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Harries LW. Dysregulated RNA processing and metabolism: a new hallmark of ageing and provocation for cellular senescence. FEBS J 2023; 290:1221-1234. [PMID: 35460337 DOI: 10.1111/febs.16462] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/28/2022] [Accepted: 04/21/2022] [Indexed: 12/23/2022]
Abstract
The human genome is capable of producing hundreds of thousands of different proteins and non-coding RNAs from <20 000 genes, in a co-ordinated and regulated fashion. This is achieved by a collection of phenomena known as mRNA processing and metabolism, and encompasses events in the life cycle of an RNA from synthesis to degradation. These factors are critical determinants of cellular adaptability and plasticity, which allows the cell to adjust its transcriptomic output in response to its internal and external environment. Evidence is building that dysfunctional RNA processing and metabolism may be a key contributor to the development of cellular senescence. Senescent cells by definition have exited cell cycle, but have gained functional features such as the secretion of the senescence-associated secretory phenotype (SASP), a known driver of chronic disease and perhaps even ageing itself. In this review, I will outline the impact of dysregulated mRNA processing and metabolism on senescence and ageing at the level of genes, cells and systems, and describe the mechanisms by which progressive deterioration in these processes may impact senescence and organismal ageing. Finally, I will present the evidence implicating this important process as a new hallmark of ageing, which could be harnessed in the future to develop new senotherapeutic interventions for chronic disease.
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Hu J, Li P, Shi B, Tie J. Importin β1 mediates nuclear import of the factors associated with nonsense-mediated RNA decay. Biochem Biophys Res Commun 2021; 542:34-39. [PMID: 33486189 DOI: 10.1016/j.bbrc.2021.01.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 12/15/2022]
Abstract
In eukaryotic cells, nonsense-mediated RNA decay (NMD) is an essential physiological mechanism coupled to translation, regulating the stability of abnormal RNA containing premature termination codon (PTC) and a significant fraction of normal transcriptomes. So far, the molecular regulation mechanism of NMD pathway is far from fully elucidated. Previously, we observed the interaction between importin β1 (Impβ1) and UPF1, a core factor of NMD. Here, we demonstrated that Impβ1 knockdown stabilized NMD reporters, and Impβ1 and UPF1 interacted and co-regulated an extensive number of target transcripts. Furthermore, Impβ1 affected the interaction between UPF1 and SMG5 or MAGOH, and the nuclear distributions of UPF1, SMG1, SMG5 and MAGOH. Besides, Ran knockdown extremely promoted the dissociation of UPF1 from SMG5 or MAGOH. Our findings provide molecular insight into the potential function of Impβ1in nonsense-mediated RNA decay.
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Affiliation(s)
- Jianran Hu
- Department of Biological Science and Technology, Changzhi University, Changzhi, 046011, China.
| | - Ping Li
- Department of Biological Science and Technology, Changzhi University, Changzhi, 046011, China
| | - Baozhong Shi
- Department of Biological Science and Technology, Changzhi University, Changzhi, 046011, China
| | - Jun Tie
- Department of Biological Science and Technology, Changzhi University, Changzhi, 046011, China
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Bera M, Kalyana Sundaram RV. Chromosome Territorial Organization Drives Efficient Protein Complex Formation: A Hypothesis. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2019; 92:541-548. [PMID: 31543715 PMCID: PMC6747946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In eukaryotes, chromosomes often form a transcriptional kissing loop during interphase. We propose that these kissing loops facilitate the formation of protein complexes. mRNA transcripts from these loops could cluster together into phase-separated nuclear granules. Their export into the ER could be ensured by guided diffusion through the inter-chromatin space followed by association with nuclear baskets and export factors. Inside the ER, these mRNAs would form a translation hub. Juxtaposed translation of these mRNAs would increase the cis/trans protein complex assembly among the nascent protein chains. Eukaryotes might employ this pathway to increase complex formation efficiency.
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Affiliation(s)
- Manindra Bera
- To whom all correspondence should be addressed: Manindra Bera, Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT USA, 06520; Tel: 203-737-3269,
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4
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Li Y, Junod SL, Ruba A, Kelich JM, Yang W. Nuclear export of mRNA molecules studied by SPEED microscopy. Methods 2019; 153:46-62. [PMID: 30125665 PMCID: PMC7138453 DOI: 10.1016/j.ymeth.2018.08.005] [Citation(s) in RCA: 10] [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: 05/31/2018] [Revised: 07/19/2018] [Accepted: 08/10/2018] [Indexed: 12/30/2022] Open
Abstract
The nuclear exit of messenger RNA (mRNA) molecules through the nuclear pore complex (NPC) is an essential step in the translation process of all proteins. The current limitations of conventional fluorescence and electron microscopy have prevented elucidation of how mRNA exports through the NPCs of live cells. In the recent years, various single-molecule fluorescence (SMF) microscopy techniques have been developed to improve the temporal and spatial resolutions of live-cell imaging allowing a more comprehensive understanding of the dynamics of mRNA export through native NPCs. In this review, we firstly evaluate the necessity of single-molecule live-cell microscopy in the study of mRNA nuclear export. Then, we highlight the application of single-point edge-excitation sub-diffraction (SPEED) microscopy that combines high-speed SMF microscopy and a 2D-to-3D transformation algorithm in the studies of nuclear transport kinetics and route for mRNAs. Finally, we summarize the new features of mRNA nuclear export found with SPEED microscopy as well as the reliability and accuracy of SPEED microscopy in mapping the 3D spatial locations of transport routes adopted by proteins and mRNAs through the NPCs.
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Affiliation(s)
- Yichen Li
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - Samuel L Junod
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - Andrew Ruba
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - Joseph M Kelich
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, PA, USA.
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Kiselev AM, Stepanova IS, Adonin LS, Batalova FM, Parfenov VN, Bogolyubov DS, Podgornaya OI. The exon junction complex factor Y14 is dynamic in the nucleus of the beetle Tribolium castaneum during late oogenesis. Mol Cytogenet 2017; 10:41. [PMID: 29151891 PMCID: PMC5679382 DOI: 10.1186/s13039-017-0342-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 10/27/2017] [Indexed: 12/02/2022] Open
Abstract
Background The oocyte chromosomes of the red flour beetle, Tribolium castaneum, are gathered into a knot, forming a karyosphere at the diplotene stage of meiotic prophase. Chromatin rearrangement, which is a characteristic feature of oocyte maturation, is well documented. The T. castaneum karyosphere is surrounded by a complex extrachromosomal structure termed the karyosphere capsule. The capsule contains the vast majority of oocyte RNA. We have previously shown using a BrUTP assay that oocyte chromosomes in T. castaneum maintain residual transcription up to the very end of oocyte maturation. Karyosphere transcription requires evidently not only transcription factors but also mRNA processing factors, including the components of the exon junction complex with its core component, the splicing factor Y14. We employed a gene engineering approach with injection of mRNA derived from the Myc-tagged Y14 plasmid-based construct in order to monitor the newly synthesized fusion protein in the oocyte nuclei. Results Our preliminary data have been presented as a brief correspondence elsewhere. Here, we provide a full-length article including immunoelectron-microscopy localization data on Y14–Myc distribution in the nucleus of previtellogenic and vitellogenic oocytes. The injections of the fusion protein Y14–Myc mRNA into the oocytes showed a dynamic pattern of the protein distribution. At the previtellogenic stage, there are two main locations for the protein: SC35 domains (the analogues of interchromatin granule clusters or nuclear speckles) and the karyosphere capsule. At the vitellogenic stage, SC35 domains were devoid of labels, and Y14–Myc was found in the perichromatin region of the karyosphere, presumably at the places of residual transcription. We show that karyosphere formation is accompanied by the movement of a nuclear protein while the residual transcription occurs during genome inactivation. Conclusions Our data indicate that the karyosphere capsule, being a destination site for a protein involved in mRNA splicing and export, is not only a specializes part of nuclear matrix separating the karyosphere from the products of chromosome activity, as believed previously, but represents a special nuclear compartment involved in the processes of gene expression in the case the karyosphere retains residual transcription activity. Electronic supplementary material The online version of this article (10.1186/s13039-017-0342-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Artem M Kiselev
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064 Russia.,Federal Almazov North-West Medical Research Centre, St. Petersburg, 197341 Russia.,ITMO University, Institute of Translational Medicine, St. Petersburg, 197101 Russia
| | - Irina S Stepanova
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064 Russia
| | - Leonid S Adonin
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064 Russia
| | - Florina M Batalova
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064 Russia
| | - Vladimir N Parfenov
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064 Russia
| | - Dmitry S Bogolyubov
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064 Russia
| | - Olga I Podgornaya
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064 Russia.,Department of Cytology and Histology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034 Russia.,Far Eastern Federal University, School of Biomedicine, Vladivostok, 690950 Russia
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6
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Mamon LA, Ginanova VR, Kliver SF, Yakimova AO, Atsapkina AA, Golubkova EV. RNA-binding proteins of the NXF (nuclear export factor) family and their connection with the cytoskeleton. Cytoskeleton (Hoboken) 2017; 74:161-169. [PMID: 28296067 DOI: 10.1002/cm.21362] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 03/04/2017] [Accepted: 03/08/2017] [Indexed: 02/05/2023]
Abstract
The mutual relationship between mRNA and the cytoskeleton can be seen from two points of view. On the one hand, the cytoskeleton is necessary for mRNA trafficking and anchoring to subcellular domains. On the other hand, cytoskeletal growth and rearrangement require the translation of mRNAs that are connected to the cytoskeleton. β-actin mRNA localization may influence dynamic changes in the actin cytoskeleton. In the cytoplasm, long-lived mRNAs exist in the form of RNP (ribonucleoprotein) complexes, where they interact with RNA-binding proteins, including NXF (Nuclear eXport Factor). Dm NXF1 is an evolutionarily conserved protein in Drosophila melanogaster that has orthologs in different animals. The universal function of nxf1 genes is the nuclear export of different mRNAs in various organisms. In this mini-review, we briefly discuss the evidence demonstrating that Dm NXF1 fulfils not only universal but also specialized cytoplasmic functions. This protein is detected not only in the nucleus but also in the cytoplasm. It is a component of neuronal granules. Dm NXF1 marks nuclear division spindles during early embryogenesis and the dense body on one side of the elongated spermatid nuclei. The characteristic features of sbr mutants (sbr10 and sbr5 ) are impairment of chromosome segregation and spindle formation anomalies during female meiosis. sbr12 mutant sterile males with immobile spermatozoa exhibit disturbances in the axoneme, mitochondrial derivatives and cytokinesis. These data allow us to propose that the Dm NXF1 proteins transport certain mRNAs in neurites and interact with localized mRNAs that are necessary for dynamic changes of the cytoskeleton.
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Affiliation(s)
- L A Mamon
- Department of Genetics and Biotechnology, Faculty of Biology, St Petersburg State University Universitetskaya nab. 7-9, Saint-Petersburg, 199034, Russia
| | - V R Ginanova
- Department of Genetics and Biotechnology, Faculty of Biology, St Petersburg State University Universitetskaya nab. 7-9, Saint-Petersburg, 199034, Russia
| | - S F Kliver
- Department of Genetics and Biotechnology, Faculty of Biology, St Petersburg State University Universitetskaya nab. 7-9, Saint-Petersburg, 199034, Russia
| | - A O Yakimova
- Department of Genetics and Biotechnology, Faculty of Biology, St Petersburg State University Universitetskaya nab. 7-9, Saint-Petersburg, 199034, Russia
| | - A A Atsapkina
- Department of Genetics and Biotechnology, Faculty of Biology, St Petersburg State University Universitetskaya nab. 7-9, Saint-Petersburg, 199034, Russia
| | - E V Golubkova
- Department of Genetics and Biotechnology, Faculty of Biology, St Petersburg State University Universitetskaya nab. 7-9, Saint-Petersburg, 199034, Russia
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Kutsenko A, Svensson T, Nystedt B, Lundeberg J, Björk P, Sonnhammer E, Giacomello S, Visa N, Wieslander L. The Chironomus tentans genome sequence and the organization of the Balbiani ring genes. BMC Genomics 2014; 15:819. [PMID: 25261295 PMCID: PMC4192438 DOI: 10.1186/1471-2164-15-819] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 09/22/2014] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The polytene nuclei of the dipteran Chironomus tentans (Ch. tentans) with their Balbiani ring (BR) genes constitute an exceptional model system for studies of the expression of endogenous eukaryotic genes. Here, we report the first draft genome of Ch. tentans and characterize its gene expression machineries and genomic architecture of the BR genes. RESULTS The genome of Ch. tentans is approximately 200 Mb in size, and has a low GC content (31%) and a low repeat fraction (15%) compared to other Dipteran species. Phylogenetic inference revealed that Ch. tentans is a sister clade to mosquitoes, with a split 150-250 million years ago. To characterize the Ch. tentans gene expression machineries, we identified potential orthologus sequences to more than 600 Drosophila melanogaster (D. melanogaster) proteins involved in the expression of protein-coding genes. We report novel data on the organization of the BR gene loci, including a novel putative BR gene, and we present a model for the organization of chromatin bundles in the BR2 puff based on genic and intergenic in situ hybridizations. CONCLUSIONS We show that the molecular machineries operating in gene expression are largely conserved between Ch. tentans and D. melanogaster, and we provide enhanced insight into the organization and expression of the BR genes. Our data strengthen the generality of the BR genes as a unique model system and provide essential background for in-depth studies of the biogenesis of messenger ribonucleoprotein complexes.
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Affiliation(s)
- Alexey Kutsenko
- />Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE 106 91 Stockholm, Sweden
- />Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE 171 21 Solna, Sweden
| | - Thomas Svensson
- />Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE 171 21 Solna, Sweden
| | - Björn Nystedt
- />Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE 171 21 Solna, Sweden
- />Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE 752 37 Uppsala, Sweden
| | - Joakim Lundeberg
- />Science for Life Laboratory, KTH, Royal Institute of Technology, Science for Life Laboratory, SE 171 65 Solna, Sweden
| | - Petra Björk
- />Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE 106 91 Stockholm, Sweden
| | - Erik Sonnhammer
- />Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE 171 21 Solna, Sweden
- />Department of Biochemistry and Biophysics, Stockholm University, SE 106 91 Stockholm, Sweden
| | - Stefania Giacomello
- />Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE 171 21 Solna, Sweden
| | - Neus Visa
- />Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE 106 91 Stockholm, Sweden
| | - Lars Wieslander
- />Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE 106 91 Stockholm, Sweden
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Björk P, Wieslander L. Mechanisms of mRNA export. Semin Cell Dev Biol 2014; 32:47-54. [PMID: 24813364 DOI: 10.1016/j.semcdb.2014.04.027] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 04/17/2014] [Indexed: 02/02/2023]
Abstract
Release of properly processed and assembled mRNPs from the actively transcribing genes, movement of the mRNPs through the interchromatin and interaction with the Nuclear Pore Complexes, leading to cytoplasmic export, are essential steps of eukaryotic gene expression. Here, we review these intranuclear gene expression steps.
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Affiliation(s)
- Petra Björk
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Lars Wieslander
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden.
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Kaminski T, Siebrasse JP, Kubitscheck U. A single molecule view on Dbp5 and mRNA at the nuclear pore. Nucleus 2013; 4:8-13. [PMID: 23324459 DOI: 10.4161/nucl.23386] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Numerous molecular details of intracellular mRNA processing have been revealed in recent years. However, the export process of single native mRNA molecules, the actual translocation through the nuclear pore complex (NPC), could not yet be examined in vivo. The problem is observing mRNA molecules without interfering with their native behavior. We used a protein-based labeling approach to visualize single native mRNPs in live salivary gland cells of Chironomus tentans, an iconic system used for decades to study the mRNA life cycle. Recombinant hrp36, the C. tentans homolog of mammalian hnRNP A1, was fluorescence labeled and microinjected into living cells, where it was integrated into nascent mRNPs. Intranuclear trajectories of single mRNPs, including their NPC passage, were observed with high space and time resolution employing a custom-built light sheet fluorescence microscope. We analyzed the kinetics and dynamics of mRNP export and started to study its mechanism and regulation by measuring the turnover-kinetics of single Dbp5 at the NPC.
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Affiliation(s)
- Tim Kaminski
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, Bonn, Germany
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Ma J, Liu Z, Michelotti N, Pitchiaya S, Veerapaneni R, Androsavich JR, Walter NG, Yang W. High-resolution three-dimensional mapping of mRNA export through the nuclear pore. Nat Commun 2013; 4:2414. [PMID: 24008311 PMCID: PMC3800679 DOI: 10.1038/ncomms3414] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 08/08/2013] [Indexed: 11/10/2022] Open
Abstract
The flow of genetic information is regulated by selective nucleocytoplasmic transport of messenger RNA:protein complexes (mRNPs) through the nuclear pore complexes (NPCs) of eukaryotic cells. However, the three-dimensional (3D) pathway taken by mRNPs as they transit through the NPC, and the kinetics and selectivity of transport, remain obscure. Here we employ single-molecule fluorescence microscopy with an unprecedented spatiotemporal accuracy of 8 nm and 2 ms to provide new insights into the mechanism of nuclear mRNP export in live human cells. We find that mRNPs exiting the nucleus are decelerated and selected at the centre of the NPC, and adopt a fast-slow-fast diffusion pattern during their brief, ~12 ms, interaction with the NPC. A 3D reconstruction of the export route indicates that mRNPs primarily interact with the periphery on the nucleoplasmic side and in the centre of the NPC, without entering the central axial conduit utilized for passive diffusion of small molecules, and eventually dissociate on the cytoplasmic side.
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Affiliation(s)
- Jiong Ma
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - Zhen Liu
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - Nicole Michelotti
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Physics, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Ram Veerapaneni
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - John R. Androsavich
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nils G. Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
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11
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Mamon LA, Kliver SF, Golubkova EV. Evolutionarily conserved features of the retained intron in alternative transcripts of the <i>nxf1</i> (nuclear export factor) genes in different organisms. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/ojgen.2013.33018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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12
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Nuclear export of single native mRNA molecules observed by light sheet fluorescence microscopy. Proc Natl Acad Sci U S A 2012; 109:9426-31. [PMID: 22615357 DOI: 10.1073/pnas.1201781109] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Nuclear export of mRNA is a key transport process in eukaryotic cells. To investigate it, we labeled native mRNP particles in living Chironomus tentans salivary gland cells with fluorescent hrp36, the hnRNP A1 homolog, and the nuclear envelope by fluorescent NTF2. Using light sheet microscopy, we traced single native mRNA particles across the nuclear envelope. The particles were observed to often probe nuclear pore complexes (NPC) at their nuclear face, and in only 25% of the cases yielded actual export. The complete export process took between 65 ms up to several seconds. A rate-limiting step was observed, which could be assigned to the nuclear basket of the pore and might correspond to a repositioning and unfolding of mRNPs before the actual translocation. Analysis of single fluorescent Dbp5 molecules, the RNA helicase essential for mRNA export, revealed that Dbp5 most often approached the cytoplasmic face of the NPC, and exhibited a binding duration of approximately 55 ms. Our results have allowed a refinement of the current models for mRNA export.
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Meier I. mRNA export and sumoylation-Lessons from plants. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:531-7. [PMID: 22306659 DOI: 10.1016/j.bbagrm.2012.01.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 01/15/2012] [Accepted: 01/19/2012] [Indexed: 01/22/2023]
Abstract
SUMO is a small ubiquitin-related protein modifier that is involved in a number of biological processes, including transcription, DNA repair, genome stability, and chromatin organization. Its potential role in mRNA biogenesis is less well investigated. The biogenesis of mRNA is closely coupled to transcription as well as mRNA nuclear export and several of the involved proteins have dual roles and appear in several complexes. Recently, SUMO-proteome analyses have discovered a number of these proteins as putative targets of SUMO regulation. In the model plant Arabidopsis thaliana, several mutants as well as environmental conditions have been identified that show a close correlation between over- and under-sumoylation of nuclear proteins and mRNA export retention. Three new plant SUMO-proteome studies add to the list of potentially sumoylated RNA-related proteins. Here, the emerging connection between SUMO and mRNA export is compared across kingdoms and its potential mechanistic role is discussed. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing.
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Affiliation(s)
- Iris Meier
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA.
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Katahira J. mRNA export and the TREX complex. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:507-13. [PMID: 22178508 DOI: 10.1016/j.bbagrm.2011.12.001] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 11/29/2011] [Accepted: 12/01/2011] [Indexed: 02/08/2023]
Abstract
Over the past few decades, we have learned that eukaryotes have evolved sophisticated means to coordinate the nuclear export of mRNAs with different steps of gene expression. This functional orchestration is important for the maintenance of the efficiency and fidelity of gene expression processes. The TREX (TRanscription-EXport) complex is an evolutionarily conserved multiprotein complex that plays a major role in the functional coupling of different steps during mRNA biogenesis, including mRNA transcription, processing, decay, and nuclear export. Furthermore, recent gene knockout studies in mice have revealed that the metazoan TREX complex is required for cell differentiation and development, likely because this complex regulates the expression of key genes. These newly identified roles for the TREX complex suggest the existence of a relationship between mRNA nuclear biogenesis and more complex cellular processes. This review describes the functional roles of the TREX complex in gene expression and the nuclear export of mRNAs. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing.
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Affiliation(s)
- Jun Katahira
- Biomolecular Networks Laboratories, Graduate School of Frontier Biosciences, Osaka University, Yamadaoka, Suita, Osaka, Japan.
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15
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Brechalov AV, Gurskii DY, Georgieva SG, Shidlovskii YV. Functioning of macromolecular complexes at successive stages of gene expression as self-coordinated molecular machines. Biophysics (Nagoya-shi) 2011. [DOI: 10.1134/s0006350911050034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Buratti E, Baralle FE. TDP-43: new aspects of autoregulation mechanisms in RNA binding proteins and their connection with human disease. FEBS J 2011; 278:3530-8. [DOI: 10.1111/j.1742-4658.2011.08257.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Sánchez-Álvarez M, Sánchez-Hernández N, Suñé C. Spatial Organization and Dynamics of Transcription Elongation and Pre-mRNA Processing in Live Cells. GENETICS RESEARCH INTERNATIONAL 2011; 2011:626081. [PMID: 22567362 PMCID: PMC3335512 DOI: 10.4061/2011/626081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 09/05/2011] [Indexed: 11/25/2022]
Abstract
During the last 30 years, systematic biochemical and functional studies have significantly expanded our knowledge of the transcriptional molecular components and the pre-mRNA processing machinery of the cell. However, our current understanding of how these functions take place spatiotemporally within the highly compartmentalized eukaryotic nucleus remains limited. Moreover, it is increasingly clear that “the whole is more than the sum of its parts” and that an understanding of the dynamic coregulation of genes is essential for fully characterizing complex biological phenomena and underlying diseases. Recent technological advances in light microscopy in addition to novel cell and molecular biology approaches have led to the development of new tools, which are being used to address these questions and may contribute to achieving an integrated and global understanding of how the genome works at a cellular level. Here, we review major hallmarks and novel insights in RNA polymerase II activity and pre-mRNA processing in the context of nuclear organization, as well as new concepts and challenges arising from our ability to gather extensive dynamic information at the single-cell resolution.
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Affiliation(s)
- Miguel Sánchez-Álvarez
- Dynamical Cell Systems Team, Section of Cellular and Molecular Biology, The Institute of Cancer Research, London SW3 6JB, UK
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