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Joshua IM, Lin M, Mardjuki A, Mazzola A, Höfken T. A Protein-Protein Interaction Analysis Suggests a Wide Range of New Functions for the p21-Activated Kinase (PAK) Ste20. Int J Mol Sci 2023; 24:15916. [PMID: 37958899 PMCID: PMC10647699 DOI: 10.3390/ijms242115916] [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: 09/20/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
The p21-activated kinases (PAKs) are important signaling proteins. They contribute to a surprisingly wide range of cellular processes and play critical roles in a number of human diseases including cancer, neurological disorders and cardiac diseases. To get a better understanding of PAK functions, mechanisms and integration of various cellular activities, we screened for proteins that bind to the budding yeast PAK Ste20 as an example, using the split-ubiquitin technique. We identified 56 proteins, most of them not described previously as Ste20 interactors. The proteins fall into a small number of functional categories such as vesicle transport and translation. We analyzed the roles of Ste20 in glucose metabolism and gene expression further. Ste20 has a well-established role in the adaptation to changing environmental conditions through the stimulation of mitogen-activated protein kinase (MAPK) pathways which eventually leads to transcription factor activation. This includes filamentous growth, an adaptation to nutrient depletion. Here we show that Ste20 also induces filamentous growth through interaction with nuclear proteins such as Sac3, Ctk1 and Hmt1, key regulators of gene expression. Combining our observations and the data published by others, we suggest that Ste20 has several new and unexpected functions.
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Affiliation(s)
| | - Meng Lin
- Institute of Biochemistry, Kiel University, 24118 Kiel, Germany
| | - Ariestia Mardjuki
- Division of Biosciences, Brunel University London, Uxbridge UB8 3PH, UK; (I.M.J.)
| | - Alessandra Mazzola
- Division of Biosciences, Brunel University London, Uxbridge UB8 3PH, UK; (I.M.J.)
- Department of Biopathology and Medical and Forensic Biotechnologies, University of Palermo, 90133 Palermo, Italy
| | - Thomas Höfken
- Division of Biosciences, Brunel University London, Uxbridge UB8 3PH, UK; (I.M.J.)
- Institute of Biochemistry, Kiel University, 24118 Kiel, Germany
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Kuang Z, Ke J, Hong J, Zhu Z, Niu L. Structural assembly of the nucleic-acid-binding Thp3-Csn12-Sem1 complex functioning in mRNA splicing. Nucleic Acids Res 2022; 50:8882-8897. [PMID: 35904806 PMCID: PMC9410885 DOI: 10.1093/nar/gkac634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 06/26/2022] [Accepted: 07/21/2022] [Indexed: 12/02/2022] Open
Abstract
PCI domain proteins play important roles in post-transcriptional gene regulation. In the TREX-2 complex, PCI domain-containing Sac3 and Thp1 proteins and accessory Sem1 protein form a ternary complex required for mRNA nuclear export. In contrast, structurally related Thp3–Csn12–Sem1 complex mediates pre-mRNA splicing. In this study, we determined the structure of yeast Thp3186–470–Csn12–Sem1 ternary complex at 2.9 Å resolution. Both Thp3 and Csn12 structures have a typical PCI structural fold, characterized by a stack of α-helices capped by a C-terminal winged-helix (WH) domain. The overall structure of Thp3186–470–Csn12–Sem1 complex has an inverted V-shape with Thp3 and Csn12 forming the two sides. A fishhook-shaped Sem1 makes extensive contacts on Csn12 to stabilize its conformation. The overall structure of Thp3186–470–Csn12–Sem1 complex resembles the previously reported Sac3–Thp1–Sem1 complex, but also has significant structural differences. The C-terminal WH domains of Thp3 and Csn12 form a continuous surface to bind different forms of nucleic acids with micromolar affinity. Mutation of the basic residues in the WH domains of Thp3 and Csn12 affects nucleic acid binding in vitro and mRNA splicing in vivo. The Thp3–Csn12–Sem1 structure provides a foundation for further exploring the structural elements required for its specific recruitment to spliceosome for pre-mRNA splicing.
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Affiliation(s)
- Zhiling Kuang
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, Anhui 230026, China.,School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jiyuan Ke
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Northwest corner of Susong Rd & Guanhai Rd, Hefei, Anhui 230601, China
| | - Jiong Hong
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Zhongliang Zhu
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, Anhui 230026, China.,School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Liwen Niu
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, Anhui 230026, China.,School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
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3
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Aguilera P, Dubarry M, Hardy J, Lisby M, Simon MN, Géli V. Telomeric C-circles localize at nuclear pore complexes in Saccharomyces cerevisiae. EMBO J 2022; 41:e108736. [PMID: 35147992 PMCID: PMC8922269 DOI: 10.15252/embj.2021108736] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 11/09/2022] Open
Abstract
As in human cells, yeast telomeres can be maintained in cells lacking telomerase activity by recombination-based mechanisms known as ALT (Alternative Lengthening of Telomeres). A hallmark of ALT human cancer cells are extrachromosomal telomeric DNA elements called C-circles, whose origin and function have remained unclear. Here, we show that extrachromosomal telomeric C-circles in yeast can be detected shortly after senescence crisis and concomitantly with the production of survivors arising from "type II" recombination events. We uncover that C-circles bind to the nuclear pore complex (NPC) and to the SAGA-TREX2 complex, similar to other non-centromeric episomal DNA. Disrupting the integrity of the SAGA/TREX2 complex affects both C-circle binding to NPCs and type II telomere recombination, suggesting that NPC tethering of C-circles facilitates formation and/or propagation of the long telomere repeats characteristic of type II survivors. Furthermore, we find that disruption of the nuclear diffusion barrier impairs type II recombination. These results support a model in which concentration of C-circles at NPCs benefits type II telomere recombination, highlighting the importance of spatial coordination in ALT-type mechanisms of telomere maintenance.
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Affiliation(s)
- Paula Aguilera
- Marseille Cancer Research Center (CRCM), U1068 Inserm, UMR7258 CNRS, Institut Paoli-Calmettes, Equipe labellisée Ligue, Aix Marseille University, Marseille, France
| | - Marion Dubarry
- Marseille Cancer Research Center (CRCM), U1068 Inserm, UMR7258 CNRS, Institut Paoli-Calmettes, Equipe labellisée Ligue, Aix Marseille University, Marseille, France
| | - Julien Hardy
- Marseille Cancer Research Center (CRCM), U1068 Inserm, UMR7258 CNRS, Institut Paoli-Calmettes, Equipe labellisée Ligue, Aix Marseille University, Marseille, France
| | - Michael Lisby
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Marie-Noëlle Simon
- Marseille Cancer Research Center (CRCM), U1068 Inserm, UMR7258 CNRS, Institut Paoli-Calmettes, Equipe labellisée Ligue, Aix Marseille University, Marseille, France
| | - Vincent Géli
- Marseille Cancer Research Center (CRCM), U1068 Inserm, UMR7258 CNRS, Institut Paoli-Calmettes, Equipe labellisée Ligue, Aix Marseille University, Marseille, France
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Woldegebriel R, Kvist J, Andersson N, Õunap K, Reinson K, Wojcik MH, Bijlsma EK, Hoffer MJV, Ryan MM, Stark Z, Walsh M, Cuppen I, van den Boogaard MJH, Bharucha-Goebel D, Donkervoort S, Winchester S, Zori R, Bönnemann CG, Maroofian R, O’Connor E, Houlden H, Zhao F, Carpén O, White M, Sreedharan J, Stewart M, Ylikallio E, Tyynismaa H. Distinct effects on mRNA export factor GANP underlie neurological disease phenotypes and alter gene expression depending on intron content. Hum Mol Genet 2020; 29:1426-1439. [PMID: 32202298 PMCID: PMC7297229 DOI: 10.1093/hmg/ddaa051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 11/15/2022] Open
Abstract
Defects in the mRNA export scaffold protein GANP, encoded by the MCM3AP gene, cause autosomal recessive early-onset peripheral neuropathy with or without intellectual disability. We extend here the phenotypic range associated with MCM3AP variants, by describing a severely hypotonic child and a sibling pair with a progressive encephalopathic syndrome. In addition, our analysis of skin fibroblasts from affected individuals from seven unrelated families indicates that disease variants result in depletion of GANP except when they alter critical residues in the Sac3 mRNA binding domain. GANP depletion was associated with more severe phenotypes compared with the Sac3 variants. Patient fibroblasts showed transcriptome alterations that suggested intron content-dependent regulation of gene expression. For example, all differentially expressed intronless genes were downregulated, including ATXN7L3B, which couples mRNA export to transcription activation by association with the TREX-2 and SAGA complexes. Our results provide insight into the molecular basis behind genotype-phenotype correlations in MCM3AP-associated disease and suggest mechanisms by which GANP defects might alter RNA metabolism.
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Affiliation(s)
- Rosa Woldegebriel
- Stem Cells and Metabolism Research Program, Research Programs Unit, University of Helsinki, 00290 Helsinki, Finland
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Jouni Kvist
- Stem Cells and Metabolism Research Program, Research Programs Unit, University of Helsinki, 00290 Helsinki, Finland
| | - Noora Andersson
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Karit Reinson
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Monica H Wojcik
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Divisions of Genetics and Genomics and Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Mariëtte J V Hoffer
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Monique M Ryan
- Murdoch Children’s Research Institute, Melbourne 3052, Australia
- Royal Children’s Hospital, Melbourne 3052, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne 3052, Australia
| | - Zornitza Stark
- Murdoch Children’s Research Institute, Melbourne 3052, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne 3052, Australia
| | - Maie Walsh
- Murdoch Children’s Research Institute, Melbourne 3052, Australia
| | - Inge Cuppen
- Department of Pediatric Neurology, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Diana Bharucha-Goebel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Division of Neurology, Children's National Health System, Washington, DC, USA
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Sara Winchester
- Child Neurology Center of Northwest Florida, Pensacola, FL, USA
| | - Roberto Zori
- Division of Genetics and Metabolism, University of Florida, Gainesville, FL, USA
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Institute of Neurology, London WC1N 3BG, UK
| | - Emer O’Connor
- Department of Neuromuscular Disorders, UCL Institute of Neurology, London WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Institute of Neurology, London WC1N 3BG, UK
| | - Fang Zhao
- Department of Pathology and Genetics, HUSLAB Laboratories, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Olli Carpén
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Matthew White
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Jemeen Sreedharan
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Murray Stewart
- MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Emil Ylikallio
- Stem Cells and Metabolism Research Program, Research Programs Unit, University of Helsinki, 00290 Helsinki, Finland
- Clinical Neurosciences, Neurology, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Henna Tyynismaa
- Stem Cells and Metabolism Research Program, Research Programs Unit, University of Helsinki, 00290 Helsinki, Finland
- Department of Medical and Clinical Genetics, University of Helsinki, 00290 Helsinki, Finland
- Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
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Xie Y, Ren Y. Mechanisms of nuclear mRNA export: A structural perspective. Traffic 2019; 20:829-840. [PMID: 31513326 DOI: 10.1111/tra.12691] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 08/26/2019] [Indexed: 12/28/2022]
Abstract
Export of mRNA from the nucleus to the cytoplasm is a critical process for all eukaryotic gene expression. As mRNA is synthesized, it is packaged with a myriad of RNA-binding proteins to form ribonucleoprotein particles (mRNPs). For each step in the processes of maturation and export, mRNPs must have the correct complement of proteins. Much of the mRNA export pathway revolves around the heterodimeric export receptor yeast Mex67•Mtr2/human NXF1•NXT1, which is recruited to signal the completion of nuclear mRNP assembly, mediates mRNP targeting/translocation through the nuclear pore complex (NPC), and is displaced at the cytoplasmic side of the NPC to release the mRNP into the cytoplasm. Directionality of the transport is governed by at least two DEAD-box ATPases, yeast Sub2/human UAP56 in the nucleus and yeast Dbp5/human DDX19 at the cytoplasmic side of the NPC, which respectively mediate the association and dissociation of Mex67•Mtr2/NXF1•NXT1 onto the mRNP. Here we review recent progress from structural studies of key constituents in different steps of nuclear mRNA export. These findings have laid the foundation for further studies to obtain a comprehensive mechanistic view of the mRNA export pathway.
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Affiliation(s)
- Yihu Xie
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Yi Ren
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
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