1
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Yoon SB, Chen L, Robinson IE, Khatib TO, Arthur RA, Claussen H, Zohbi NM, Wu H, Mouw JK, Marcus AI. Subpopulation commensalism promotes Rac1-dependent invasion of single cells via laminin-332. J Cell Biol 2024; 223:e202308080. [PMID: 38551497 PMCID: PMC10982113 DOI: 10.1083/jcb.202308080] [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: 08/28/2023] [Revised: 02/02/2024] [Accepted: 03/11/2024] [Indexed: 04/02/2024] Open
Abstract
Phenotypic heterogeneity poses a significant hurdle for cancer treatment but is under-characterized in the context of tumor invasion. Amidst the range of phenotypic heterogeneity across solid tumor types, collectively invading cells and single cells have been extensively characterized as independent modes of invasion, but their intercellular interactions have rarely been explored. Here, we isolated collectively invading cells and single cells from the heterogeneous 4T1 cell line and observed extensive transcriptional and epigenetic diversity across these subpopulations. By integrating these datasets, we identified laminin-332 as a protein complex exclusively secreted by collectively invading cells. Live-cell imaging revealed that laminin-332 derived from collectively invading cells increased the velocity and directionality of single cells. Despite collectively invading and single cells having similar expression of the integrin α6β4 dimer, single cells demonstrated higher Rac1 activation upon laminin-332 binding to integrin α6β4. This mechanism suggests a novel commensal relationship between collectively invading and single cells, wherein collectively invading cells promote the invasive potential of single cells through a laminin-332/Rac1 axis.
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Affiliation(s)
- Sung Bo Yoon
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Luxiao Chen
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
| | - Isaac E. Robinson
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Tala O. Khatib
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Robert A. Arthur
- Emory Integrated Computational Core, Emory University, Atlanta, GA, USA
| | - Henry Claussen
- Emory Integrated Computational Core, Emory University, Atlanta, GA, USA
| | - Najdat M. Zohbi
- Graduate Medical Education, Piedmont Macon Medical, Macon, GA, USA
| | - Hao Wu
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Janna K. Mouw
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Adam I. Marcus
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
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2
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Cozzolino K, Sanford L, Hunter S, Molison K, Erickson B, Jones T, Courvan MCS, Ajit D, Galbraith MD, Espinosa JM, Bentley DL, Allen MA, Dowell RD, Taatjes DJ. Mediator kinase inhibition suppresses hyperactive interferon signaling in Down syndrome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.05.547813. [PMID: 37461585 PMCID: PMC10349994 DOI: 10.1101/2023.07.05.547813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Hyperactive interferon (IFN) signaling is a hallmark of Down syndrome (DS), a condition caused by trisomy 21 (T21); strategies that normalize IFN signaling could benefit this population. Mediator-associated kinases CDK8 and CDK19 drive inflammatory responses through incompletely understood mechanisms. Using sibling-matched cell lines with/without T21, we investigated Mediator kinase function in the context of hyperactive IFN in DS over a 45min - 24h timeframe. Activation of IFN-response genes was suppressed in cells treated with the CDK8/CDK19 inhibitor cortistatin A (CA), and this occurred through rapid suppression of IFN-responsive transcription factor activity. Moreover, we discovered that CDK8/CDK19 affect splicing, a novel means by which Mediator kinases control gene expression. To further probe Mediator kinase function, we completed cytokine screens and untargeted metabolomics experiments. Cytokines are master regulators of inflammatory responses; by screening 105 different cytokine proteins, we show that Mediator kinases help drive IFN-dependent cytokine responses at least in part through transcriptional regulation of cytokine genes and receptors. Metabolomics revealed that Mediator kinase inhibition altered core metabolic pathways, including broad up-regulation of anti-inflammatory lipid mediators, whose levels were elevated during hyperactive IFN signaling. A subset of these lipid mediators (e.g. oleamide, desmosterol) serve as ligands for nuclear receptors PPAR and LXR, and activation of these receptors occurred specifically during hyperactive IFN signaling in CA-treated cells, revealing a mechanistic link between Mediator kinase activity and nuclear receptor function. Collectively, our results identify new mechanisms by which CDK8/CDK19 regulate gene expression, and establish that Mediator kinase inhibition antagonizes IFN signaling through transcriptional, metabolic, and cytokine responses, with implications for DS and other chronic inflammatory conditions.
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Affiliation(s)
- Kira Cozzolino
- Dept. of Biochemistry, University of Colorado, Boulder, CO, 80303, USA
| | - Lynn Sanford
- Dept. of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, 80303, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO, 80303, USA
| | - Samuel Hunter
- Dept. of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, 80303, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO, 80303, USA
| | - Kayla Molison
- Dept. of Biochemistry, University of Colorado, Boulder, CO, 80303, USA
| | - Benjamin Erickson
- Dept. Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- UC-Denver RNA Bioscience Initiative
| | - Taylor Jones
- Dept. of Biochemistry, University of Colorado, Boulder, CO, 80303, USA
| | - Meaghan C S Courvan
- Dept. of Biochemistry, University of Colorado, Boulder, CO, 80303, USA
- Dept. of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, 80303, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO, 80303, USA
- Crnic Institute Boulder Branch
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Deepa Ajit
- Metabolon, Inc., Durham, North Carolina, USA
| | - Matthew D Galbraith
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Dept. of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Joaquin M Espinosa
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Dept. of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - David L Bentley
- Dept. Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- UC-Denver RNA Bioscience Initiative
| | - Mary A Allen
- BioFrontiers Institute, University of Colorado, Boulder, CO, 80303, USA
| | - Robin D Dowell
- Dept. of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, 80303, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO, 80303, USA
| | - Dylan J Taatjes
- Dept. of Biochemistry, University of Colorado, Boulder, CO, 80303, USA
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3
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DiCandia MA, Edwards AN, Alcaraz YB, Monteiro MP, Lee CD, Vargas Cuebas G, Bagchi P, McBride SM. A conserved switch controls virulence, sporulation, and motility in C. difficile. PLoS Pathog 2024; 20:e1012224. [PMID: 38739653 PMCID: PMC11115286 DOI: 10.1371/journal.ppat.1012224] [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: 10/09/2023] [Revised: 05/23/2024] [Accepted: 04/25/2024] [Indexed: 05/16/2024] Open
Abstract
Spore formation is required for environmental survival and transmission of the human enteropathogenic Clostridioides difficile. In all bacterial spore formers, sporulation is regulated through activation of the master response regulator, Spo0A. However, the factors and mechanisms that directly regulate C. difficile Spo0A activity are not defined. In the well-studied Bacillus species, Spo0A is directly inactivated by Spo0E, a small phosphatase. To understand Spo0E function in C. difficile, we created a null mutation of the spo0E ortholog and assessed sporulation and physiology. The spo0E mutant produced significantly more spores, demonstrating Spo0E represses C. difficile sporulation. Unexpectedly, the spo0E mutant also exhibited increased motility and toxin production, and enhanced virulence in animal infections. We uncovered that Spo0E interacts with both Spo0A and the toxin and motility regulator, RstA. Direct interactions between Spo0A, Spo0E, and RstA constitute a previously unknown molecular switch that coordinates sporulation with motility and toxin production. Reinvestigation of Spo0E function in B. subtilis revealed that Spo0E induced motility, demonstrating Spo0E regulation of motility and sporulation among divergent species. Further, 3D structural analyses of Spo0E revealed specific and exclusive interactions between Spo0E and binding partners in C. difficile and B. subtilis that provide insight into the conservation of this regulatory mechanism among different species.
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Affiliation(s)
- Michael A. DiCandia
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, United States of America
| | - Adrianne N. Edwards
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, United States of America
| | - Ysabella B. Alcaraz
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, United States of America
| | - Marcos P. Monteiro
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, United States of America
| | - Cheyenne D. Lee
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, United States of America
| | - Germán Vargas Cuebas
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, United States of America
| | - Pritha Bagchi
- Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, United States of America
| | - Shonna M. McBride
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, United States of America
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4
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Knippler CM, Arnst JL, Robinson IE, Matsuk V, Khatib TO, Harvey RD, Shanmugam M, Mouw JK, Fu H, Ganesh T, Marcus AI. Bisbiguanide analogs induce mitochondrial stress to inhibit lung cancer cell invasion. iScience 2024; 27:109591. [PMID: 38632988 PMCID: PMC11022046 DOI: 10.1016/j.isci.2024.109591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 01/18/2024] [Accepted: 03/25/2024] [Indexed: 04/19/2024] Open
Abstract
Targeting cancer metabolism to limit cellular energy and metabolite production is an attractive therapeutic approach. Here, we developed analogs of the bisbiguanide, alexidine, to target lung cancer cell metabolism and assess a structure-activity relationship (SAR). The SAR led to the identification of two analogs, AX-4 and AX-7, that limit cell growth via G1/G0 cell-cycle arrest and are tolerated in vivo with favorable pharmacokinetics. Mechanistic evaluation revealed that AX-4 and AX-7 induce potent mitochondrial defects; mitochondrial cristae were deformed and the mitochondrial membrane potential was depolarized. Additionally, cell metabolism was rewired, as indicated by reduced oxygen consumption and mitochondrial ATP production, with an increase in extracellular lactate. Importantly, AX-4 and AX-7 impacted overall cell behavior, as these compounds reduced collective cell invasion. Taken together, our study establishes a class of bisbiguanides as effective mitochondria and cell invasion disrupters, and proposes bisbiguanides as promising approaches to limiting cancer metastasis.
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Affiliation(s)
- Christina M. Knippler
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Jamie L. Arnst
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
- Department of Medicine, Division of Endocrinology, Emory University, Atlanta, GA 30322, USA
| | - Isaac E. Robinson
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30318, USA
| | - Veronika Matsuk
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
- Graduate Program in Cancer Biology, Emory University, Atlanta, GA 30322, USA
| | - Tala O. Khatib
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
- Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University, Atlanta, GA 30322, USA
| | - R. Donald Harvey
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
- Department of Pharmacology and Chemical Biology, Emory University, Atlanta, GA 30322, USA
| | - Mala Shanmugam
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Janna K. Mouw
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Haian Fu
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
- Department of Pharmacology and Chemical Biology, Emory University, Atlanta, GA 30322, USA
| | - Thota Ganesh
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
- Department of Pharmacology and Chemical Biology, Emory University, Atlanta, GA 30322, USA
| | - Adam I. Marcus
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
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5
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Lee CM, Jarrell ZR, Lee HY, Singer G, Tran VT, Orr M, Jones DP, Go YM. Protein S-palmitoylation enhances profibrotic signaling in response to cadmium. Toxicol Appl Pharmacol 2024; 483:116806. [PMID: 38195004 PMCID: PMC10923080 DOI: 10.1016/j.taap.2024.116806] [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: 09/21/2023] [Revised: 12/26/2023] [Accepted: 01/03/2024] [Indexed: 01/11/2024]
Abstract
Cadmium (Cd) is a naturally occurring, toxic environmental metal found in foods. Humans do not have an efficient mechanism for Cd elimination; thus, Cd burden in humans increases with age. Cell and mouse studies show that Cd burden from low environmental levels of exposure impacts lung cell metabolism, proliferation signaling and cell growth as part of disease-promoting profibrotic responses in the lungs. Prior integrative analysis of metabolomics and transcriptomics identified the zDHHC11 transcript as a central functional hub in response to Cd dose. zDHHC11 encodes a protein S-palmitoyltransferase, but no evidence is available for effects of Cd on protein S-palmitoylation. In the present research, we studied palmitoylation changes in response to Cd and found increased protein S-palmitoylation in human lung fibroblasts that was inhibited by 2-bromopalmitate (2-BP), an irreversible palmitoyltransferase inhibitor. Mass spectrometry-based proteomics showed palmitoylation of proteins involved in divalent metal transport and in fibrotic signaling. Mechanistic studies showed that 2-BP inhibited palmitoylation of divalent metal ion transporter ZIP14 and also inhibited cellular Cd uptake. Transcription analyses showed that Cd stimulated transforming growth factor (TGF)-β1 and β3 expression within 8 h and lung fibrotic markers α-smooth muscle actin, matrix metalloproteinase-2, and collagen 1α1 gene expression and that these effects were blocked by 2-BP. Because 2-BP also blocked palmitoylation of proteins controlled by TGFβ1, these results show that palmitoylation impacts Cd-dependent fibrotic signaling both by enhancing cellular Cd accumulation and by supporting post-translational processing of TGFβ1-dependent proteins.
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Affiliation(s)
- Choon-Myung Lee
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Zachery R Jarrell
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ho Young Lee
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Grant Singer
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - ViLinh Thi Tran
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Michael Orr
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Dean P Jones
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA.
| | - Young-Mi Go
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA.
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6
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Heinrich S, Hondele M, Marchand D, Derrer CP, Zedan M, Oswald A, Malinovska L, Uliana F, Khawaja S, Mancini R, Grunwald D, Weis K. Glucose stress causes mRNA retention in nuclear Nab2 condensates. Cell Rep 2024; 43:113593. [PMID: 38113140 DOI: 10.1016/j.celrep.2023.113593] [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: 03/10/2022] [Revised: 10/12/2023] [Accepted: 11/30/2023] [Indexed: 12/21/2023] Open
Abstract
Nuclear mRNA export via nuclear pore complexes is an essential step in eukaryotic gene expression. Although factors involved in mRNA transport have been characterized, a comprehensive mechanistic understanding of this process and its regulation is lacking. Here, we use single-RNA imaging in yeast to show that cells use mRNA retention to control mRNA export during stress. We demonstrate that, upon glucose withdrawal, the essential RNA-binding factor Nab2 forms RNA-dependent condensate-like structures in the nucleus. This coincides with a reduced abundance of the DEAD-box ATPase Dbp5 at the nuclear pore. Depleting Dbp5, and consequently blocking mRNA export, is necessary and sufficient to trigger Nab2 condensation. The state of Nab2 condensation influences the extent of nuclear mRNA accumulation and can be recapitulated in vitro, where Nab2 forms RNA-dependent liquid droplets. We hypothesize that cells use condensation to regulate mRNA export and control gene expression during stress.
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Affiliation(s)
- Stephanie Heinrich
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland.
| | - Maria Hondele
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland; Biozentrum, Center for Molecular Life Sciences, University of Basel, 4056 Basel, Switzerland
| | - Désirée Marchand
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Carina Patrizia Derrer
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Mostafa Zedan
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Alexandra Oswald
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Liliana Malinovska
- Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Federico Uliana
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Sarah Khawaja
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Roberta Mancini
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - David Grunwald
- University of Massachusetts Chan Medical School, RNA Therapeutics Institute, Worcester, MA 01605, USA
| | - Karsten Weis
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland.
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7
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Han Y, Bagchi P, Yun CC. Regulation of the intestinal Na +/H + exchanger NHE3 by AMP-activated kinase is dependent on phosphorylation of NHE3 at S555 and S563. Am J Physiol Cell Physiol 2024; 326:C50-C59. [PMID: 38047302 PMCID: PMC11192475 DOI: 10.1152/ajpcell.00540.2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 12/05/2023]
Abstract
Electroneutral NaCl transport by Na+/H+ exchanger 3 (NHE3, SLC9A3) is the major Na+ absorptive mechanism in the intestine and decreased NHE3 activity contributes to diarrhea. Patients with diabetes often experience gastrointestinal adverse effects and medications are often a culprit for chronic diarrhea in type 2 diabetes (T2D). We have shown previously that metformin, the most widely prescribed drug for the treatment of T2D, induces diarrhea by inhibition of Na+/H+ exchanger 3 (NHE3) in rodent models of T2D. Metformin was shown to activate AMP-activated protein kinase (AMPK), but AMPK-independent glycemic effects of metformin are also known. The current study is undertaken to determine whether metformin inhibits NHE3 by activation of AMPK and the mechanism by which NHE3 is inhibited by AMPK. Inhibition of NHE3 by metformin was abolished by knockdown of AMPK-α1 or AMPK-α2. AMPK activation by 5-aminoimidazole-4-carboxamide ribonucleoside (AICAR) phosphorylated NHE3 at S555. S555 is the primary site of phosphorylation by protein kinase A (PKA), but AMPK phosphorylated S555 independently of PKA. Using Mass spectrometry, we found S563 as a newly recognized phosphorylation site in NHE3. Altering either S555 or S563 to Ala was sufficient to block the inhibition of NHE3 activity by AMPK. NHE3 inhibition is dependent on ubiquitination by the E3 ubiquitin ligase Nedd4-2 and metformin was shown to induce NHE3 internalization via Nedd4-2-mediated ubiquitination. AICAR did not increase NHE3 ubiquitination when S555 or S563 was mutated. We conclude that AMPK activation inhibits NHE3 activity and NHE3 inhibition is associated with phosphorylation of NHE3 at S555 and S563.NEW & NOTEWORTHY We show that AMP-activated protein kinase (AMPK) phosphorylates NHE3 at S555 and S563 to inhibit NHE3 activity in intestinal epithelial cells. Phosphorylation of NHE3 by AMPK is necessary for ubiquitination of NHE3.
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Affiliation(s)
- Yiran Han
- Gastroenterology Research, Atlanta Veterans Administration Medical Center, Decatur, Georgia, United States
- Division of Digestive Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States
| | - Pritha Bagchi
- Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, United States
| | - C Chris Yun
- Gastroenterology Research, Atlanta Veterans Administration Medical Center, Decatur, Georgia, United States
- Division of Digestive Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia, United States
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8
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Parra-Rivas LA, Madhivanan K, Aulston BD, Wang L, Prakashchand DD, Boyer NP, Saia-Cereda VM, Branes-Guerrero K, Pizzo DP, Bagchi P, Sundar VS, Tang Y, Das U, Scott DA, Rangamani P, Ogawa Y, Subhojit Roy. Serine-129 phosphorylation of α-synuclein is an activity-dependent trigger for physiologic protein-protein interactions and synaptic function. Neuron 2023; 111:4006-4023.e10. [PMID: 38128479 PMCID: PMC10766085 DOI: 10.1016/j.neuron.2023.11.020] [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: 02/28/2023] [Revised: 10/08/2023] [Accepted: 11/19/2023] [Indexed: 12/23/2023]
Abstract
Phosphorylation of α-synuclein at the serine-129 site (α-syn Ser129P) is an established pathologic hallmark of synucleinopathies and a therapeutic target. In physiologic states, only a fraction of α-syn is phosphorylated at this site, and most studies have focused on the pathologic roles of this post-translational modification. We found that unlike wild-type (WT) α-syn, which is widely expressed throughout the brain, the overall pattern of α-syn Ser129P is restricted, suggesting intrinsic regulation. Surprisingly, preventing Ser129P blocked activity-dependent synaptic attenuation by α-syn-thought to reflect its normal function. Exploring mechanisms, we found that neuronal activity augments Ser129P, which is a trigger for protein-protein interactions that are necessary for mediating α-syn function at the synapse. AlphaFold2-driven modeling and membrane-binding simulations suggest a scenario where Ser129P induces conformational changes that facilitate interactions with binding partners. Our experiments offer a new conceptual platform for investigating the role of Ser129 in synucleinopathies, with implications for drug development.
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Affiliation(s)
- Leonardo A Parra-Rivas
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Kayalvizhi Madhivanan
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Brent D Aulston
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Lina Wang
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Dube Dheeraj Prakashchand
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Nicholas P Boyer
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Veronica M Saia-Cereda
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Kristen Branes-Guerrero
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Donald P Pizzo
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Pritha Bagchi
- Emory Integrated Proteomics Core, Emory University, Atlanta, GA, USA
| | - V S Sundar
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Yong Tang
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Utpal Das
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA; Department of Neurosciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - David A Scott
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Yuki Ogawa
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Subhojit Roy
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA; Department of Neurosciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA.
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9
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Jalloh B, Lancaster CL, Rounds JC, Brown BE, Leung SW, Banerjee A, Morton DJ, Bienkowski RS, Fasken MB, Kremsky IJ, Tegowski M, Meyer K, Corbett A, Moberg K. The Drosophila Nab2 RNA binding protein inhibits m 6A methylation and male-specific splicing of Sex lethal transcript in female neuronal tissue. eLife 2023; 12:e64904. [PMID: 37458420 PMCID: PMC10351920 DOI: 10.7554/elife.64904] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 06/23/2023] [Indexed: 07/20/2023] Open
Abstract
The Drosophila polyadenosine RNA binding protein Nab2, which is orthologous to a human protein lost in a form of inherited intellectual disability, controls adult locomotion, axon projection, dendritic arborization, and memory through a largely undefined set of target RNAs. Here, we show a specific role for Nab2 in regulating splicing of ~150 exons/introns in the head transcriptome and focus on retention of a male-specific exon in the sex determination factor Sex-lethal (Sxl) that is enriched in female neurons. Previous studies have revealed that this splicing event is regulated in females by N6-methyladenosine (m6A) modification by the Mettl3 complex. At a molecular level, Nab2 associates with Sxl pre-mRNA in neurons and limits Sxl m6A methylation at specific sites. In parallel, reducing expression of the Mettl3, Mettl3 complex components, or the m6A reader Ythdc1 rescues mutant phenotypes in Nab2 flies. Overall, these data identify Nab2 as an inhibitor of m6A methylation and imply significant overlap between Nab2 and Mettl3 regulated RNAs in neuronal tissue.
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Affiliation(s)
- Binta Jalloh
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
- Graduate Program in Genetics and Molecular Biology, Emory UniversityAtlantaUnited States
| | - Carly L Lancaster
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
- Graduate Program in Biochemistry, Cell and Developmental Biology, Emory UniversityAtlantaUnited States
| | - J Christopher Rounds
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
- Graduate Program in Genetics and Molecular Biology, Emory UniversityAtlantaUnited States
| | - Brianna E Brown
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
| | - Sara W Leung
- Department of Biology, Emory UniversityAtlantaUnited States
| | - Ayan Banerjee
- Department of Biology, Emory UniversityAtlantaUnited States
| | - Derrick J Morton
- Department of Biology, Emory UniversityAtlantaUnited States
- Emory Institutional Research and Academic Career Development Award (IRACDA), Fellowships in Research and Science Teaching (FIRST) Postdoctoral FellowshipAtlantaUnited States
| | - Rick S Bienkowski
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
- Graduate Program in Genetics and Molecular Biology, Emory UniversityAtlantaUnited States
| | - Milo B Fasken
- Department of Biology, Emory UniversityAtlantaUnited States
| | | | - Matthew Tegowski
- Department of Biochemistry, Duke University School of MedicineDurhamUnited States
| | - Kate Meyer
- Department of Biochemistry, Duke University School of MedicineDurhamUnited States
- Department of Neurobiology, Duke University School of MedicineDurhamUnited States
| | - Anita Corbett
- Department of Biology, Emory UniversityAtlantaUnited States
| | - Ken Moberg
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
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10
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Zhao J, Veeranan-Karmegam R, Baker FC, Mysona BA, Bagchi P, Liu Y, Smith SB, Gonsalvez GB, Bollinger KE. Defining the ligand-dependent proximatome of the sigma 1 receptor. Front Cell Dev Biol 2023; 11:1045759. [PMID: 37351276 PMCID: PMC10284605 DOI: 10.3389/fcell.2023.1045759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 05/16/2023] [Indexed: 06/24/2023] Open
Abstract
Sigma 1 Receptor (S1R) is a therapeutic target for a wide spectrum of pathological conditions ranging from neurodegenerative diseases to cancer and COVID-19. S1R is ubiquitously expressed throughout the visceral organs, nervous, immune and cardiovascular systems. It is proposed to function as a ligand-dependent molecular chaperone that modulates multiple intracellular signaling pathways. The purpose of this study was to define the S1R proximatome under native conditions and upon binding to well-characterized ligands. This was accomplished by fusing the biotin ligase, Apex2, to the C terminus of S1R. Cells stably expressing S1R-Apex or a GFP-Apex control were used to map proximal proteins. Biotinylated proteins were labeled under native conditions and in a ligand dependent manner, then purified and identified using quantitative mass spectrometry. Under native conditions, S1R biotinylates over 200 novel proteins, many of which localize within the endomembrane system (endoplasmic reticulum, Golgi, secretory vesicles) and function within the secretory pathway. Under conditions of cellular exposure to either S1R agonist or antagonist, results show enrichment of proteins integral to secretion, extracellular matrix formation, and cholesterol biosynthesis. Notably, Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK9) displays increased binding to S1R under conditions of treatment with Haloperidol, a well-known S1R antagonist; whereas Low density lipoprotein receptor (LDLR) binds more efficiently to S1R upon treatment with (+)-Pentazocine ((+)-PTZ), a classical S1R agonist. Furthermore, we demonstrate that the ligand bound state of S1R correlates with specific changes to the cellular secretome. Our results are consistent with the postulated role of S1R as an intracellular chaperone and further suggest important and novel functionalities related to secretion and cholesterol metabolism.
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Affiliation(s)
- Jing Zhao
- Department of Ophthalmology, Medical College of Georgia at Augusta University, Augusta, GA, United States
- Culver Vision Discovery Institute, Augusta, GA, United States
| | - Rajalakshmi Veeranan-Karmegam
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, GA, United States
| | - Frederick C. Baker
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, GA, United States
| | - Barbara A. Mysona
- Department of Ophthalmology, Medical College of Georgia at Augusta University, Augusta, GA, United States
- Culver Vision Discovery Institute, Augusta, GA, United States
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, GA, United States
| | - Pritha Bagchi
- Emory Integrated Proteomics Core, Emory University, Atlanta, GA, United States
| | - Yutao Liu
- Culver Vision Discovery Institute, Augusta, GA, United States
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, GA, United States
| | - Sylvia B. Smith
- Department of Ophthalmology, Medical College of Georgia at Augusta University, Augusta, GA, United States
- Culver Vision Discovery Institute, Augusta, GA, United States
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, GA, United States
| | - Graydon B. Gonsalvez
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, GA, United States
| | - Kathryn E. Bollinger
- Department of Ophthalmology, Medical College of Georgia at Augusta University, Augusta, GA, United States
- Culver Vision Discovery Institute, Augusta, GA, United States
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, GA, United States
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11
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Kwiatek L, Landry-Voyer AM, Latour M, Yague-Sanz C, Bachand F. PABPN1 prevents the nuclear export of an unspliced RNA with a constitutive transport element and controls human gene expression via intron retention. RNA (NEW YORK, N.Y.) 2023; 29:644-662. [PMID: 36754576 PMCID: PMC10158996 DOI: 10.1261/rna.079294.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/12/2023] [Indexed: 05/06/2023]
Abstract
Intron retention is a type of alternative splicing where one or more introns remain unspliced in a polyadenylated transcript. Although many viral systems are known to translate proteins from mRNAs with retained introns, restriction mechanisms generally prevent export and translation of incompletely spliced mRNAs. Here, we provide evidence that the human nuclear poly(A)-binding protein, PABPN1, functions in such restrictions. Using a reporter construct in which nuclear export of an incompletely spliced mRNA is enhanced by a viral constitutive transport element (CTE), we show that PABPN1 depletion results in a significant increase in export and translation from the unspliced CTE-containing transcript. Unexpectedly, we find that inactivation of poly(A)-tail exosome targeting by depletion of PAXT components had no effect on export and translation of the unspliced reporter mRNA, suggesting a mechanism largely independent of nuclear RNA decay. Interestingly, a PABPN1 mutant selectively defective in stimulating poly(A) polymerase elongation strongly enhanced the expression of the unspliced, but not of intronless, reporter transcripts. Analysis of RNA-seq data also revealed that PABPN1 controls the expression of many human genes via intron retention. Notably, PABPN1-dependent intron retention events mostly affected 3'-terminal introns and were insensitive to PAXT and NEXT deficiencies. Our findings thus disclose a role for PABPN1 in restricting nuclear export of intron-retained transcripts and reinforce the interdependence between terminal intron splicing, 3' end processing, and polyadenylation.
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Affiliation(s)
- Lauren Kwiatek
- RNA Group, Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada J1E 4K8
| | - Anne-Marie Landry-Voyer
- RNA Group, Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada J1E 4K8
| | - Mélodie Latour
- RNA Group, Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada J1E 4K8
| | - Carlo Yague-Sanz
- RNA Group, Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada J1E 4K8
| | - Francois Bachand
- RNA Group, Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada J1E 4K8
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12
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DiCandia MA, Edwards AN, Lee CD, Monteiro MP, Cuebas GNV, Bagchi P, McBride SM. A Conserved Switch Controls Virulence, Sporulation, and Motility in C. difficile. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.28.534590. [PMID: 37034656 PMCID: PMC10081167 DOI: 10.1101/2023.03.28.534590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Spore formation is required for environmental survival and transmission of the human enteropathogenic Clostridioides difficile . In all bacterial spore formers, sporulation is regulated through activation of the master response regulator, Spo0A. However, the factors and mechanisms that directly regulate C. difficile Spo0A activity are not defined. In the well-studied Bacillus species, Spo0A is directly inactivated by Spo0E, a small phosphatase. To understand Spo0E function in C. difficile , we created a null mutation of the spo0E ortholog and assessed sporulation and physiology. The spo0E mutant produced significantly more spores, demonstrating Spo0E represses C. difficile sporulation. Unexpectedly, the spo0E mutant also exhibited increased motility and toxin production, and enhanced virulence in animal infections. We uncovered that Spo0E interacts with both Spo0A and the toxin and motility regulator, RstA. Direct interactions between Spo0A, Spo0E, and RstA constitute a previously unknown molecular switch that coordinates sporulation with motility and toxin production. Reinvestigation of Spo0E function in B. subtilis revealed that Spo0E induced motility, demonstrating Spo0E regulation of motility and sporulation among divergent species. Further, we found that Spo0E orthologs are widespread among prokaryotes, suggesting that Spo0E performs conserved regulatory functions in diverse bacteria.
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13
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Keil P, Wulf A, Kachariya N, Reuscher S, Hühn K, Silbern I, Altmüller J, Keller M, Stehle R, Zarnack K, Sattler M, Urlaub H, Sträßer K. Npl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA. Nucleic Acids Res 2022; 51:831-851. [PMID: 36583366 PMCID: PMC9881175 DOI: 10.1093/nar/gkac1206] [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: 07/22/2022] [Revised: 11/25/2022] [Accepted: 12/07/2022] [Indexed: 12/31/2022] Open
Abstract
RNA-binding proteins (RBPs) control every RNA metabolic process by multiple protein-RNA and protein-protein interactions. Their roles have largely been analyzed by crude mutations, which abrogate multiple functions at once and likely impact the structural integrity of the large ribonucleoprotein particles (RNPs) these proteins function in. Using UV-induced RNA-protein crosslinking of entire cells, protein complex purification and mass spectrometric analysis, we identified >100 in vivo RNA crosslinks in 16 nuclear mRNP components in Saccharomyces cerevisiae. For functional analysis, we chose Npl3, which displayed crosslinks in its two RNA recognition motifs (RRMs) and in the connecting flexible linker region. Both RRM domains and the linker uniquely contribute to RNA recognition as revealed by NMR and structural analyses. Interestingly, mutations in these regions cause different phenotypes, indicating distinct functions of the different RNA-binding domains. Notably, an npl3-Linker mutation strongly impairs recruitment of several mRNP components to chromatin and incorporation of other mRNP components into nuclear mRNPs, establishing a so far unknown function of Npl3 in nuclear mRNP assembly. Taken together, our integrative analysis uncovers a specific function of the RNA-binding activity of the nuclear mRNP component Npl3. This approach can be readily applied to RBPs in any RNA metabolic process.
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Affiliation(s)
| | | | | | - Samira Reuscher
- Buchmann Institute for Molecular Life Sciences (BMLS) & Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt a.M., Germany
| | - Kristin Hühn
- Institute of Biochemistry, FB08, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Ivan Silbern
- Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Goettingen, University Medical Center Goettingen, Institute of Clinical Chemistry, Robert-Koch-Strasse 40, 37075 Goettingen, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), University of Cologne, Weyertal 115b, 50931 Cologne, Germany,Technology platform genomics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Mario Keller
- Buchmann Institute for Molecular Life Sciences (BMLS) & Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt a.M., Germany
| | - Ralf Stehle
- Bavarian NMR Center (BNMRZ), Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany,Institute of Structural Biology, Helmholtz Center Munich, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS) & Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt a.M., Germany,Cardio-Pulmonary Institute (CPI), EXC 2026, 35392 Giessen, Germany
| | | | | | - Katja Sträßer
- To whom correspondence should be addressed. Tel: +49 641 99 35400; Fax: +49 641 99 35409;
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14
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Bensidoun P, Reiter T, Montpetit B, Zenklusen D, Oeffinger M. Nuclear mRNA metabolism drives selective basket assembly on a subset of nuclear pore complexes in budding yeast. Mol Cell 2022; 82:3856-3871.e6. [PMID: 36220102 PMCID: PMC10300651 DOI: 10.1016/j.molcel.2022.09.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 06/24/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022]
Abstract
To determine which transcripts should reach the cytoplasm for translation, eukaryotic cells have established mechanisms to regulate selective mRNA export through the nuclear pore complex (NPC). The nuclear basket, a substructure of the NPC protruding into the nucleoplasm, is thought to function as a stable platform where mRNA-protein complexes (mRNPs) are rearranged and undergo quality control prior to export, ensuring that only mature mRNAs reach the cytoplasm. Here, we use proteomic, genetic, live-cell, and single-molecule resolution microscopy approaches in budding yeast to demonstrate that basket formation is dependent on RNA polymerase II transcription and subsequent mRNP processing. We further show that while all NPCs can bind Mlp1, baskets assemble only on a subset of nucleoplasmic NPCs, and these basket-containing NPCs associate a distinct protein and RNA interactome. Taken together, our data point toward NPC heterogeneity and an RNA-dependent mechanism for functionalization of NPCs in budding yeast through nuclear basket assembly.
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Affiliation(s)
- Pierre Bensidoun
- Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada; Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Taylor Reiter
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, USA
| | - Ben Montpetit
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, USA
| | - Daniel Zenklusen
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, QC, Canada.
| | - Marlene Oeffinger
- Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada; Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, QC, Canada; Division of Experimental Medicine, McGill University, Montréal, QC, Canada.
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15
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Rosa-Mercado NA, Steitz JA. Who let the DoGs out? - biogenesis of stress-induced readthrough transcripts. Trends Biochem Sci 2022; 47:206-217. [PMID: 34489151 PMCID: PMC8840951 DOI: 10.1016/j.tibs.2021.08.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/27/2021] [Accepted: 08/10/2021] [Indexed: 01/22/2023]
Abstract
Readthrough transcription caused by inefficient 3'-end cleavage of nascent mRNAs has emerged as a hallmark of the mammalian cellular stress response and results in the production of long noncoding RNAs known as downstream-of-gene (DoG)-containing transcripts. DoGs arise from around 10% of human protein-coding genes and are retained in the nucleus. They are produced minutes after cell exposure to stress and can be detected hours after stress removal. However, their biogenesis and the role(s) that DoGs or their production play in the cellular stress response are incompletely understood. We discuss findings that implicate host and viral proteins in the mechanisms underlying DoG production, as well as the transcriptional landscapes that accompany DoG induction under different stress conditions.
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Affiliation(s)
- Nicolle A Rosa-Mercado
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT, USA.
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16
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Rounds JC, Corgiat EB, Ye C, Behnke JA, Kelly SM, Corbett AH, Moberg KH. The disease-associated proteins Drosophila Nab2 and Ataxin-2 interact with shared RNAs and coregulate neuronal morphology. Genetics 2022; 220:iyab175. [PMID: 34791182 PMCID: PMC8733473 DOI: 10.1093/genetics/iyab175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 09/27/2021] [Indexed: 01/05/2023] Open
Abstract
Nab2 encodes the Drosophila melanogaster member of a conserved family of zinc finger polyadenosine RNA-binding proteins (RBPs) linked to multiple steps in post-transcriptional regulation. Mutation of the Nab2 human ortholog ZC3H14 gives rise to an autosomal recessive intellectual disability but understanding of Nab2/ZC3H14 function in metazoan nervous systems is limited, in part because no comprehensive identification of metazoan Nab2/ZC3H14-associated RNA transcripts has yet been conducted. Moreover, many Nab2/ZC3H14 functional protein partnerships remain unidentified. Here, we present evidence that Nab2 genetically interacts with Ataxin-2 (Atx2), which encodes a neuronal translational regulator, and that these factors coordinately regulate neuronal morphology, circadian behavior, and adult viability. We then present the first high-throughput identifications of Nab2- and Atx2-associated RNAs in Drosophila brain neurons using RNA immunoprecipitation-sequencing (RIP-Seq). Critically, the RNA interactomes of each RBP overlap, and Nab2 exhibits high specificity in its RNA associations in neurons in vivo, associating with a small fraction of all polyadenylated RNAs. The identities of shared associated transcripts (e.g., drk, me31B, stai) and of transcripts specific to Nab2 or Atx2 (e.g., Arpc2 and tea) promise insight into neuronal functions of, and genetic interactions between, each RBP. Consistent with prior biochemical studies, Nab2-associated neuronal RNAs are overrepresented for internal A-rich motifs, suggesting these sequences may partially mediate Nab2 target selection. These data support a model where Nab2 functionally opposes Atx2 in neurons, demonstrate Nab2 shares associated neuronal RNAs with Atx2, and reveal Drosophila Nab2 associates with a more specific subset of polyadenylated mRNAs than its polyadenosine affinity alone may suggest.
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Affiliation(s)
- J Christopher Rounds
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Edwin B Corgiat
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Changtian Ye
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Joseph A Behnke
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Seth M Kelly
- Department of Biology, The College of Wooster, Wooster, OH 44691, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Kenneth H Moberg
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
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17
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Baker FC, Neiswender H, Veeranan-Karmegam R, Gonsalvez GB. In vivo proximity biotin ligation identifies the interactome of Egalitarian, a Dynein cargo adaptor. Development 2021; 148:dev199935. [PMID: 35020877 PMCID: PMC8645207 DOI: 10.1242/dev.199935] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/18/2021] [Indexed: 06/21/2024]
Abstract
Numerous motors of the Kinesin family contribute to plus-end-directed microtubule transport. However, almost all transport towards the minus-end of microtubules involves Dynein. Understanding the mechanism by which Dynein transports this vast diversity of cargo is the focus of intense research. In selected cases, adaptors that link a particular cargo with Dynein have been identified. However, the sheer diversity of cargo suggests that additional adaptors must exist. We used the Drosophila egg chamber as a model to address this issue. Within egg chambers, Egalitarian is required for linking mRNA with Dynein. However, in the absence of Egalitarian, Dynein transport into the oocyte is severely compromised. This suggests that additional cargoes might be linked to Dynein in an Egalitarian-dependent manner. We therefore used proximity biotin ligation to define the interactome of Egalitarian. This approach yielded several novel interacting partners, including P body components and proteins that associate with Dynein in mammalian cells. We also devised and validated a nanobody-based proximity biotinylation strategy that can be used to define the interactome of any GFP-tagged protein.
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Affiliation(s)
| | | | | | - Graydon B. Gonsalvez
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA 30912, USA
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18
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Lu YY, Krebber H. Nuclear mRNA Quality Control and Cytoplasmic NMD Are Linked by the Guard Proteins Gbp2 and Hrb1. Int J Mol Sci 2021; 22:ijms222011275. [PMID: 34681934 PMCID: PMC8541090 DOI: 10.3390/ijms222011275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/13/2021] [Accepted: 10/17/2021] [Indexed: 12/23/2022] Open
Abstract
Pre-mRNA splicing is critical for cells, as defects in this process can lead to altered open reading frames and defective proteins, potentially causing neurodegenerative diseases and cancer. Introns are removed in the nucleus and splicing is documented by the addition of exon-junction-complexes (EJCs) at exon-exon boundaries. This “memory” of splicing events is important for the ribosome, which translates the RNAs in the cytoplasm. In case a stop codon was detected before an EJC, translation is blocked and the RNA is eliminated by the nonsense-mediated decay (NMD). In the model organism Saccharomyces cerevisiae, two guard proteins, Gbp2 and Hrb1, have been identified as nuclear quality control factors for splicing. In their absence, intron-containing mRNAs leak into the cytoplasm. Their presence retains transcripts until the process is completed and they release the mRNAs by recruitment of the export factor Mex67. On transcripts that experience splicing problems, these guard proteins recruit the nuclear RNA degradation machinery. Interestingly, they continue their quality control function on exported transcripts. They support NMD by inhibiting translation and recruiting the cytoplasmic degradation factors. In this way, they link the nuclear and cytoplasmic quality control systems. These discoveries are also intriguing for humans, as homologues of these guard proteins are present also in multicellular organisms. Here, we provide an overview of the quality control mechanisms of pre-mRNA splicing, and present Gbp2 and Hrb1, as well as their human counterparts, as important players in these pathways.
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19
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Gorkhali R, Tian L, Dong B, Bagchi P, Deng X, Pawar S, Duong D, Fang N, Seyfried N, Yang J. Extracellular calcium alters calcium-sensing receptor network integrating intracellular calcium-signaling and related key pathway. Sci Rep 2021; 11:20576. [PMID: 34663830 PMCID: PMC8523568 DOI: 10.1038/s41598-021-00067-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 09/29/2021] [Indexed: 12/21/2022] Open
Abstract
G-protein-coupled receptors (GPCRs) are a target for over 34% of current drugs. The calcium-sensing receptor (CaSR), a family C GPCR, regulates systemic calcium (Ca2+) homeostasis that is critical for many physiological, calciotropical, and noncalciotropical outcomes in multiple organs. However, the mechanisms by which extracellular Ca2+ (Ca2+ex) and the CaSR mediate networks of intracellular Ca2+-signaling and players involved throughout the life cycle of CaSR are largely unknown. Here we report the first CaSR protein–protein interactome with 94 novel putative and 8 previously published interactors using proteomics. Ca2+ex promotes enrichment of 66% of the identified CaSR interactors, pertaining to Ca2+ dynamics, endocytosis, degradation, trafficking, and primarily to protein processing in the endoplasmic reticulum (ER). These enhanced ER-related processes are governed by Ca2+ex-activated CaSR which directly modulates ER-Ca2+ (Ca2+ER), as monitored by a novel ER targeted Ca2+-sensor. Moreover, we validated the Ca2+ex dependent colocalizations and interactions of CaSR with ER-protein processing chaperone, 78-kDa glucose regulated protein (GRP78), and with trafficking-related protein. Live cell imaging results indicated that CaSR and vesicle-associated membrane protein-associated A (VAPA) are inter-dependent during Ca2+ex induced enhancement of near-cell membrane expression. This study significantly extends the repertoire of the CaSR interactome and reveals likely novel players and pathways of CaSR participating in Ca2+ER dynamics, agonist mediated ER-protein processing and surface expression.
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Affiliation(s)
- Rakshya Gorkhali
- Department of Chemistry, Center of Diagnostics and Therapeutics, Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA, 30303, USA
| | - Li Tian
- Department of Chemistry, Center of Diagnostics and Therapeutics, Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA, 30303, USA
| | - Bin Dong
- Department of Chemistry, Center of Diagnostics and Therapeutics, Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA, 30303, USA
| | - Pritha Bagchi
- Emory Integrated Proteomics Core, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Xiaonan Deng
- Department of Chemistry, Center of Diagnostics and Therapeutics, Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA, 30303, USA
| | - Shrikant Pawar
- Department of Biology, Center of Diagnostics and Therapeutics, Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA, 30303, USA
| | - Duc Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Ning Fang
- Department of Chemistry, Center of Diagnostics and Therapeutics, Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA, 30303, USA
| | - Nicholas Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jenny Yang
- Department of Chemistry, Center of Diagnostics and Therapeutics, Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA, 30303, USA.
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20
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Corgiat EB, List SM, Rounds JC, Corbett AH, Moberg KH. The RNA-binding protein Nab2 regulates the proteome of the developing Drosophila brain. J Biol Chem 2021; 297:100877. [PMID: 34139237 PMCID: PMC8260979 DOI: 10.1016/j.jbc.2021.100877] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 06/07/2021] [Accepted: 06/13/2021] [Indexed: 12/14/2022] Open
Abstract
The human ZC3H14 gene, which encodes a ubiquitously expressed polyadenosine zinc finger RNA-binding protein, is mutated in an inherited form of autosomal recessive, nonsyndromic intellectual disability. To gain insight into neurological functions of ZC3H14, we previously developed a Drosophila melanogaster model of ZC3H14 loss by deleting the fly ortholog, Nab2. Studies in this invertebrate model revealed that Nab2 controls final patterns of neuron projection within fully developed adult brains, but the role of Nab2 during development of the Drosophila brain is not known. Here, we identify roles for Nab2 in controlling the dynamic growth of axons in the developing brain mushroom bodies, which support olfactory learning and memory, and regulating abundance of a small fraction of the total brain proteome. The group of Nab2-regulated brain proteins, identified by quantitative proteomic analysis, includes the microtubule-binding protein Futsch, the neuronal Ig-family transmembrane protein turtle, the glial:neuron adhesion protein contactin, the Rac GTPase-activating protein tumbleweed, and the planar cell polarity factor Van Gogh, which collectively link Nab2 to the processes of brain morphogenesis, neuroblast proliferation, circadian sleep/wake cycles, and synaptic development. Overall, these data indicate that Nab2 controls the abundance of a subset of brain proteins during the active process of wiring the pupal brain mushroom body and thus provide a window into potentially conserved functions of the Nab2/ZC3H14 RNA-binding proteins in neurodevelopment.
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Affiliation(s)
- Edwin B Corgiat
- Department of Cell Biology, Emory University School of Medicine, Emory University, Atlanta, Georgia, USA; Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia, USA; Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Sara M List
- Graduate Program in Neuroscience, Emory University, Atlanta, Georgia, USA
| | - J Christopher Rounds
- Department of Cell Biology, Emory University School of Medicine, Emory University, Atlanta, Georgia, USA; Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia, USA; Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, Georgia, USA.
| | - Kenneth H Moberg
- Department of Cell Biology, Emory University School of Medicine, Emory University, Atlanta, Georgia, USA.
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21
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Bensidoun P, Zenklusen D, Oeffinger M. Choosing the right exit: How functional plasticity of the nuclear pore drives selective and efficient mRNA export. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1660. [PMID: 33938148 DOI: 10.1002/wrna.1660] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/30/2021] [Accepted: 04/04/2021] [Indexed: 12/17/2022]
Abstract
The nuclear pore complex (NPC) serves as a central gate for mRNAs to transit from the nucleus to the cytoplasm. The ability for mRNAs to get exported is linked to various upstream nuclear processes including co-transcriptional RNP assembly and processing, and only export competent mRNPs are thought to get access to the NPC. While the nuclear pore is generally viewed as a monolithic structure that serves as a mediator of transport driven by transport receptors, more recent evidence suggests that the NPC might be more heterogenous than previously believed, both in its composition or in the selective treatment of cargo that seek access to the pore, providing functional plasticity to mRNA export. In this review, we consider the interconnected processes of nuclear mRNA metabolism that contribute and mediate export competence. Furthermore, we examine different aspects of NPC heterogeneity, including the role of the nuclear basket and its associated complexes in regulating selective and/or efficient binding to and transport through the pore. This article is categorized under: RNA Export and Localization > Nuclear Export/Import RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Pierre Bensidoun
- Systems Biology, Institut de Recherches Cliniques de Montréal, Montréal, Canada.,Département de Biochimie et Médecine Moléculaire, Faculté de médecine, Université de Montréal, Montréal, Canada
| | - Daniel Zenklusen
- Département de Biochimie et Médecine Moléculaire, Faculté de médecine, Université de Montréal, Montréal, Canada
| | - Marlene Oeffinger
- Systems Biology, Institut de Recherches Cliniques de Montréal, Montréal, Canada.,Département de Biochimie et Médecine Moléculaire, Faculté de médecine, Université de Montréal, Montréal, Canada.,Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Canada
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22
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Alqawlaq S, Livne-Bar I, Williams D, D'Ercole J, Leung SW, Chan D, Tuccitto A, Datti A, Wrana JL, Corbett AH, Schmitt-Ulms G, Sivak JM. An endogenous PI3K interactome promoting astrocyte-mediated neuroprotection identifies a novel association with RNA-binding protein ZC3H14. J Biol Chem 2021; 296:100118. [PMID: 33234594 PMCID: PMC7948738 DOI: 10.1074/jbc.ra120.015389] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 11/06/2022] Open
Abstract
Astrocytes can support neuronal survival through a range of secreted signals that protect against neurotoxicity, oxidative stress, and apoptotic cascades. Thus, analyzing the effects of the astrocyte secretome may provide valuable insight into these neuroprotective mechanisms. Previously, we characterized a potent neuroprotective activity mediated by retinal astrocyte conditioned media (ACM) on retinal and cortical neurons in metabolic stress models. However, the molecular mechanism underlying this complex activity in neuronal cells has remained unclear. Here, a chemical genetics screen of kinase inhibitors revealed phosphoinositide 3-kinase (PI3K) as a central player transducing ACM-mediated neuroprotection. To identify additional proteins contributing to the protective cascade, endogenous PI3K was immunoprecipitated from neuronal cells exposed to ACM or control media, followed by MS/MS proteomic analyses. These data pointed toward a relatively small number of proteins that coimmunoprecipitated with PI3K, and surprisingly only five were regulated by the ACM signal. These hits included expected PI3K interactors, such as the platelet-derived growth factor receptor A (PDGFRA), as well as novel RNA-binding protein interactors ZC3H14 (zinc finger CCCH-type containing 14) and THOC1 (THO complex protein 1). In particular, ZC3H14 has recently emerged as an important RNA-binding protein with multiple roles in posttranscriptional regulation. In validation studies, we show that PI3K recruitment of ZC3H14 is necessary for PDGF-induced neuroprotection and that this interaction is present in primary retinal ganglion cells. Thus, we identified a novel non-cell autonomous neuroprotective signaling cascade mediated through PI3K that requires recruitment of ZC3H14 and may present a promising strategy to promote astrocyte-secreted prosurvival signals.
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Affiliation(s)
- Samih Alqawlaq
- Department of Vision Science, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada; Department of Ophthalmology and Vision Science, University of Toronto School of Medicine, Toronto, Ontario, Canada
| | - Izhar Livne-Bar
- Department of Vision Science, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada; Department of Ophthalmology and Vision Science, University of Toronto School of Medicine, Toronto, Ontario, Canada
| | - Declan Williams
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Ontario, Canada
| | - Joseph D'Ercole
- Department of Vision Science, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada; Department of Ophthalmology and Vision Science, University of Toronto School of Medicine, Toronto, Ontario, Canada
| | - Sara W Leung
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Darren Chan
- Department of Vision Science, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada; Department of Ophthalmology and Vision Science, University of Toronto School of Medicine, Toronto, Ontario, Canada
| | - Alessandra Tuccitto
- Department of Vision Science, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada; Department of Ophthalmology and Vision Science, University of Toronto School of Medicine, Toronto, Ontario, Canada
| | - Alessandro Datti
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Jeffrey L Wrana
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Gerold Schmitt-Ulms
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Ontario, Canada
| | - Jeremy M Sivak
- Department of Vision Science, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada; Department of Ophthalmology and Vision Science, University of Toronto School of Medicine, Toronto, Ontario, Canada.
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23
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Wu M, Karadoulama E, Lloret-Llinares M, Rouviere JO, Vaagensø CS, Moravec M, Li B, Wang J, Wu G, Gockert M, Pelechano V, Jensen TH, Sandelin A. The RNA exosome shapes the expression of key protein-coding genes. Nucleic Acids Res 2020; 48:8509-8528. [PMID: 32710631 PMCID: PMC7470964 DOI: 10.1093/nar/gkaa594] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/29/2020] [Accepted: 07/03/2020] [Indexed: 12/20/2022] Open
Abstract
The ribonucleolytic exosome complex is central for nuclear RNA degradation, primarily targeting non-coding RNAs. Still, the nuclear exosome could have protein-coding (pc) gene-specific regulatory activities. By depleting an exosome core component, or components of exosome adaptor complexes, we identify ∼2900 transcription start sites (TSSs) from within pc genes that produce exosome-sensitive transcripts. At least 1000 of these overlap with annotated mRNA TSSs and a considerable portion of their transcripts share the annotated mRNA 3′ end. We identify two types of pc-genes, both employing a single, annotated TSS across cells, but the first type primarily produces full-length, exosome-sensitive transcripts, whereas the second primarily produces prematurely terminated transcripts. Genes within the former type often belong to immediate early response transcription factors, while genes within the latter are likely transcribed as a consequence of their proximity to upstream TSSs on the opposite strand. Conversely, when genes have multiple active TSSs, alternative TSSs that produce exosome-sensitive transcripts typically do not contribute substantially to overall gene expression, and most such transcripts are prematurely terminated. Our results display a complex landscape of sense transcription within pc-genes and imply a direct role for nuclear RNA turnover in the regulation of a subset of pc-genes.
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Affiliation(s)
- Mengjun Wu
- The Bioinformatics Centre, Department of Biology and Biotech and Research Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
| | - Evdoxia Karadoulama
- The Bioinformatics Centre, Department of Biology and Biotech and Research Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark
| | - Marta Lloret-Llinares
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark.,European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jerome Olivier Rouviere
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark
| | - Christian Skov Vaagensø
- The Bioinformatics Centre, Department of Biology and Biotech and Research Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
| | - Martin Moravec
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark
| | - Bingnan Li
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna 171 65, Sweden
| | - Jingwen Wang
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna 171 65, Sweden
| | - Guifen Wu
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark
| | - Maria Gockert
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna 171 65, Sweden
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology and Biotech and Research Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
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24
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A Genetic Screen Links the Disease-Associated Nab2 RNA-Binding Protein to the Planar Cell Polarity Pathway in Drosophila melanogaster. G3-GENES GENOMES GENETICS 2020; 10:3575-3583. [PMID: 32817074 PMCID: PMC7534439 DOI: 10.1534/g3.120.401637] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Mutations in the gene encoding the ubiquitously expressed RNA-binding protein ZC3H14 result in a non-syndromic form of autosomal recessive intellectual disability in humans. Studies in Drosophila have defined roles for the ZC3H14 ortholog, Nab2 (aka Drosophila Nab2 or dNab2), in axon guidance and memory due in part to interaction with a second RNA-binding protein, the fly Fragile X homolog Fmr1, and coregulation of shared Nab2-Fmr1 target mRNAs. Despite these advances, neurodevelopmental mechanisms that underlie defective axonogenesis in Nab2 mutants remain undefined. Nab2 null phenotypes in the brain mushroom bodies (MBs) resemble defects caused by alleles that disrupt the planar cell polarity (PCP) pathway, which regulates planar orientation of static and motile cells via a non-canonical arm of the Wnt/Wg pathway. A kinked bristle phenotype in surviving Nab2 mutant adults additionally suggests a defect in F-actin polymerization and bundling, a PCP-regulated processes. To test for Nab2-PCP genetic interactions, a collection of PCP mutant alleles was screened for modification of a rough-eye phenotype produced by Nab2 overexpression in the eye (GMR> Nab2) and, subsequently, for modification of a viability defect among Nab2 nulls. Multiple PCP alleles dominantly modify GMR> Nab2 eye roughening and a subset rescue low survival and thoracic bristle kinking in Nab2 zygotic nulls. Collectively, these genetic interactions identify the PCP pathway as a potential target of the Nab2 RNA-binding protein in developing eye and wing tissues and suggest that altered PCP signaling could contribute to neurological defects that result from loss of Drosophila Nab2 or its vertebrate ortholog ZC3H14.
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25
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Alpert T, Straube K, Carrillo Oesterreich F, Herzel L, Neugebauer KM. Widespread Transcriptional Readthrough Caused by Nab2 Depletion Leads to Chimeric Transcripts with Retained Introns. Cell Rep 2020; 33:108324. [PMID: 33113357 DOI: 10.1016/j.celrep.2020.108324] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 09/15/2020] [Accepted: 10/07/2020] [Indexed: 01/26/2023] Open
Abstract
Nascent RNA sequencing has revealed that pre-mRNA splicing can occur shortly after introns emerge from RNA polymerase II (RNA Pol II). Differences in co-transcriptional splicing profiles suggest regulation by cis- and/or trans-acting factors. Here, we use single-molecule intron tracking (SMIT) to identify a cohort of regulators by machine learning in budding yeast. Of these, Nab2 displays reduced co-transcriptional splicing when depleted. Unexpectedly, these splicing defects are attributable to aberrant "intrusive" transcriptional readthrough from upstream genes, as revealed by long-read sequencing. Transcripts that originate from the intron-containing gene's own transcription start site (TSS) are efficiently spliced, indicating no direct role of Nab2 in splicing per se. This work highlights the coupling between transcription, splicing, and 3' end formation in the context of gene organization along chromosomes. We conclude that Nab2 is required for proper 3' end processing, which ensures gene-specific control of co-transcriptional RNA processing.
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Affiliation(s)
- Tara Alpert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Korinna Straube
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | | | - Lydia Herzel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
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26
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Minocha R, Popova V, Kopytova D, Misiak D, Hüttelmaier S, Georgieva S, Sträßer K. Mud2 functions in transcription by recruiting the Prp19 and TREX complexes to transcribed genes. Nucleic Acids Res 2019; 46:9749-9763. [PMID: 30053068 PMCID: PMC6182176 DOI: 10.1093/nar/gky640] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 07/20/2018] [Indexed: 01/31/2023] Open
Abstract
The different steps of gene expression are intimately linked to coordinate and regulate this complex process. During transcription, numerous RNA-binding proteins are already loaded onto the nascent mRNA and package the mRNA into a messenger ribonucleoprotein particle (mRNP). These RNA-binding proteins are often also involved in other steps of gene expression than mRNA packaging. For example, TREX functions in transcription, mRNP packaging and nuclear mRNA export. Previously, we showed that the Prp19 splicing complex (Prp19C) is needed for efficient transcription as well as TREX occupancy at transcribed genes. Here, we show that the splicing factor Mud2 interacts with Prp19C and is needed for Prp19C occupancy at transcribed genes in Saccharomyces cerevisiae. Interestingly, Mud2 is not only recruited to intron-containing but also to intronless genes indicating a role in transcription. Indeed, we show for the first time that Mud2 functions in transcription. Furthermore, these functions of Mud2 are likely evolutionarily conserved as Mud2 is also recruited to an intronless gene and interacts with Prp19C in Drosophila melanogaster. Taken together, we classify Mud2 as a novel transcription factor that is necessary for the recruitment of mRNA-binding proteins to the transcription machinery. Thus, Mud2 is a multifunctional protein important for transcription, splicing and most likely also mRNP packaging.
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Affiliation(s)
- Rashmi Minocha
- Institute of Biochemistry, Justus Liebig University, Giessen 35392, Germany
| | - Varvara Popova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Daria Kopytova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Danny Misiak
- Institute of Molecular Medicine, Martin-Luther-University Halle Wittenberg, Halle 06120, Germany
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Martin-Luther-University Halle Wittenberg, Halle 06120, Germany
| | - Sofia Georgieva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Katja Sträßer
- Institute of Biochemistry, Justus Liebig University, Giessen 35392, Germany
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27
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Morris KJ, Corbett AH. The polyadenosine RNA-binding protein ZC3H14 interacts with the THO complex and coordinately regulates the processing of neuronal transcripts. Nucleic Acids Res 2019; 46:6561-6575. [PMID: 29912477 PMCID: PMC6061872 DOI: 10.1093/nar/gky446] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 06/13/2018] [Indexed: 12/14/2022] Open
Abstract
The polyadenosine RNA-binding protein ZC3H14 is important in RNA processing. Although ZC3H14 is ubiquitously expressed, mutation of the ZC3H14 gene causes a non-syndromic form of intellectual disability. Here, we examine the function of ZC3H14 in the brain by identifying ZC3H14-interacting proteins using unbiased mass spectrometry. Through this analysis, we identified physical interactions between ZC3H14 and multiple RNA processing factors. Notably, proteins that comprise the THO complex were amongst the most enriched proteins. We demonstrate that ZC3H14 physically interacts with THO components and that these proteins are required for proper RNA processing, as loss of ZC3H14 or THO components leads to extended bulk poly(A) tail length. Furthermore, we identified the transcripts Atp5g1 and Psd95 as shared RNA targets of ZC3H14 and the THO complex. Our data suggest that ZC3H14 and the THO complex are important for proper processing of Atp5g1 and Psd95 RNA, as depletion of ZC3H14 or THO components leads to decreased steady-state levels of each mature transcript accompanied by accumulation of Atp5g1 and Psd95 pre-mRNA in the cytoplasm. Taken together, this work provides the first unbiased identification of nuclear ZC3H14-interacting proteins from the brain and links the functions of ZC3H14 and the THO complex in the processing of RNA.
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Affiliation(s)
- Kevin J Morris
- Department of Biology, Emory University, Atlanta, GA 30322, USA.,Graduate Program in Biochemistry, Cell and Developmental Biology, James T. Laney Graduate School, Emory University, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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28
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Abstract
In eukaryotes, the separation of translation from transcription by the nuclear envelope enables mRNA modifications such as capping, splicing, and polyadenylation. These modifications are mediated by a spectrum of ribonuclear proteins that associate with preRNA transcripts, coordinating the different steps and coupling them to nuclear export, ensuring that only mature transcripts reach the cytoplasmic translation machinery. Although the components of this machinery have been identified and considerable functional insight has been achieved, a number of questions remain outstanding about mRNA nuclear export and how it is integrated into the nuclear phase of the gene expression pathway. Nuclear export factors mediate mRNA transit through nuclear pores to the cytoplasm, after which these factors are removed from the mRNA, preventing transcripts from returning to the nucleus. However, as outlined in this review, several aspects of the mechanism by which transport factor binding and release are mediated remain unclear, as are the roles of accessory nuclear components in these processes. Moreover, the mechanisms by which completion of mRNA splicing and polyadenylation are recognized, together with how they are coordinated with nuclear export, also remain only partially characterized. One attractive hypothesis is that dissociating poly(A) polymerase from the cleavage and polyadenylation machinery could signal completion of mRNA maturation and thereby provide a mechanism for initiating nuclear export. The impressive array of genetic, molecular, cellular, and structural data that has been generated about these systems now provides many of the tools needed to define the precise mechanisms involved in these processes and how they are integrated.
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Affiliation(s)
- Murray Stewart
- From the MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
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29
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Fasken MB, Corbett AH, Stewart M. Structure-function relationships in the Nab2 polyadenosine-RNA binding Zn finger protein family. Protein Sci 2019; 28:513-523. [PMID: 30578643 PMCID: PMC6371209 DOI: 10.1002/pro.3565] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 12/15/2018] [Accepted: 12/17/2018] [Indexed: 12/12/2022]
Abstract
The poly(A) RNA binding Zn finger ribonucleoprotein Nab2 functions to control the length of 3' poly(A) tails in Saccharomyces cerevisiae as well as contributing to the integration of the nuclear export of mature mRNA with preceding steps in the nuclear phase of the gene expression pathway. Nab2 is constructed from an N-terminal PWI-fold domain, followed by QQQP and RGG motifs and then seven CCCH Zn fingers. The nuclear pore-associated proteins Gfd1 and Mlp1 bind to opposite sides of the Nab2 N-terminal domain and function in the nuclear export of mRNA, whereas the Zn fingers, especially fingers 5-7, bind to A-rich regions of mature transcripts and function to regulate poly(A) tail length as well as mRNA compaction prior to nuclear export. Nab2 Zn fingers 5-7 have a defined spatial arrangement, with fingers 5 and 7 arranged on one side of the cluster and finger 6 on the other side. This spatial arrangement facilitates the dimerization of Nab2 when bound to adenine-rich RNAs and regulates both the termination of 3' polyadenylation and transcript compaction. Nab2 also functions to coordinate steps in the nuclear phase of the gene expression pathway, such as splicing and polyadenylation, with the generation of mature mRNA and its nuclear export. Nab2 orthologues in higher Eukaryotes have similar domain structures and play roles associated with the regulation of splicing and polyadenylation. Importantly, mutations in the gene encoding the human Nab2 orthologue ZC3H14 and cause intellectual disability.
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Affiliation(s)
- Milo B Fasken
- Department of Biology, Emory University, Atlanta, Georgia 30322
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, Georgia 30322
| | - Murray Stewart
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
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30
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Escaping nuclear decay: the significance of mRNA export for gene expression. Curr Genet 2018; 65:473-476. [DOI: 10.1007/s00294-018-0913-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 11/24/2018] [Accepted: 11/28/2018] [Indexed: 12/12/2022]
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31
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Tudek A, Lloret-Llinares M, Jensen TH. The multitasking polyA tail: nuclear RNA maturation, degradation and export. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0169. [PMID: 30397105 DOI: 10.1098/rstb.2018.0169] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2018] [Indexed: 12/17/2022] Open
Abstract
A polyA (pA) tail is an essential modification added to the 3' ends of a wide range of RNAs at different stages of their metabolism. Here, we describe the main sources of polyadenylation and outline their underlying biochemical interactions within the nuclei of budding yeast Saccharomyces cerevisiae, human cells and, when relevant, the fission yeast Schizosaccharomyces pombe Polyadenylation mediated by the S. cerevisiae Trf4/5 enzymes, and their human homologues PAPD5/7, typically leads to the 3'-end trimming or complete decay of non-coding RNAs. By contrast, the primary function of canonical pA polymerases (PAPs) is to produce stable and nuclear export-competent mRNAs. However, this dichotomy is becoming increasingly blurred, at least in S. pombe and human cells, where polyadenylation mediated by canonical PAPs may also result in transcript decay.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.
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Affiliation(s)
- Agnieszka Tudek
- Department of Molecular Biology and Genetics, Aarhus University, C. F. Møllers Allé 3, building 1130, 8000 Aarhus C, Denmark
| | - Marta Lloret-Llinares
- Department of Molecular Biology and Genetics, Aarhus University, C. F. Møllers Allé 3, building 1130, 8000 Aarhus C, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C. F. Møllers Allé 3, building 1130, 8000 Aarhus C, Denmark
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Qadota H, Matsunaga Y, Bagchi P, Lange KI, Carrier KJ, Pols WV, Swartzbaugh E, Wilson KJ, Srayko M, Pallas DC, Benian GM. Protein phosphatase 2A is crucial for sarcomere organization in Caenorhabditis elegans striated muscle. Mol Biol Cell 2018; 29:2084-2097. [PMID: 29949401 PMCID: PMC6232960 DOI: 10.1091/mbc.e18-03-0192] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/12/2018] [Accepted: 06/18/2018] [Indexed: 01/06/2023] Open
Abstract
Protein phosphatase 2A (PP2A) is a heterotrimer composed of single catalytic and scaffolding subunits and one of several possible regulatory subunits. We identified PPTR-2, a regulatory subunit of PP2A, as a binding partner for the giant muscle protein UNC-89 (obscurin) in Caenorhabditis elegans. PPTR-2 is required for sarcomere organization when its paralogue, PPTR-1, is deficient. PPTR-2 localizes to the sarcomere at dense bodies and M-lines, colocalizing with UNC-89 at M-lines. PP2A components in C. elegans include one catalytic subunit LET-92, one scaffolding subunit (PAA-1), and five regulatory subunits (SUR-6, PPTR-1, PPTR-2, RSA-1, and CASH-1). In adult muscle, loss of function in any of these subunits results in sarcomere disorganization. rsa-1 mutants show an interesting phenotype: one of the two myosin heavy chains, MHC A, localizes as closely spaced double lines rather than single lines. This "double line" phenotype is found in rare missense mutants of the head domain of MHC B myosin, such as unc-54(s74). Analysis of phosphoproteins in the unc-54(s74) mutant revealed two additional phosphoserines in the nonhelical tailpiece of MHC A. Antibodies localize PPTR-1, PAA-1, and SUR-6 to I-bands and RSA-1 to M-lines and I-bands. Therefore, PP2A localizes to sarcomeres and functions in the assembly or maintenance of sarcomeres.
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Affiliation(s)
- Hiroshi Qadota
- Department of Pathology, Emory University, Atlanta, GA 30322
| | - Yohei Matsunaga
- Department of Pathology, Emory University, Atlanta, GA 30322
| | - Pritha Bagchi
- Emory Integrated Proteomics Core, Emory University, Atlanta, GA 30322
| | - Karen I. Lange
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Karma J. Carrier
- Department of Biochemistry and Winship Cancer Institute, Emory University, Atlanta, GA 30322
| | | | | | | | - Martin Srayko
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - David C. Pallas
- Department of Biochemistry and Winship Cancer Institute, Emory University, Atlanta, GA 30322
| | - Guy M. Benian
- Department of Pathology, Emory University, Atlanta, GA 30322
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Bresson S, Tollervey D. Surveillance-ready transcription: nuclear RNA decay as a default fate. Open Biol 2018; 8:170270. [PMID: 29563193 PMCID: PMC5881035 DOI: 10.1098/rsob.170270] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/23/2018] [Indexed: 12/21/2022] Open
Abstract
Eukaryotic cells synthesize enormous quantities of RNA from diverse classes, most of which are subject to extensive processing. These processes are inherently error-prone, and cells have evolved robust quality control mechanisms to selectively remove aberrant transcripts. These surveillance pathways monitor all aspects of nuclear RNA biogenesis, and in addition remove nonfunctional transcripts arising from spurious transcription and a host of non-protein-coding RNAs (ncRNAs). Surprisingly, this is largely accomplished with only a handful of RNA decay enzymes. It has, therefore, been unclear how these factors efficiently distinguish between functional RNAs and huge numbers of diverse transcripts that must be degraded. Here we describe how bona fide transcripts are specifically protected, particularly by 5' and 3' modifications. Conversely, a plethora of factors associated with the nascent transcripts all act to recruit the RNA quality control, surveillance and degradation machinery. We conclude that initiating RNAPII is 'surveillance ready', with degradation being a default fate for all transcripts that lack specific protective features. We further postulate that this promiscuity is a key feature that allowed the proliferation of vast numbers of ncRNAs in eukaryotes, including humans.
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Affiliation(s)
- Stefan Bresson
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - David Tollervey
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
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Rha J, Jones SK, Fidler J, Banerjee A, Leung SW, Morris KJ, Wong JC, Inglis GAS, Shapiro L, Deng Q, Cutler AA, Hanif AM, Pardue MT, Schaffer A, Seyfried NT, Moberg KH, Bassell GJ, Escayg A, García PS, Corbett AH. The RNA-binding protein, ZC3H14, is required for proper poly(A) tail length control, expression of synaptic proteins, and brain function in mice. Hum Mol Genet 2018; 26:3663-3681. [PMID: 28666327 DOI: 10.1093/hmg/ddx248] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 06/20/2017] [Indexed: 12/30/2022] Open
Abstract
A number of mutations in genes that encode ubiquitously expressed RNA-binding proteins cause tissue specific disease. Many of these diseases are neurological in nature revealing critical roles for this class of proteins in the brain. We recently identified mutations in a gene that encodes a ubiquitously expressed polyadenosine RNA-binding protein, ZC3H14 (Zinc finger CysCysCysHis domain-containing protein 14), that cause a nonsyndromic, autosomal recessive form of intellectual disability. This finding reveals the molecular basis for disease and provides evidence that ZC3H14 is essential for proper brain function. To investigate the role of ZC3H14 in the mammalian brain, we generated a mouse in which the first common exon of the ZC3H14 gene, exon 13 is removed (Zc3h14Δex13/Δex13) leading to a truncated ZC3H14 protein. We report here that, as in the patients, Zc3h14 is not essential in mice. Utilizing these Zc3h14Δex13/Δex13mice, we provide the first in vivo functional characterization of ZC3H14 as a regulator of RNA poly(A) tail length. The Zc3h14Δex13/Δex13 mice show enlarged lateral ventricles in the brain as well as impaired working memory. Proteomic analysis comparing the hippocampi of Zc3h14+/+ and Zc3h14Δex13/Δex13 mice reveals dysregulation of several pathways that are important for proper brain function and thus sheds light onto which pathways are most affected by the loss of ZC3H14. Among the proteins increased in the hippocampi of Zc3h14Δex13/Δex13 mice compared to control are key synaptic proteins including CaMK2a. This newly generated mouse serves as a tool to study the function of ZC3H14 in vivo.
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Affiliation(s)
- Jennifer Rha
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University, Atlanta, GA 30322, USA
| | - Stephanie K Jones
- Department of Biology.,Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, GA 30322, USA
| | - Jonathan Fidler
- Department of Anesthesiology, Emory University School of Medicine & Research Division, Atlanta VA Medical Center, Atlanta, GA 30322, USA
| | | | | | - Kevin J Morris
- Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University, Atlanta, GA 30322, USA.,Department of Biology
| | - Jennifer C Wong
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - George Andrew S Inglis
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, GA 30322, USA.,Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Lindsey Shapiro
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, GA 30322, USA.,Graduate Program in Neuroscience, Emory University, Atlanta, GA 30322, USA
| | - Qiudong Deng
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Alicia A Cutler
- Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University, Atlanta, GA 30322, USA.,Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Adam M Hanif
- Department of Opthamology, Emory University School of Medicine & Research Division, & Atlanta VA Medical Center, Atlanta, GA 30322, USA
| | - Machelle T Pardue
- Department of Opthamology, Emory University School of Medicine & Research Division, & Atlanta VA Medical Center, Atlanta, GA 30322, USA
| | - Ashleigh Schaffer
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4955, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kenneth H Moberg
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Gary J Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Andrew Escayg
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, GA 30322, USA
| | - Paul S García
- Department of Anesthesiology, Emory University School of Medicine & Research Division, Atlanta VA Medical Center, Atlanta, GA 30322, USA
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Björk P, Wieslander L. Integration of mRNP formation and export. Cell Mol Life Sci 2017; 74:2875-2897. [PMID: 28314893 PMCID: PMC5501912 DOI: 10.1007/s00018-017-2503-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/06/2017] [Accepted: 03/07/2017] [Indexed: 12/13/2022]
Abstract
Expression of protein-coding genes in eukaryotes relies on the coordinated action of many sophisticated molecular machineries. Transcription produces precursor mRNAs (pre-mRNAs) and the active gene provides an environment in which the pre-mRNAs are processed, folded, and assembled into RNA–protein (RNP) complexes. The dynamic pre-mRNPs incorporate the growing transcript, proteins, and the processing machineries, as well as the specific protein marks left after processing that are essential for export and the cytoplasmic fate of the mRNPs. After release from the gene, the mRNPs move by diffusion within the interchromatin compartment, making up pools of mRNPs. Here, splicing and polyadenylation can be completed and the mRNPs recruit the major export receptor NXF1. Export competent mRNPs interact with the nuclear pore complex, leading to export, concomitant with compositional and conformational changes of the mRNPs. We summarize the integrated nuclear processes involved in the formation and export of mRNPs.
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Affiliation(s)
- Petra Björk
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Lars Wieslander
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
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Fasken MB, Corbett AH. Links between mRNA splicing, mRNA quality control, and intellectual disability. RNA & DISEASE 2016; 3:e1448. [PMID: 27868086 PMCID: PMC5113822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023] Open
Abstract
In recent years, the impairment of RNA binding proteins that play key roles in the post-transcriptional regulation of gene expression has been linked to numerous neurological diseases. These RNA binding proteins perform critical mRNA processing steps in the nucleus, including splicing, polyadenylation, and export. In many cases, these RNA binding proteins are ubiquitously expressed raising key questions about why only brain function is impaired. Recently, mutations in the ZC3H14 gene, encoding an evolutionarily conserved, polyadenosine RNA binding protein, have been linked to a nonsyndromic form of autosomal recessive intellectual disability. Thus far, research on ZC3H14 and its Nab2 orthologs in budding yeast and Drosophila reveals that ZC3H14/Nab2 is important for mRNA processing and neuronal patterning. Two recent studies now provide evidence that ZC3H14/Nab2 may function in the quality control of mRNA splicing and export and could help to explain the molecular defects that cause neuronal dysfunction and lead to an inherited form of intellectual disability. These studies on ZC3H14/Nab2 reveal new clues to the puzzle of why loss of the ubiquitously expressed ZC3H14 protein specifically affects neurons.
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Affiliation(s)
- Milo B Fasken
- Department of Biology, Emory University, 1510 Clifton Rd., NE RRC 1021, Atlanta, GA 30322, U.S.A
| | - Anita H Corbett
- Department of Biology, Emory University, 1510 Clifton Rd., NE RRC 1021, Atlanta, GA 30322, U.S.A
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Wigington CP, Morris KJ, Newman LE, Corbett AH. The Polyadenosine RNA-binding Protein, Zinc Finger Cys3His Protein 14 (ZC3H14), Regulates the Pre-mRNA Processing of a Key ATP Synthase Subunit mRNA. J Biol Chem 2016; 291:22442-22459. [PMID: 27563065 DOI: 10.1074/jbc.m116.754069] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 08/25/2016] [Indexed: 12/23/2022] Open
Abstract
Polyadenosine RNA-binding proteins (Pabs) regulate multiple steps in gene expression. This protein family includes the well studied Pabs, PABPN1 and PABPC1, as well as the newly characterized Pab, zinc finger CCCH-type containing protein 14 (ZC3H14). Mutations in ZC3H14 are linked to a form of intellectual disability. To probe the function of ZC3H14, we performed a transcriptome-wide analysis of cells depleted of either ZC3H14 or the control Pab, PABPN1. Depletion of PABPN1 affected ∼17% of expressed transcripts, whereas ZC3H14 affected only ∼1% of expressed transcripts. To assess the function of ZC3H14 in modulating target mRNAs, we selected the gene encoding the ATP synthase F0 subunit C (ATP5G1) transcript. Knockdown of ZC3H14 significantly reduced ATP5G1 steady-state mRNA levels. Consistent with results suggesting that ATP5G1 turnover increases upon depletion of ZC3H14, double knockdown of ZC3H14 and the nonsense-mediated decay factor, UPF1, rescues ATP5G1 transcript levels. Furthermore, fractionation reveals an increase in the amount of ATP5G1 pre-mRNA that reaches the cytoplasm when ZC3H14 is depleted and that ZC3H14 binds to ATP5G1 pre-mRNA in the nucleus. These data support a role for ZC3H14 in ensuring proper nuclear processing and retention of ATP5G1 pre-mRNA. Consistent with the observation that ATP5G1 is a rate-limiting component for ATP synthase activity, knockdown of ZC3H14 decreases cellular ATP levels and causes mitochondrial fragmentation. These data suggest that ZC3H14 modulates pre-mRNA processing of select mRNA transcripts and plays a critical role in regulating cellular energy levels, observations that have broad implications for proper neuronal function.
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Affiliation(s)
- Callie P Wigington
- From the Department of Biochemistry and.,the Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, Georgia 30322
| | - Kevin J Morris
- From the Department of Biochemistry and.,the Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, Georgia 30322
| | - Laura E Newman
- From the Department of Biochemistry and.,the Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, Georgia 30322
| | - Anita H Corbett
- From the Department of Biochemistry and .,the Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, Georgia 30322
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