratory of Translational Genomics, CIBIO - Centre for Integrative Biology, University of Trento, Italy
| | - Nicola Cornella
- Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento (TN), Italy
| | - Lisa Gasperini
- Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento (TN), Italy
| | - Lorenzo Lunelli
- Laboratory of Biomolecular Sequence and Structure Analysis for Health, Fondazione Bruno Kessler, Via Sommarive 18, 38123 Povo (TN), Italy
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, CIBIO - Centre for Integrative Biology, University of Trento, Italy
| | - Gabriella Viero
- Institute of Biophysics, CNR-Italian National Council for Research, via Sommarive 18, 38123 Trento (TN), Italy
| | - Paolo Macchi
- Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento (TN), Italy
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27
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Plasma assisted surface treatments of biomaterials. Biophys Chem 2017; 229:151-164. [DOI: 10.1016/j.bpc.2017.07.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/06/2017] [Accepted: 07/06/2017] [Indexed: 02/02/2023]
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28
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Abstract
Fluorescence nanoscopy uniquely combines minimally invasive optical access to the internal nanoscale structure and dynamics of cells and tissues with molecular detection specificity. While the basic physical principles of 'super-resolution' imaging were discovered in the 1990s, with initial experimental demonstrations following in 2000, the broad application of super-resolution imaging to address cell-biological questions has only more recently emerged. Nanoscopy approaches have begun to facilitate discoveries in cell biology and to add new knowledge. One current direction for method improvement is the ambition to quantitatively account for each molecule under investigation and assess true molecular colocalization patterns via multi-colour analyses. In pursuing this goal, the labelling of individual molecules to enable their visualization has emerged as a central challenge. Extending nanoscale imaging into (sliced) tissue and whole-animal contexts is a further goal. In this Review we describe the successes to date and discuss current obstacles and possibilities for further development.
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29
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Purification, identification, and functional analysis of polysomes from the human pathogen Staphylococcus aureus. Methods 2017; 117:59-66. [DOI: 10.1016/j.ymeth.2016.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/21/2016] [Accepted: 10/06/2016] [Indexed: 12/14/2022] Open
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30
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Morisaki T, Lyon K, DeLuca KF, DeLuca JG, English BP, Zhang Z, Lavis LD, Grimm JB, Viswanathan S, Looger LL, Lionnet T, Stasevich TJ. Real-time quantification of single RNA translation dynamics in living cells. Science 2016; 352:1425-9. [PMID: 27313040 DOI: 10.1126/science.aaf0899] [Citation(s) in RCA: 246] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/28/2016] [Indexed: 12/14/2022]
Abstract
Although messenger RNA (mRNA) translation is a fundamental biological process, it has never been imaged in real time in vivo with single-molecule precision. To achieve this, we developed nascent chain tracking (NCT), a technique that uses multi-epitope tags and antibody-based fluorescent probes to quantify protein synthesis dynamics at the single-mRNA level. NCT reveals an elongation rate of ~10 amino acids per second, with initiation occurring stochastically every ~30 seconds. Polysomes contain ~1 ribosome every 200 to 900 nucleotides and are globular rather than elongated in shape. By developing multicolor probes, we showed that most polysomes act independently; however, a small fraction (~5%) form complexes in which two distinct mRNAs can be translated simultaneously. The sensitivity and versatility of NCT make it a powerful new tool for quantifying mRNA translation kinetics.
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Affiliation(s)
- Tatsuya Morisaki
- Department of Biochemistry and Molecular Biology and Institute for Genome Architecture and Function, Colorado State University, Fort Collins, CO, USA
| | - Kenneth Lyon
- Department of Biochemistry and Molecular Biology and Institute for Genome Architecture and Function, Colorado State University, Fort Collins, CO, USA
| | - Keith F DeLuca
- Department of Biochemistry and Molecular Biology and Institute for Genome Architecture and Function, Colorado State University, Fort Collins, CO, USA
| | - Jennifer G DeLuca
- Department of Biochemistry and Molecular Biology and Institute for Genome Architecture and Function, Colorado State University, Fort Collins, CO, USA
| | - Brian P English
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Zhengjian Zhang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Sarada Viswanathan
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Loren L Looger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Timothee Lionnet
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology and Institute for Genome Architecture and Function, Colorado State University, Fort Collins, CO, USA
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31
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Lunelli L, Bernabò P, Bolner A, Vaghi V, Marchioretto M, Viero G. Peering at Brain Polysomes with Atomic Force Microscopy. J Vis Exp 2016. [PMID: 27023752 DOI: 10.3791/53851] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The translational machinery, i.e., the polysome or polyribosome, is one of the biggest and most complex cytoplasmic machineries in cells. Polysomes, formed by ribosomes, mRNAs, several proteins and non-coding RNAs, represent integrated platforms where translational controls take place. However, while the ribosome has been widely studied, the organization of polysomes is still lacking comprehensive understanding. Thus much effort is required in order to elucidate polysome organization and any novel mechanism of translational control that may be embedded. Atomic force microscopy (AFM) is a type of scanning probe microscopy that allows the acquisition of 3D images at nanoscale resolution. Compared to electron microscopy (EM) techniques, one of the main advantages of AFM is that it can acquire thousands of images both in air and in solution, enabling the sample to be maintained under near physiological conditions without any need for staining and fixing procedures. Here, a detailed protocol for the accurate purification of polysomes from mouse brain and their deposition on mica substrates is described. This protocol enables polysome imaging in air and liquid with AFM and their reconstruction as three-dimensional objects. Complementary to cryo-electron microscopy (cryo-EM), the proposed method can be conveniently used for systematically analyzing polysomes and studying their organization.
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Affiliation(s)
- Lorenzo Lunelli
- Laboratory of Biomolecular Sequence and Structure Analysis for Health, Fondazione Bruno Kessler
| | | | | | - Valentina Vaghi
- Laboratory of Biomolecular Sequence and Structure Analysis for Health, Fondazione Bruno Kessler
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Lauria F, Tebaldi T, Lunelli L, Struffi P, Gatto P, Pugliese A, Brigotti M, Montanaro L, Ciribilli Y, Inga A, Quattrone A, Sanguinetti G, Viero G. RiboAbacus: a model trained on polyribosome images predicts ribosome density and translational efficiency from mammalian transcriptomes. Nucleic Acids Res 2015; 43:e153. [PMID: 26240374 PMCID: PMC4678843 DOI: 10.1093/nar/gkv781] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 07/20/2015] [Indexed: 01/14/2023] Open
Abstract
Fluctuations in mRNA levels only partially contribute to determine variations in mRNA availability for translation, producing the well-known poor correlation between transcriptome and proteome data. Recent advances in microscopy now enable researchers to obtain high resolution images of ribosomes on transcripts, providing precious snapshots of translation in vivo. Here we propose RiboAbacus, a mathematical model that for the first time incorporates imaging data in a predictive model of transcript-specific ribosome densities and translational efficiencies. RiboAbacus uses a mechanistic model of ribosome dynamics, enabling the quantification of the relative importance of different features (such as codon usage and the 5′ ramp effect) in determining the accuracy of predictions. The model has been optimized in the human Hek-293 cell line to fit thousands of images of human polysomes obtained by atomic force microscopy, from which we could get a reference distribution of the number of ribosomes per mRNA with unmatched resolution. After validation, we applied RiboAbacus to three case studies of known transcriptome-proteome datasets for estimating the translational efficiencies, resulting in an increased correlation with corresponding proteomes. RiboAbacus is an intuitive tool that allows an immediate estimation of crucial translation properties for entire transcriptomes, based on easily obtainable transcript expression levels.
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Affiliation(s)
- Fabio Lauria
- Institute of Biophysics, CNR Unit at Trento, Via alla Cascata, 56/C-38123 Povo (TN), Italy
| | - Toma Tebaldi
- Laboratory of Translational Genomics, Centre for Integrative Biology, Via delle Regole, 101-38123 Mattarello (TN), Italy
| | - Lorenzo Lunelli
- Laboratory of Biomolecular Sequence and Structure Analysis for Health, Fondazione Bruno Kessler, Via Sommarive, 18-38123 Povo (TN), Italy
| | - Paolo Struffi
- Laboratory of Translational Genomics, Centre for Integrative Biology, Via delle Regole, 101-38123 Mattarello (TN), Italy
| | - Pamela Gatto
- Laboratory of Translational Genomics, Centre for Integrative Biology, Via delle Regole, 101-38123 Mattarello (TN), Italy
| | - Andrea Pugliese
- Mathematics Department, University of Trento, Via Sommarive, 14-38123 Povo (TN), Italy
| | - Maurizio Brigotti
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Via S. Giacomo, 14-40126 Bologna, Italy
| | - Lorenzo Montanaro
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Via S. Giacomo, 14-40126 Bologna, Italy
| | - Yari Ciribilli
- Laboratory of Transcriptional Networks, Centre for Integrative Biology, Via delle Regole, 101-38123 Mattarello (TN), Italy
| | - Alberto Inga
- Laboratory of Transcriptional Networks, Centre for Integrative Biology, Via delle Regole, 101-38123 Mattarello (TN), Italy
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, Centre for Integrative Biology, Via delle Regole, 101-38123 Mattarello (TN), Italy
| | - Guido Sanguinetti
- School of Informatics, University of Edinburgh, 10 Crichton Street, Edinburgh, Midlothian EH8 9AB, UK
| | - Gabriella Viero
- Institute of Biophysics, CNR Unit at Trento, Via alla Cascata, 56/C-38123 Povo (TN), Italy
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Bernabò P, Lunelli L, Quattrone A, Jousson O, Lencioni V, Viero G. Studying translational control in non-model stressed organisms by polysomal profiling. JOURNAL OF INSECT PHYSIOLOGY 2015; 76:30-35. [PMID: 25796968 DOI: 10.1016/j.jinsphys.2015.03.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 01/30/2015] [Accepted: 03/15/2015] [Indexed: 06/04/2023]
Abstract
In stressed organisms, strategic proteins are selectively translated even if the global process of protein synthesis is compromised. The determination of protein concentrations in tissues of non-model organisms (thus with limited genomic information) is challenging due to the absence of specific antibodies. Moreover, estimating protein levels quantifying transcriptional responses may be misleading, because translational control mechanisms uncouple protein and mRNAs abundances. Translational control is increasingly recognized as a hub where regulation of gene expression converges to shape proteomes, but it is almost completely overlooked in molecular ecology studies. An interesting approach to study translation and its control mechanisms is the analysis of variations of gene-specific translational efficiencies by quantifying mRNAs associated to ribosomes. In this paper, we propose a robust and streamlined pipeline for purifying ribosome-associated mRNAs and calculating global and gene-specific translation efficiencies from non-model insect's species. This method might found applications in molecular ecology to study responses to environmental stressors in non-model organisms.
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Affiliation(s)
- Paola Bernabò
- Institute of Biophysics, CNR Unit at Trento, Italy; Centre for Integrative Biology, Mattarello, Trento, Italy; Section of Invertebrate Zoology and Hydrobiology, MUSE-Museo delle Scienze, Trento, Italy
| | - Lorenzo Lunelli
- Laboratory of Biomolecular Sequence and Structure Analysis for Health, Fondazione Bruno Kessler, Trento, Italy
| | | | | | - Valeria Lencioni
- Section of Invertebrate Zoology and Hydrobiology, MUSE-Museo delle Scienze, Trento, Italy
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