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Xie Y, Clarke BP, Xie D, Mei M, Bhat P, Hill PS, Angelos AE, Çağatay T, Haider M, Collier SE, Chambers MG, Aksenova V, Dasso M, Fontoura BMA, Ren Y. Structures and mRNP remodeling mechanism of the TREX-2 complex. Structure 2025; 33:566-582.e6. [PMID: 39862860 PMCID: PMC11890942 DOI: 10.1016/j.str.2024.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 06/18/2024] [Accepted: 12/27/2024] [Indexed: 01/27/2025]
Abstract
mRNAs are packaged with proteins into messenger ribonucleoprotein complexes (mRNPs) in the nucleus. mRNP assembly and export are of fundamental importance for all eukaryotic gene expression. Before export to the cytoplasm, mRNPs undergo dynamic remodeling governed by the DEAD-box helicase DDX39B (yeast Sub2). DDX39B/Sub2 primarily functions in the nucleus and leaves the mRNP prior to export through the nuclear pore complex; however, the underlying mechanisms remain elusive. Here, we identify the conserved TREX-2 complex as the long-sought factor that facilitates DDX39B/Sub2 to complete the mRNP remodeling cycle. Our crystallographic and cryoelectron microscopy (cryo-EM) analyses demonstrate that TREX-2 modulates the activities of DDX39B/Sub2 through multiple interactions. Critically, a conserved "trigger loop" from TREX-2 splits the two RecA domains of DDX39B/Sub2 and promotes the removal of DDX39B/Sub2 from mRNP. Our findings suggest that TREX-2 coordinates with DDX39B/Sub2 and the human export receptor NXF1-NXT1 (yeast Mex67-Mtr2) to complete the final steps of nuclear mRNP assembly.
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Affiliation(s)
- Yihu Xie
- Department of Biochemistry, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA.
| | - Bradley P Clarke
- Department of Biochemistry, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN 37232, USA
| | - Dongqi Xie
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Menghan Mei
- Department of Biochemistry, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN 37232, USA
| | - Prasanna Bhat
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Pate S Hill
- Department of Biochemistry, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN 37232, USA
| | - Alexia E Angelos
- Department of Biochemistry, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN 37232, USA
| | - Tolga Çağatay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mariam Haider
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Scott E Collier
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Melissa G Chambers
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Vasilisa Aksenova
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mary Dasso
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Beatriz M A Fontoura
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yi Ren
- Department of Biochemistry, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA.
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Clarke BP, Angelos AE, Mei M, Hill PS, Xie Y, Ren Y. Cryo-EM structure of the CBC-ALYREF complex. eLife 2024; 12:RP91432. [PMID: 39282949 PMCID: PMC11405014 DOI: 10.7554/elife.91432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2024] Open
Abstract
In eukaryotes, RNAs transcribed by RNA Pol II are modified at the 5' end with a 7-methylguanosine (m7G) cap, which is recognized by the nuclear cap binding complex (CBC). The CBC plays multiple important roles in mRNA metabolism, including transcription, splicing, polyadenylation, and export. It promotes mRNA export through direct interaction with a key mRNA export factor, ALYREF, which in turn links the TRanscription and EXport (TREX) complex to the 5' end of mRNA. However, the molecular mechanism for CBC-mediated recruitment of the mRNA export machinery is not well understood. Here, we present the first structure of the CBC in complex with an mRNA export factor, ALYREF. The cryo-EM structure of CBC-ALYREF reveals that the RRM domain of ALYREF makes direct contact with both the NCBP1 and NCBP2 subunits of the CBC. Comparing CBC-ALYREF with other cellular complexes containing CBC and/or ALYREF components provides insights into the coordinated events during mRNA transcription, splicing, and export.
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Affiliation(s)
- Bradley P Clarke
- Department of Biochemistry, Vanderbilt University School of Medicine Basic SciencesNashvilleUnited States
| | - Alexia E Angelos
- Department of Biochemistry, Vanderbilt University School of Medicine Basic SciencesNashvilleUnited States
| | - Menghan Mei
- Department of Biochemistry, Vanderbilt University School of Medicine Basic SciencesNashvilleUnited States
| | - Pate S Hill
- Department of Biochemistry, Vanderbilt University School of Medicine Basic SciencesNashvilleUnited States
| | - Yihu Xie
- Department of Biochemistry, Vanderbilt University School of Medicine Basic SciencesNashvilleUnited States
| | - Yi Ren
- Department of Biochemistry, Vanderbilt University School of Medicine Basic SciencesNashvilleUnited States
- Center for Structural Biology, Vanderbilt University School of Medicine Basic SciencesNashvilleUnited States
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Qiu Y, Kang YM, Korfmann C, Pouyet F, Eckford A, Palazzo AF. The GC-content at the 5' ends of human protein-coding genes is undergoing mutational decay. Genome Biol 2024; 25:219. [PMID: 39138526 PMCID: PMC11323403 DOI: 10.1186/s13059-024-03364-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 07/31/2024] [Indexed: 08/15/2024] Open
Abstract
BACKGROUND In vertebrates, most protein-coding genes have a peak of GC-content near their 5' transcriptional start site (TSS). This feature promotes both the efficient nuclear export and translation of mRNAs. Despite the importance of GC-content for RNA metabolism, its general features, origin, and maintenance remain mysterious. We investigate the evolutionary forces shaping GC-content at the transcriptional start site (TSS) of genes through both comparative genomic analysis of nucleotide substitution rates between different species and by examining human de novo mutations. RESULTS Our data suggests that GC-peaks at TSSs were present in the last common ancestor of amniotes, and likely that of vertebrates. We observe that in apes and rodents, where recombination is directed away from TSSs by PRDM9, GC-content at the 5' end of protein-coding gene is currently undergoing mutational decay. In canids, which lack PRDM9 and perform recombination at TSSs, GC-content at the 5' end of protein-coding is increasing. We show that these patterns extend into the 5' end of the open reading frame, thus impacting synonymous codon position choices. CONCLUSIONS Our results indicate that the dynamics of this GC-peak in amniotes is largely shaped by historic patterns of recombination. Since decay of GC-content towards the mutation rate equilibrium is the default state for non-functional DNA, the observed decrease in GC-content at TSSs in apes and rodents indicates that the GC-peak is not being maintained by selection on most protein-coding genes in those species.
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Affiliation(s)
- Yi Qiu
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5G1M1, Canada
| | - Yoon Mo Kang
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5G1M1, Canada
| | - Christopher Korfmann
- Department of Electrical Engineering and Computer Science, York University, Toronto, Ontario, M3J1P3, Canada
| | - Fanny Pouyet
- Laboratoire Interdisciplinaire des Sciences du Numérique, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Andrew Eckford
- Department of Electrical Engineering and Computer Science, York University, Toronto, Ontario, M3J1P3, Canada
| | - Alexander F Palazzo
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5G1M1, Canada.
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Banerjee S, Nagasawa C, Widen S, Garcia-Blanco M. Parsing the roles of DExD-box proteins DDX39A and DDX39B in alternative RNA splicing. Nucleic Acids Res 2024; 52:8534-8551. [PMID: 38801080 PMCID: PMC11317157 DOI: 10.1093/nar/gkae431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 05/01/2024] [Accepted: 05/12/2024] [Indexed: 05/29/2024] Open
Abstract
DExD-box RNA proteins DDX39A and DDX39B are highly homologous paralogs that are conserved in vertebrates. They are required for energy-driven reactions involved in RNA processing. Although we have some understanding of how their functions overlap in RNA nuclear export, our knowledge of whether or not these proteins have specific or redundant functions in RNA splicing is limited. Our previous work has shown that DDX39B is responsible for regulating the splicing of important immune transcripts IL7R and FOXP3. In this study, we aimed to investigate whether DDX39A, a highly homologous paralog of DDX39B, plays a similar role in regulating alternative RNA splicing. We find that DDX39A and DDX39B have significant redundancy in their gene targets, but there are targets that uniquely require one or the other paralog. For instance, DDX39A is incapable of complementing defective splicing of IL7R exon 6 when DDX39B is depleted. This exon and other cassette exons that specifically depend on DDX39B have U-poor/C-rich polypyrimidine tracts in the upstream intron and this variant polypyrimidine tract is required for DDX39B dependency. This study provides evidence that despite a high degree of functional redundancy, DDX39A and DDX39B are selectively required for the splicing of specific pre-mRNAs.
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Affiliation(s)
- Shefali Banerjee
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA 22903, USA
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Chloe K Nagasawa
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA 22903, USA
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550, USA
- Human Pathophysiology and Translational Medicine Program, Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX 77555-5302, USA
| | - Steven G Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Mariano A Garcia-Blanco
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA 22903, USA
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550, USA
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Rödel A, Weig I, Tiedemann S, Schwartz U, Längst G, Moehle C, Grasser M, Grasser KD. Arabidopsis mRNA export factor MOS11: molecular interactions and role in abiotic stress responses. THE NEW PHYTOLOGIST 2024; 243:180-194. [PMID: 38650347 DOI: 10.1111/nph.19773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/01/2024] [Indexed: 04/25/2024]
Abstract
Transcription and export (TREX) is a multi-subunit complex that links synthesis, processing and export of mRNAs. It interacts with the RNA helicase UAP56 and export factors such as MOS11 and ALYs to facilitate nucleocytosolic transport of mRNAs. Plant MOS11 is a conserved, but sparsely researched RNA-binding export factor, related to yeast Tho1 and mammalian CIP29/SARNP. Using biochemical approaches, the domains of Arabidopsis thaliana MOS11 required for interaction with UAP56 and RNA-binding were identified. Further analyses revealed marked genetic interactions between MOS11 and ALY genes. Cell fractionation in combination with transcript profiling demonstrated that MOS11 is required for export of a subset of mRNAs that are shorter and more GC-rich than MOS11-independent transcripts. The central α-helical domain of MOS11 proved essential for physical interaction with UAP56 and for RNA-binding. MOS11 is involved in the nucleocytosolic transport of mRNAs that are upregulated under stress conditions and accordingly mos11 mutant plants turned out to be sensitive to elevated NaCl concentrations and heat stress. Collectively, our analyses identify functional interaction domains of MOS11. In addition, the results establish that mRNA export is critically involved in the plant response to stress conditions and that MOS11 plays a prominent role at this.
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Affiliation(s)
- Amelie Rödel
- Cell Biology & Plant Biochemistry, Biochemistry Center, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Ina Weig
- Cell Biology & Plant Biochemistry, Biochemistry Center, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Sophie Tiedemann
- Cell Biology & Plant Biochemistry, Biochemistry Center, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Uwe Schwartz
- NGS Analysis Center, Biology and Pre-Clinical Medicine, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Gernot Längst
- Institute for Biochemistry III, Biochemistry Center, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Christoph Moehle
- Center of Excellence for Fluorescent Bioanalytics (KFB), University of Regensburg, Am Biopark 9, D-93053, Regensburg, Germany
| | - Marion Grasser
- Cell Biology & Plant Biochemistry, Biochemistry Center, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Klaus D Grasser
- Cell Biology & Plant Biochemistry, Biochemistry Center, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
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Yellamaty R, Sharma S. Critical Cellular Functions and Mechanisms of Action of the RNA Helicase UAP56. J Mol Biol 2024; 436:168604. [PMID: 38729260 PMCID: PMC11168752 DOI: 10.1016/j.jmb.2024.168604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/24/2024] [Accepted: 05/03/2024] [Indexed: 05/12/2024]
Abstract
Posttranscriptional maturation and export from the nucleus to the cytoplasm are essential steps in the normal processing of many cellular RNAs. The RNA helicase UAP56 (U2AF associated protein 56; also known as DDX39B) has emerged as a critical player in facilitating and co-transcriptionally linking these steps. Originally identified as a helicase involved in pre-mRNA splicing, UAP56 has been shown to facilitate formation of the A complex during spliceosome assembly. Additionally, it has been found to be critical for interactions between components of the exon junction and transcription and export complexes to promote the loading of export receptors. Although it appears to be structurally similar to other helicase superfamily 2 members, UAP56's ability to interact with multiple different protein partners allows it to perform its various cellular functions. Herein, we describe the structure-activity relationship studies that identified protein interactions of UAP56 and its human paralog URH49 (UAP56-related helicase 49; also known as DDX39A) and are beginning to reveal molecular mechanisms by which interacting proteins and substrate RNAs may regulate these helicases. We also provide an overview of reports that have demonstrated less well-characterized roles for UAP56, including R-loop resolution and telomere maintenance. Finally, we discuss studies that indicate a potential pathogenic effect of UAP56 in the development of autoimmune diseases and cancer, and identify the association of somatic and genetic mutations in UAP56 with neurodevelopmental disorders.
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Affiliation(s)
- Ryan Yellamaty
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004, USA
| | - Shalini Sharma
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004, USA.
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He PC, He C. mRNA accessibility within mRNPs as a determinant of gene expression. Trends Biochem Sci 2024; 49:199-207. [PMID: 38071089 PMCID: PMC10939938 DOI: 10.1016/j.tibs.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/05/2023] [Accepted: 11/10/2023] [Indexed: 01/31/2024]
Abstract
Gene expression is a complex process requiring many control mechanisms to achieve a desired phenotype. DNA accessibility within chromatin is well established as an important determinant of gene expression. By contrast, while mRNA also associates with a complement of proteins, the exact nature of messenger ribonucleoprotein (mRNP) packaging and its functional relevance is not as clear. Recent reports indicate that exon junction complex (EJC)-mediated mRNP packaging renders exon junction-proximal regions inaccessible for m6A methylation, and that EJCs reside within the inaccessible interior of globular transcription and export (TREX) complex-associated nuclear mRNPs. We propose that 'mRNA accessibility' within mRNPs is an important determinant of gene expression that may modulate the specificity of a broad array of regulatory processes including but not limited to m6A methylation.
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Affiliation(s)
- P Cody He
- Pritzker School of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA.
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Palazzo AF, Qiu Y, Kang YM. mRNA nuclear export: how mRNA identity features distinguish functional RNAs from junk transcripts. RNA Biol 2024; 21:1-12. [PMID: 38091265 PMCID: PMC10732640 DOI: 10.1080/15476286.2023.2293339] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 11/27/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
The division of the cellular space into nucleoplasm and cytoplasm promotes quality control mechanisms that prevent misprocessed mRNAs and junk RNAs from gaining access to the translational machinery. Here, we explore how properly processed mRNAs are distinguished from both misprocessed mRNAs and junk RNAs by the presence or absence of various 'identity features'.
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Affiliation(s)
| | - Yi Qiu
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Yoon Mo Kang
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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