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Mun H, Lee S, Choi S, Jeong JH, Ko S, Chun YL, Deaton B, Yeager CT, Boyette A, Palmera J, Newman L, Zhou P, Shin S, Kim DC, Sagum CA, Bedford MT, Kim YK, Kwon J, Jung J, Chang JH, Yoon JH. Targeting of CYP2E1 by miRNAs in alcohol-induced intestine injury. Mol Cells 2024:100074. [PMID: 38901530 DOI: 10.1016/j.mocell.2024.100074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 06/22/2024] Open
Abstract
Although binge alcohol-induced gut leakage has been studied extensively in the context of reactive oxygen species (ROS)-mediated signaling, it was recently revealed that post-transcriptional regulation plays an essential role as well. Ethanol (EtOH)-inducible cytochrome P450-2E1 (CYP2E1), a key enzyme in EtOH metabolism, promotes alcohol-induced hepatic steatosis and inflammatory liver disease, at least in part by mediating changes in intestinal permeability. For instance, gut leakage and elevated intestinal permeability to endotoxins have been shown to be regulated by enhancing CYP2E1 mRNA and CYP2E1 protein levels. Although it is understood that EtOH promotes CYP2E1 induction and activation, the mechanisms that regulate CYP2E1 expression in the context of intestinal damage remain poorly defined. Specific miRNAs, including miR-132, miR-212, miR-378, and miR-552, have been shown to repress the expression of CYP2E1, suggesting that these miRNAs contribute to EtOH-induced intestinal injury. Here, we have shown that CYP2E1 expression is regulated post-transcriptionally through miRNA-mediated degradation, as follows: 1) the RNA-binding protein AU-binding Factor 1 (AUF1) binds mature miRNAs, including CYP2E1-targeting miRNAs, and this binding modulates the degradation of corresponding target mRNAs upon EtOH treatment; 2) the Serine/Threonine kinase MST1 mediates oxidative stress-induced phosphorylation of AUF1. Those findings suggest that ROS-mediated signaling modulates AUF1/miRNA interaction through MST1-mediated phosphorylation. Thus, our study demonstrates the critical functions of AUF1 phosphorylation by MST1 in the decay of miRNAs targeting CYP2E1, the stabilization of CYP2E1 mRNA in the presence of EtOH, and the relationship of this pathway to subsequent intestinal injury.
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Affiliation(s)
- Hyejin Mun
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA; Department of Oncology Science, University of Oklahoma, Oklahoma City, OK 73104, USA
| | - Sungyul Lee
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Suyoung Choi
- Department of Infection Biology, College of Medicine, Chungnam National University, Daejeon 35015, Korea; Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea; Brain Korea 21 FOUR Project for Medical Science, Chungnam National University, Daejeon 35015, Korea
| | - Ji-Hoon Jeong
- Department of Oncology Science, University of Oklahoma, Oklahoma City, OK 73104, USA
| | - Seungbeom Ko
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Yoo Lim Chun
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA; Department of Anatomy and Neurobiology, College of Medicine, Kyung Hee University, 26, Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea
| | - Benjamin Deaton
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Clay T Yeager
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Audrey Boyette
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Juliana Palmera
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - London Newman
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Ping Zhou
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Soona Shin
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Dong-Chan Kim
- Division of Medical Device R&D Center, NQ-Lab, Inc., 16827, Republic of Korea
| | - Cari A Sagum
- Department of Epigenetics and Molecular Carcinogenesis, the University of Texas MD, Anderson Cancer Center, Houston, TX 77030, USA
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, the University of Texas MD, Anderson Cancer Center, Houston, TX 77030, USA
| | - Young-Kook Kim
- Department of Biochemistry, Chonnam National University Medical School, Hwasun 58128, Republic of Korea
| | - Jaeyul Kwon
- Department of Infection Biology, College of Medicine, Chungnam National University, Daejeon 35015, Korea; Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea; Brain Korea 21 FOUR Project for Medical Science, Chungnam National University, Daejeon 35015, Korea; Department of Medical Education, College of Medicine, Chungnam National University, Daejeon 35015, Korea; Translational Immunology Institute, Chungnam National University, Daejeon 35015, Korea
| | - Junyang Jung
- Department of Anatomy and Neurobiology, College of Medicine, Kyung Hee University, 26, Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea.
| | - Jeong Ho Chang
- Department of Biology Education, Kyungpook National University, Daegu 41566, Republic of Korea.
| | - Je-Hyun Yoon
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA; Department of Oncology Science, University of Oklahoma, Oklahoma City, OK 73104, USA.
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Glauninger H, Bard JA, Wong Hickernell CJ, Airoldi EM, Li W, Singer RH, Paul S, Fei J, Sosnick TR, Wallace EWJ, Drummond DA. Transcriptome-wide mRNA condensation precedes stress granule formation and excludes stress-induced transcripts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589678. [PMID: 38659805 PMCID: PMC11042329 DOI: 10.1101/2024.04.15.589678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Stress-induced condensation of mRNA and proteins into stress granules is conserved across eukaryotes, yet the function, formation mechanisms, and relation to well-studied conserved transcriptional responses remain largely unresolved. Stress-induced exposure of ribosome-free mRNA following translational shutoff is thought to cause condensation by allowing new multivalent RNA-dependent interactions, with RNA length and associated interaction capacity driving increased condensation. Here we show that, in striking contrast, virtually all mRNA species condense in response to multiple unrelated stresses in budding yeast, length plays a minor role, and instead, stress-induced transcripts are preferentially excluded from condensates, enabling their selective translation. Using both endogenous genes and reporter constructs, we show that translation initiation blockade, rather than resulting ribosome-free RNA, causes condensation. These translation initiation-inhibited condensates (TIICs) are biochemically detectable even when stress granules, defined as microscopically visible foci, are absent or blocked. TIICs occur in unstressed yeast cells, and, during stress, grow before the appearance of visible stress granules. Stress-induced transcripts are excluded from TIICs primarily due to the timing of their expression, rather than their sequence features. Together, our results reveal a simple system by which cells redirect translational activity to newly synthesized transcripts during stress, with broad implications for cellular regulation in changing conditions.
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Affiliation(s)
- Hendrik Glauninger
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL, USA
- Interdisciplinary Scientist Training Program, The University of Chicago, Chicago, IL, USA
| | - Jared A.M. Bard
- Department of Biology, Texas A&M University, College Station, TX, USA
| | | | - Edo M. Airoldi
- Fox School of Business and Management, Temple University, Philadelphia, PA, USA
| | - Weihan Li
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Robert H. Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sneha Paul
- Department of Biochemistry & Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Jingyi Fei
- Department of Biochemistry & Molecular Biology, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - Tobin R. Sosnick
- Department of Biochemistry & Molecular Biology, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | | | - D. Allan Drummond
- Department of Biochemistry & Molecular Biology, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, USA
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Joshua IM, Lin M, Mardjuki A, Mazzola A, Höfken T. A Protein-Protein Interaction Analysis Suggests a Wide Range of New Functions for the p21-Activated Kinase (PAK) Ste20. Int J Mol Sci 2023; 24:15916. [PMID: 37958899 PMCID: PMC10647699 DOI: 10.3390/ijms242115916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
The p21-activated kinases (PAKs) are important signaling proteins. They contribute to a surprisingly wide range of cellular processes and play critical roles in a number of human diseases including cancer, neurological disorders and cardiac diseases. To get a better understanding of PAK functions, mechanisms and integration of various cellular activities, we screened for proteins that bind to the budding yeast PAK Ste20 as an example, using the split-ubiquitin technique. We identified 56 proteins, most of them not described previously as Ste20 interactors. The proteins fall into a small number of functional categories such as vesicle transport and translation. We analyzed the roles of Ste20 in glucose metabolism and gene expression further. Ste20 has a well-established role in the adaptation to changing environmental conditions through the stimulation of mitogen-activated protein kinase (MAPK) pathways which eventually leads to transcription factor activation. This includes filamentous growth, an adaptation to nutrient depletion. Here we show that Ste20 also induces filamentous growth through interaction with nuclear proteins such as Sac3, Ctk1 and Hmt1, key regulators of gene expression. Combining our observations and the data published by others, we suggest that Ste20 has several new and unexpected functions.
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Affiliation(s)
| | - Meng Lin
- Institute of Biochemistry, Kiel University, 24118 Kiel, Germany
| | - Ariestia Mardjuki
- Division of Biosciences, Brunel University London, Uxbridge UB8 3PH, UK; (I.M.J.)
| | - Alessandra Mazzola
- Division of Biosciences, Brunel University London, Uxbridge UB8 3PH, UK; (I.M.J.)
- Department of Biopathology and Medical and Forensic Biotechnologies, University of Palermo, 90133 Palermo, Italy
| | - Thomas Höfken
- Division of Biosciences, Brunel University London, Uxbridge UB8 3PH, UK; (I.M.J.)
- Institute of Biochemistry, Kiel University, 24118 Kiel, Germany
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4
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Kramer S, Karolak NK, Odenwald J, Gabiatti B, Castañeda Londoño P, Zavřelová A, Freire E, Almeida K, Braune S, Moreira C, Eder A, Goos C, Field M, Carrington M, Holetz F, Górna M, Zoltner M. A unique mRNA decapping complex in trypanosomes. Nucleic Acids Res 2023; 51:7520-7540. [PMID: 37309887 PMCID: PMC10415143 DOI: 10.1093/nar/gkad497] [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: 12/05/2022] [Revised: 05/18/2023] [Accepted: 06/06/2023] [Indexed: 06/14/2023] Open
Abstract
Removal of the mRNA 5' cap primes transcripts for degradation and is central for regulating gene expression in eukaryotes. The canonical decapping enzyme Dcp2 is stringently controlled by assembly into a dynamic multi-protein complex together with the 5'-3'exoribonuclease Xrn1. Kinetoplastida lack Dcp2 orthologues but instead rely on the ApaH-like phosphatase ALPH1 for decapping. ALPH1 is composed of a catalytic domain flanked by C- and N-terminal extensions. We show that T. brucei ALPH1 is dimeric in vitro and functions within a complex composed of the trypanosome Xrn1 ortholog XRNA and four proteins unique to Kinetoplastida, including two RNA-binding proteins and a CMGC-family protein kinase. All ALPH1-associated proteins share a unique and dynamic localization to a structure at the posterior pole of the cell, anterior to the microtubule plus ends. XRNA affinity capture in T. cruzi recapitulates this interaction network. The ALPH1 N-terminus is not required for viability in culture, but essential for posterior pole localization. The C-terminus, in contrast, is required for localization to all RNA granule types, as well as for dimerization and interactions with XRNA and the CMGC kinase, suggesting possible regulatory mechanisms. Most significantly, the trypanosome decapping complex has a unique composition, differentiating the process from opisthokonts.
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Affiliation(s)
| | - Natalia Katarzyna Karolak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | | | - Bernardo Gabiatti
- Biocenter, University of Würzburg, Würzburg, Germany
- Carlos Chagas Institute (ICC), FIOCRUZ/PR, Curitiba, Brazil
| | | | - Anna Zavřelová
- Department of Parasitology, Faculty of Science, Charles University in Prague, Biocev, Vestec, Czech Republic
| | | | | | - Silke Braune
- Biocenter, University of Würzburg, Würzburg, Germany
| | - Claudia Moreira
- Biocenter, University of Würzburg, Würzburg, Germany
- Carlos Chagas Institute (ICC), FIOCRUZ/PR, Curitiba, Brazil
| | - Amelie Eder
- Biocenter, University of Würzburg, Würzburg, Germany
| | - Carina Goos
- Biocenter, University of Würzburg, Würzburg, Germany
| | - Mark Field
- School of Life Sciences, University of Dundee, Dundee, UK
- Biology Centre, Czech Academy of Sciences, Institute of Parasitology, České Budějovice, Czech Republic
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Fabiola Holetz
- Carlos Chagas Institute (ICC), FIOCRUZ/PR, Curitiba, Brazil
| | - Maria Wiktoria Górna
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
| | - Martin Zoltner
- Department of Parasitology, Faculty of Science, Charles University in Prague, Biocev, Vestec, Czech Republic
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Kaposi's sarcoma-associated herpesvirus (KSHV) utilizes the NDP52/CALCOCO2 selective autophagy receptor to disassemble processing bodies. PLoS Pathog 2023; 19:e1011080. [PMID: 36634147 PMCID: PMC9876383 DOI: 10.1371/journal.ppat.1011080] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 01/25/2023] [Accepted: 12/22/2022] [Indexed: 01/13/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) causes the inflammatory and angiogenic endothelial cell neoplasm, Kaposi's sarcoma (KS). We previously demonstrated that the KSHV Kaposin B (KapB) protein promotes inflammation via the disassembly of cytoplasmic ribonucleoprotein granules called processing bodies (PBs). PBs modify gene expression by silencing or degrading labile messenger RNAs (mRNAs), including many transcripts that encode inflammatory or angiogenic proteins associated with KS disease. Although our work implicated PB disassembly as one of the causes of inflammation during KSHV infection, the precise mechanism used by KapB to elicit PB disassembly was unclear. Here we reveal a new connection between the degradative process of autophagy and PB disassembly. We show that both latent KSHV infection and KapB expression enhanced autophagic flux via phosphorylation of the autophagy regulatory protein, Beclin. KapB was necessary for this effect, as infection with a recombinant virus that does not express the KapB protein did not induce Beclin phosphorylation or autophagic flux. Moreover, we showed that PB disassembly mediated by KSHV or KapB, depended on autophagy genes and the selective autophagy receptor NDP52/CALCOCO2 and that the PB scaffolding protein, Pat1b, co-immunoprecipitated with NDP52. These studies reveal a new role for autophagy and the selective autophagy receptor NDP52 in promoting PB turnover and the concomitant synthesis of inflammatory molecules during KSHV infection.
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Nabariya DK, Heinz A, Derksen S, Krauß S. Intracellular and intercellular transport of RNA organelles in CXG repeat disorders: The strength of weak ties. Front Mol Biosci 2022; 9:1000932. [PMID: 36589236 PMCID: PMC9800848 DOI: 10.3389/fmolb.2022.1000932] [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: 07/22/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
RNA is a vital biomolecule, the function of which is tightly spatiotemporally regulated. RNA organelles are biological structures that either membrane-less or surrounded by membrane. They are produced by the all the cells and indulge in vital cellular mechanisms. They include the intracellular RNA granules and the extracellular exosomes. RNA granules play an essential role in intracellular regulation of RNA localization, stability and translation. Aberrant regulation of RNA is connected to disease development. For example, in microsatellite diseases such as CXG repeat expansion disorders, the mutant CXG repeat RNA's localization and function are affected. RNA is not only transported intracellularly but can also be transported between cells via exosomes. The loading of the exosomes is regulated by RNA-protein complexes, and recent studies show that cytosolic RNA granules and exosomes share common content. Intracellular RNA granules and exosome loading may therefore be related. Exosomes can also transfer pathogenic molecules of CXG diseases from cell to cell, thereby driving disease progression. Both intracellular RNA granules and extracellular RNA vesicles may serve as a source for diagnostic and treatment strategies. In therapeutic approaches, pharmaceutical agents may be loaded into exosomes which then transport them to the desired cells/tissues. This is a promising target specific treatment strategy with few side effects. With respect to diagnostics, disease-specific content of exosomes, e.g., RNA-signatures, can serve as attractive biomarker of central nervous system diseases detecting early physiological disturbances, even before symptoms of neurodegeneration appear and irreparable damage to the nervous system occurs. In this review, we summarize the known function of cytoplasmic RNA granules and extracellular vesicles, as well as their role and dysfunction in CXG repeat expansion disorders. We also provide a summary of established protocols for the isolation and characterization of both cytoplasmic and extracellular RNA organelles.
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Affiliation(s)
| | | | | | - Sybille Krauß
- Human Biology/Neurobiology, Institute of Biology, Faculty IV, School of Science and Technology, University of Siegen, Siegen, Germany
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Liu Z, Rui T, Lin Z, Xie S, Zhou B, Fu M, Mai L, Zhu C, Wu G, Wang Y. Tumor-Associated Macrophages Promote Metastasis of Oral Squamous Cell Carcinoma via CCL13 Regulated by Stress Granule. Cancers (Basel) 2022; 14:5081. [PMID: 36291863 PMCID: PMC9657876 DOI: 10.3390/cancers14205081] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/07/2022] [Accepted: 10/13/2022] [Indexed: 11/03/2023] Open
Abstract
M2 tumor-associated macrophages (TAMs) have been a well-established promoter of oral squamous cell carcinoma (OSCC) progression. However, the mechanisms of M2 TAMs promoting OSCC metastasis have not been elucidated clearly. This study illustrated the regulatory mechanisms in which M2 TAMs enhance OSCC malignancy in a novel point of view. In this study, mass spectrometry was utilized to analyze the proteins expression profile of M2 type monocyte-derived macrophages (MDMs-M2), whose results revealed the high expression of G3BP1 in M2 macrophages. RNA sequencing analyzed the genome-wide changes upon G3BP1 knockdown in MDMs-M2 and identified that CCL13 was the most significantly downregulated inflammatory cytokines in MDMs-M2. Co-immunoprecipitation and qualitative mass spectrometry were used to identify the proteins that directly interacted with endogenous G3BP1 in MDMs-M2. Elevated stress granule (SG) formation in stressed M2 TAMs enhanced the expression of CCL13, which promoted OSCC metastasis both in vitro and in vivo. For mechanisms, we demonstrated SG formation improved DDX3Y/hnRNPF-mediated CCL13 mRNA stability, thus enhancing CCL13 expression and promoting OSCC metastasis. Collectively, our findings demonstrated for the first time the roles of CCL13 in improving OSCC metastasis and illustrated the molecular mechanisms of CCL13 expression regulated by SG, indicating that the SG-CCL13 axis can be the potential targets for TAM-navigated tumor therapy.
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Affiliation(s)
- Zhixin Liu
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510120, China
- The Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510120, China
| | - Tao Rui
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510120, China
- The Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510120, China
| | - Zhaoyu Lin
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510120, China
- The Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510120, China
- The Oral and Maxillofacial-Head and Neck Digital Precision Reconstruction Technology Research Center of Guangdong Province, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510120, China
| | - Shule Xie
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510120, China
- The Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510120, China
- The Oral and Maxillofacial-Head and Neck Digital Precision Reconstruction Technology Research Center of Guangdong Province, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510120, China
| | - Bin Zhou
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510120, China
- The Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510120, China
- The Oral and Maxillofacial-Head and Neck Digital Precision Reconstruction Technology Research Center of Guangdong Province, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510120, China
| | - Min Fu
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510120, China
- The Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510120, China
| | - Lianxi Mai
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510120, China
- The Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510120, China
| | - Chuandong Zhu
- Department of Oral and Maxillofacial Surgery, Affiliate Stomatology Hospital of Guangzhou Medical University, Guangzhou Medical University, 31 Huangsha Avenue, Guangzhou 510000, China
| | - Guotao Wu
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510120, China
| | - Youyuan Wang
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510120, China
- The Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510120, China
- The Oral and Maxillofacial-Head and Neck Digital Precision Reconstruction Technology Research Center of Guangdong Province, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510120, China
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8
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Grousl T, Vojtova J, Hasek J, Vomastek T. Yeast stress granules at a glance. Yeast 2021; 39:247-261. [PMID: 34791685 DOI: 10.1002/yea.3681] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/15/2021] [Accepted: 11/12/2021] [Indexed: 11/10/2022] Open
Abstract
The formation of stress granules (SGs), membrane-less organelles that are composed of mainly messenger ribonucleoprotein assemblies, is the result of a conserved evolutionary strategy to cellular stress. During their formation, which is triggered by robust environmental stress, SGs sequester translationally inactive mRNA molecules, which are either forwarded for further processing elsewhere or stored during a period of stress within SGs. Removal of mRNA molecules from active translation and their sequestration in SGs allows preferential translation of stress response transcripts. By affecting the specificity of mRNA translation, mRNA localization and stability, SGs are involved in the overall cellular reprogramming during periods of environmental stress and viral infection. Over the past two decades, we have learned which processes drive SGs assembly, how their composition varies under stress, and how they co-exist with other subcellular organelles. Yeast as a model has been instrumental in our understanding of SG biology. Despite the specific differences between the SGs of yeast and mammals, yeast have been shown to be a valuable tool to the study of SGs in translation-related stress response. This review summarizes the data surrounding SGs that are formed under different stress conditions in Saccharomyces cerevisiae and other yeast species. It offers a comprehensive and up-to-date view on these still somewhat mysterious entities.
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Affiliation(s)
- Tomas Grousl
- Laboratory of Cell Signalling, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jana Vojtova
- Laboratory of Cell Reproduction, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiri Hasek
- Laboratory of Cell Reproduction, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tomas Vomastek
- Laboratory of Cell Signalling, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
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9
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Tishinov K, Spang A. The mRNA decapping complex is buffered by nuclear localization. J Cell Sci 2021; 134:272313. [PMID: 34435633 DOI: 10.1242/jcs.259156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/17/2021] [Indexed: 01/08/2023] Open
Abstract
mRNA decay is a key step in regulating the cellular proteome. Processing bodies (P-bodies) are thought to be sites of mRNA decay and/or storage. P-body units assemble into P-body granules under stress conditions. How this assembly is regulated, however, remains poorly understood. Here, we show, in the yeast Saccharomyces cerevisiae, that the translational repressor Scd6 and the decapping stimulator Edc3 act partially redundantly in P-body assembly by sequestering the Dcp1-Dcp2 (denoted Dcp1/2) decapping complex in the cytoplasm and preventing it from becoming imported into the nucleus by the karyopherin β protein Kap95. One of two nuclear localization signals in Dcp2 overlaps with the RNA-binding site, suggesting an additional mechanism to regulate Dcp1/2 localization. Nuclear Dcp1/2 does not drive mRNA decay and might be stored there as a readily releasable pool, indicating a dynamic equilibrium between cytoplasmic and nuclear Dcp1/2. Cytoplasmic Dcp1/2 is linked to Dhh1 via Edc3. Functional P-bodies are present at the endoplasmic reticulum where Dcp2 potentially acts to increase the local concentration of Dhh1 through interaction with Edc3 to drive phase separation and hence P-body formation.
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Affiliation(s)
- Kiril Tishinov
- Biozentrum, University of Basel, Spitalstrasse 41, CH-4056 Basel, Switzerland
| | - Anne Spang
- Biozentrum, University of Basel, Spitalstrasse 41, CH-4056 Basel, Switzerland
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10
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Yahya G, Pérez AP, Mendoza MB, Parisi E, Moreno DF, Artés MH, Gallego C, Aldea M. Stress granules display bistable dynamics modulated by Cdk. J Cell Biol 2021; 220:211705. [PMID: 33480968 PMCID: PMC7836273 DOI: 10.1083/jcb.202005102] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 11/27/2020] [Accepted: 12/23/2020] [Indexed: 12/20/2022] Open
Abstract
Stress granules (SGs) are conserved biomolecular condensates that originate in response to many stress conditions. These membraneless organelles contain nontranslating mRNAs and a diverse subproteome, but our knowledge of their regulation and functional relevance is still incipient. Here, we describe a mutual-inhibition interplay between SGs and Cdc28, the budding yeast Cdk. Among Cdc28 interactors acting as negative modulators of Start, we have identified Whi8, an RNA-binding protein that localizes to SGs and recruits the mRNA of CLN3, the most upstream G1 cyclin, for efficient translation inhibition and Cdk inactivation under stress. However, Whi8 also contributes to recruiting Cdc28 to SGs, where it acts to promote their dissolution. As predicted by a mutual-inhibition framework, the SG constitutes a bistable system that is modulated by Cdk. Since mammalian cells display a homologous mechanism, we propose that the opposing functions of specific mRNA-binding proteins and Cdk’s subjugate SG dynamics to a conserved hysteretic switch.
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Affiliation(s)
- Galal Yahya
- Molecular Biology Institute of Barcelona, Spanish National Research Council, Catalonia, Spain.,Department of Microbiology and Immunology, Zagazig University, Zagazig, Egypt
| | - Alexis P Pérez
- Molecular Biology Institute of Barcelona, Spanish National Research Council, Catalonia, Spain.,Department of Basic Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Mònica B Mendoza
- Molecular Biology Institute of Barcelona, Spanish National Research Council, Catalonia, Spain
| | - Eva Parisi
- Molecular Biology Institute of Barcelona, Spanish National Research Council, Catalonia, Spain
| | - David F Moreno
- Molecular Biology Institute of Barcelona, Spanish National Research Council, Catalonia, Spain
| | - Marta H Artés
- Molecular Biology Institute of Barcelona, Spanish National Research Council, Catalonia, Spain
| | - Carme Gallego
- Molecular Biology Institute of Barcelona, Spanish National Research Council, Catalonia, Spain
| | - Martí Aldea
- Molecular Biology Institute of Barcelona, Spanish National Research Council, Catalonia, Spain.,Department of Basic Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
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11
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Li J, Liu X, Yin Z, Hu Z, Zhang KQ. An Overview on Identification and Regulatory Mechanisms of Long Non-coding RNAs in Fungi. Front Microbiol 2021; 12:638617. [PMID: 33995298 PMCID: PMC8113380 DOI: 10.3389/fmicb.2021.638617] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/06/2021] [Indexed: 01/04/2023] Open
Abstract
For decades, more and more long non-coding RNAs (lncRNAs) have been confirmed to play important functions in key biological processes of different organisms. At present, most identified lncRNAs and those with known functional roles are from mammalian systems. However, lncRNAs have also been found in primitive eukaryotic fungi, and they have different functions in fungal development, metabolism, and pathogenicity. In this review, we highlight some recent researches on lncRNAs in the primitive eukaryotic fungi, particularly focusing on the identification of lncRNAs and their regulatory roles in diverse biological processes.
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Affiliation(s)
- Juan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Xiaoying Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Ziyu Yin
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Zhihong Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
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12
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Borbolis F, Syntichaki P. Biological implications of decapping: beyond bulk mRNA decay. FEBS J 2021; 289:1457-1475. [PMID: 33660392 DOI: 10.1111/febs.15798] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/21/2021] [Accepted: 03/07/2021] [Indexed: 12/12/2022]
Abstract
It is well established that mRNA steady-state levels do not directly correlate with transcription rate. This is attributed to the multiple post-transcriptional mechanisms, which control both mRNA turnover and translation within eukaryotic cells. One such mechanism is the removal of the 5' end cap structure of RNAs (decapping). This 5' cap plays a fundamental role in cellular functions related to mRNA processing, transport, translation, quality control, and decay, while its chemical modifications influence the fate of cytoplasmic mRNAs. Decapping is a highly controlled process, performed by multiple decapping enzymes, and regulated by complex cellular networks. In this review, we provide an updated synopsis of 5' end modifications and functions, and give an overview of mRNA decapping enzymes, presenting their enzymatic properties. Focusing on DCP2 decapping enzyme, a major component on the 5'-3' mRNA decay pathway, we describe cis-elements and trans-acting factors that affect its activity, substrate specificity, and cellular localization. Finally, we discuss current knowledge on the biological functions of mRNA decapping and decay factors, highlighting the major questions that remain to be addressed.
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Affiliation(s)
- Fivos Borbolis
- Biomedical Research Foundation of the Academy of Athens, Center of Basic Research, Athens, Greece
| | - Popi Syntichaki
- Biomedical Research Foundation of the Academy of Athens, Center of Basic Research, Athens, Greece
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13
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Luo Y, Schofield JA, Na Z, Hann T, Simon MD, Slavoff SA. Discovery of cellular substrates of human RNA-decapping enzyme DCP2 using a stapled bicyclic peptide inhibitor. Cell Chem Biol 2020; 28:463-474.e7. [PMID: 33357462 DOI: 10.1016/j.chembiol.2020.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/29/2020] [Accepted: 12/04/2020] [Indexed: 01/23/2023]
Abstract
DCP2 is an RNA-decapping enzyme that controls the stability of human RNAs that encode factors functioning in transcription and the immune response. While >1,800 human DCP2 substrates have been identified, compensatory expression changes secondary to genetic ablation of DCP2 have complicated a complete mapping of its regulome. Cell-permeable, selective chemical inhibitors of DCP2 could provide a powerful tool to study DCP2 specificity. Here, we report phage display selection of CP21, a bicyclic peptide ligand to DCP2. CP21 has high affinity and selectivity for DCP2 and inhibits DCP2 decapping activity toward selected RNA substrates in human cells. CP21 increases formation of P-bodies, liquid condensates enriched in intermediates of RNA decay, in a manner that resembles the deletion or mutation of DCP2. We used CP21 to identify 76 previously unreported DCP2 substrates. This work demonstrates that DCP2 inhibition can complement genetic approaches to study RNA decay.
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Affiliation(s)
- Yang Luo
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Jeremy A Schofield
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06529, USA
| | - Zhenkun Na
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Tanja Hann
- Yale Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT 06520, USA
| | - Matthew D Simon
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06529, USA
| | - Sarah A Slavoff
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06529, USA.
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14
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Two- and Three-Dimensional Tracking of MFA2 mRNA Molecules in Mating Yeast. Cells 2020; 9:cells9102151. [PMID: 32977598 PMCID: PMC7650813 DOI: 10.3390/cells9102151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/15/2020] [Accepted: 09/22/2020] [Indexed: 12/14/2022] Open
Abstract
Intracellular mRNA transport contributes to the spatio-temporal regulation of mRNA function and localized translation. In the budding yeast, Saccharomyces cerevisiae, asymmetric mRNA transport localizes ~30 specific mRNAs including those encoding polarity and secretion factors, to the bud tip. The underlying process involves RNA-binding proteins (RBPs), molecular motors, processing bodies (PBs), and the actin cytoskeleton. Recently, pheromone a-factor expression in mating yeast was discovered to depend on proper localization of its mRNA, MFA2 mRNAs in conjunction with PBs cluster at the shmoo tip to form "mating bodies", from which a-factor is locally expressed. The mechanism ensuring the correct targeting of mRNA to the shmoo tip is poorly understood. Here we analyzed the kinetics and trajectories of MFA2 mRNA transport in living, alpha-factor treated yeast. Two- (2D) and three-dimensional (3D) analyses allowed us to reconstruct the granule tracks and estimate granule velocities. Tracking analysis of single MFA2 mRNA granules, labeled using a fluorescent aptamer system, demonstrated three types movement: vibrational, oscillatory and translocational. The mRNA granule transport was complex; a granule could change its movement behavior and composition during its journey to the shmoo. Processing body assembly and the actin-based motor, Myo4p, were involved in movement of MFA2 mRNA to the shmoo, but neither was required, indicating that multiple mechanisms for translocation were at play. Our visualization studies present a dynamic view of the localization mechanism in shmoo-bearing cells.
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15
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Zarnack K, Balasubramanian S, Gantier MP, Kunetsky V, Kracht M, Schmitz ML, Sträßer K. Dynamic mRNP Remodeling in Response to Internal and External Stimuli. Biomolecules 2020; 10:biom10091310. [PMID: 32932892 PMCID: PMC7565591 DOI: 10.3390/biom10091310] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/02/2020] [Accepted: 09/08/2020] [Indexed: 02/06/2023] Open
Abstract
Signal transduction and the regulation of gene expression are fundamental processes in every cell. RNA-binding proteins (RBPs) play a key role in the post-transcriptional modulation of gene expression in response to both internal and external stimuli. However, how signaling pathways regulate the assembly of RBPs with mRNAs remains largely unknown. Here, we summarize observations showing that the formation and composition of messenger ribonucleoprotein particles (mRNPs) is dynamically remodeled in space and time by specific signaling cascades and the resulting post-translational modifications. The integration of signaling events with gene expression is key to the rapid adaptation of cells to environmental changes and stress. Only a combined approach analyzing the signal transduction pathways and the changes in post-transcriptional gene expression they cause will unravel the mechanisms coordinating these important cellular processes.
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Affiliation(s)
- Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt a.M., Germany;
| | | | - Michael P. Gantier
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia;
- Department of Molecular and Translational Science, Monash University, Clayton, VIC 3800, Australia
| | - Vladislav Kunetsky
- Institute of Biochemistry, FB08, Justus Liebig University, 35392 Giessen, Germany;
| | - Michael Kracht
- Rudolf Buchheim Institute of Pharmacology, FB11, Justus Liebig University, 35392 Giessen, Germany;
| | - M. Lienhard Schmitz
- Institute of Biochemistry, FB11, Justus Liebig University, 35392 Giessen, Germany;
| | - Katja Sträßer
- Institute of Biochemistry, FB08, Justus Liebig University, 35392 Giessen, Germany;
- Correspondence:
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16
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Zhu M, Kuechler ER, Zhang J, Matalon O, Dubreuil B, Hofmann A, Loewen C, Levy ED, Gsponer J, Mayor T. Proteomic analysis reveals the direct recruitment of intrinsically disordered regions to stress granules in S. cerevisiae. J Cell Sci 2020; 133:jcs244657. [PMID: 32503941 DOI: 10.1242/jcs.244657] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/15/2020] [Indexed: 01/21/2023] Open
Abstract
Stress granules (SGs) are stress-induced membraneless condensates that store non-translating mRNA and stalled translation initiation complexes. Although metazoan SGs are dynamic compartments where proteins can rapidly exchange with their surroundings, yeast SGs seem largely static. To gain a better understanding of yeast SGs, we identified proteins that sediment after heat shock using mass spectrometry. Proteins that sediment upon heat shock are biased toward a subset of abundant proteins that are significantly enriched in intrinsically disordered regions (IDRs). Heat-induced SG localization of over 80 proteins were confirmed using microscopy, including 32 proteins not previously known to localize to SGs. We found that several IDRs were sufficient to mediate SG recruitment. Moreover, the dynamic exchange of IDRs can be observed using fluorescence recovery after photobleaching, whereas other components remain immobile. Lastly, we showed that the IDR of the Ubp3 deubiquitinase was critical for yeast SG formation. This work shows that IDRs can be sufficient for SG incorporation, can remain dynamic in vitrified SGs, and can play an important role in cellular compartmentalization upon stress.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Mang Zhu
- Michael Smith Laboratories, Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Erich R Kuechler
- Michael Smith Laboratories, Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Joyce Zhang
- Michael Smith Laboratories, Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Or Matalon
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Benjamin Dubreuil
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Analise Hofmann
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada, V6T 1Z3
| | - Chris Loewen
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada, V6T 1Z3
| | - Emmanuel D Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Joerg Gsponer
- Michael Smith Laboratories, Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Thibault Mayor
- Michael Smith Laboratories, Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
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17
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Milbury KL, Paul B, Lari A, Fowler C, Montpetit B, Stirling PC. Exonuclease domain mutants of yeast DIS3 display genome instability. Nucleus 2020; 10:21-32. [PMID: 30724665 PMCID: PMC6380420 DOI: 10.1080/19491034.2019.1578600] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The exosome functions to regulate the cellular transcriptome through RNA biogenesis, surveillance, and decay. Mutations in Dis3, a catalytic subunit of the RNA exosome with separable endonuclease and exonuclease activities, are linked to multiple myeloma. Here we report that a cancer-associated DIS3 allele, dis3E729K, provides evidence for DIS3 functioning in mitotic fidelity in yeast. This dis3E729K allele does not induce defects in 7S→5.8S rRNA processing, although it elicits a requirement for P-body function. While it does not significantly influence cell cycle progression alone, the allele reduces the efficiency of cell cycle arrest in strains with defects in kinetochore assembly. Finally, point mutations in the exonuclease domains of yeast Dis3 elicit genome instability phenotypes; however, these DIS3 mutations do not increase DNA damage or RNA processing defects that lead to the accumulation of polyadenylated RNA in the nucleus. These data suggest that specific DIS3 activities support mitotic fidelity in yeast.
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Affiliation(s)
- Karissa L Milbury
- a Terry Fox Laboratory , British Columbia Cancer Agency , Vancouver , Canada
| | - Biplab Paul
- b Department of Cell Biology , University of Alberta , Edmonton , Canada
| | - Azra Lari
- b Department of Cell Biology , University of Alberta , Edmonton , Canada
| | - Claire Fowler
- a Terry Fox Laboratory , British Columbia Cancer Agency , Vancouver , Canada
| | - Ben Montpetit
- b Department of Cell Biology , University of Alberta , Edmonton , Canada.,c Department of Viticulture and Enology , University of California , Davis , CA , USA
| | - Peter C Stirling
- a Terry Fox Laboratory , British Columbia Cancer Agency , Vancouver , Canada.,d Department of Medical Genetics , University of British Columbia , Vancouver , BC , Canada
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18
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Kozlova NV, Pichon C, Rahmouni AR. mRNA with Mammalian Codon Bias Accumulates in Yeast Mutants with Constitutive Stress Granules. Int J Mol Sci 2020; 21:ijms21041234. [PMID: 32059599 PMCID: PMC7072924 DOI: 10.3390/ijms21041234] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/04/2020] [Accepted: 02/04/2020] [Indexed: 11/19/2022] Open
Abstract
Stress granules and P bodies are cytoplasmic structures assembled in response to various stress factors and represent sites of temporary storage or decay of mRNAs. Depending on the source of stress, the formation of these structures may be driven by distinct mechanisms, but several stresses have been shown to stabilize mRNAs via inhibition of deadenylation. A recent study identified yeast gene deletion mutants with constitutive stress granules and elevated P bodies; however, the mechanisms which trigger its formation remain poorly understood. Here, we investigate the possibility of accumulating mRNA with mammalian codon bias, which we termed the model RNA, in these mutants. We found that the model RNA accumulates in dcp2 and xrn1 mutants and in four mutants with constitutive stress granules overlapping with P bodies. However, in eight other mutants with constitutive stress granules, the model RNA is downregulated, or its steady state levels vary. We further suggest that the accumulation of the model RNA is linked to its protection from the main mRNA surveillance path. However, there is no obvious targeting of the model RNA to stress granules or P bodies. Thus, accumulation of the model RNA and formation of constitutive stress granules occur independently and only some paths inducing formation of constitutive stress granules will stabilize mRNA as well.
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Affiliation(s)
- Natalia V. Kozlova
- Centre de Biophysique Moléculaire, UPR 4301 du CNRS, Rue Charles Sadron, 45071 Orléans, France;
- Correspondence: (N.V.K.); (A.R.R.)
| | - Chantal Pichon
- Centre de Biophysique Moléculaire, UPR 4301 du CNRS, Rue Charles Sadron, 45071 Orléans, France;
- Colléguim Sciences et Techniques, Université d’Orléans, 45071 Orléans, France
| | - A. Rachid Rahmouni
- Centre de Biophysique Moléculaire, UPR 4301 du CNRS, Rue Charles Sadron, 45071 Orléans, France;
- Correspondence: (N.V.K.); (A.R.R.)
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19
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Eshleman N, Luo X, Capaldi A, Buchan JR. Alterations of signaling pathways in response to chemical perturbations used to measure mRNA decay rates in yeast. RNA (NEW YORK, N.Y.) 2020; 26:10-18. [PMID: 31601735 PMCID: PMC6913126 DOI: 10.1261/rna.072892.119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/04/2019] [Indexed: 06/10/2023]
Abstract
Assessing variations in mRNA stability typically involves inhibiting transcription either globally or in a gene-specific manner. Alternatively, mRNA pulse-labeling strategies offer a means to calculate mRNA stability without inhibiting transcription. However, key stress-responsive cell signaling pathways, which affect mRNA stability, may themselves be perturbed by the approaches used to measure mRNA stability, leading to artifactual results. Here, we have focused on common strategies to measure mRNA half-lives in yeast and determined that commonly used transcription inhibitors thiolutin and 1,10 phenanthroline inhibit TORC1 signaling, PKC signaling, and partially activate HOG signaling. Additionally, 4-thiouracil (4tU), a uracil analog used in mRNA pulse-labeling approaches, modestly induces P-bodies, mRNA-protein granules implicated in storage and decay of nontranslating mRNA. Thiolutin also induces P-bodies, whereas phenanthroline has no effect. Doxycycline, which controls "Tet On/Tet Off" regulatable promoters, shows no impact on the above signaling pathways or P-bodies. In summary, our data argues that broad-acting transcriptional inhibitors are problematic for determining mRNA half-life, particularly if studying the impacts of the TORC1, HOG, or PKC pathway on mRNA stability. Regulatable promoter systems are a preferred approach for individual mRNA half-life studies, with 4tU labeling representing a good approach to global mRNA half-life analysis, despite modestly inducing P-bodies.
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Affiliation(s)
- Nichole Eshleman
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Xiangxia Luo
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Andrew Capaldi
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - J Ross Buchan
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
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20
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Joshua IM, Höfken T. Ste20 and Cla4 modulate the expression of the glycerol biosynthesis enzyme Gpd1 by a novel MAPK-independent pathway. Biochem Biophys Res Commun 2019; 517:611-616. [PMID: 31395335 DOI: 10.1016/j.bbrc.2019.07.072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 07/19/2019] [Indexed: 11/29/2022]
Abstract
p21-activated kinases (PAKs) are important signalling molecules with a wide range of functions. In budding yeast, the main PAKs Ste20 and Cla4 regulate the response to hyperosmotic stress, which is an excellent model for the adaptation to changing environmental conditions. In this pathway, the only known function of Ste20 and Cla4 is the activation of a mitogen-activated protein kinase (MAPK) cascade through Ste11. This eventually leads to increased transcription of glycerol biosynthesis genes, the most important response to hyperosmotic shock. Here, we show that Ste20 and Cla4 not only stimulate transcription, they also bind to the glycerol biosynthesis enzymes Gpd1, Gpp1 and Gpp2. Protein levels of Gpd1, the enzyme that catalyzes the rate limiting step in glycerol synthesis, positively correlate with glucose availability. Using a chemical genetics approach, we find that simultaneous inactivation of STE20 and CLA4 reduces the glucose-induced increase of Gpd1 levels, whereas the deletion of either STE20 or CLA4 alone has no effect. This is also observed for the hyperosmotic stress-induced increase of Gpd1 levels. Importantly, under both conditions the deletion of STE11 has no effect on Gpd1 induction. These observations suggest that Ste20 and Cla4 not only have a role in the transcriptional regulation of GPD1 through Ste11. They also seem to modulate GPD1 expression at another level such as translation or protein degradation.
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Affiliation(s)
| | - Thomas Höfken
- Division of Biosciences, Brunel University London, UK.
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21
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Mutlu N, Sheidy DT, Hsu A, Jeong HS, Wozniak KJ, Kumar A. A Stress-Responsive Signaling Network Regulating Pseudohyphal Growth and Ribonucleoprotein Granule Abundance in Saccharomyces cerevisiae. Genetics 2019; 213:705-720. [PMID: 31455721 PMCID: PMC6781900 DOI: 10.1534/genetics.119.302538] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 08/21/2019] [Indexed: 11/18/2022] Open
Abstract
The budding yeast Saccharomyces cerevisiae undergoes a stress-responsive transition to a pseudohyphal growth form in which cells elongate and remain connected in multicellular filaments. Pseudohyphal growth is regulated through conserved signaling networks that control cell growth and the response to glucose or nitrogen limitation in metazoans. These networks are incompletely understood, and our studies identify the TORC1- and PKA-regulated kinase Ksp1p as a key stress-responsive signaling effector in the yeast pseudohyphal growth response. The kinase-defective ksp1-K47D allele results in decreased pseudohyphal morphology at the cellular and colony level, indicating that Ksp1p kinase signaling is required for pseudohyphal filamentation. To determine the functional consequences of Ksp1p signaling, we implemented transcriptional profiling and quantitative phosphoproteomic analysis of ksp1-K47D on a global scale. Ksp1p kinase signaling maintains wild-type transcript levels of many pathways for amino acid synthesis and metabolism, relevant for the regulation of translation under conditions of nutrient stress. Proteins in stress-responsive ribonucleoprotein granules are regulated post-translationally by Ksp1p, and the Ksp1p-dependent phosphorylation sites S176 in eIF4G/Tif4631p and S436 in Pbp1p are required for wild-type levels of pseudohyphal growth and Protein Kinase A pathway activity. Pbp1p and Tif4631p localize in stress granules, and the ksp1 null mutant shows elevated abundance of Pbp1p puncta relative to wild-type. Collectively, the Ksp1p kinase signaling network integrates polarized pseudohyphal morphogenesis and translational regulation through the stress-responsive transcriptional control of pathways for amino acid metabolism and post-translational modification of translation factors affecting stress granule abundance.
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Affiliation(s)
- Nebibe Mutlu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Daniel T Sheidy
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | | | - Han Seol Jeong
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Katherine J Wozniak
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Anuj Kumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
- Program in Molecular and Cellular Biology, University of Michigan, Ann Arbor, Michigan 48109
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22
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Cuevas-Bermúdez A, Garrido-Godino AI, Navarro F. A novel yeast chromatin-enriched fractions purification approach, yChEFs, for the chromatin-associated protein analysis used for chromatin-associated and RNA-dependent chromatin-associated proteome studies from Saccharomyces cerevisiae. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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23
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Kroschwald S, Munder MC, Maharana S, Franzmann TM, Richter D, Ruer M, Hyman AA, Alberti S. Different Material States of Pub1 Condensates Define Distinct Modes of Stress Adaptation and Recovery. Cell Rep 2018; 23:3327-3339. [DOI: 10.1016/j.celrep.2018.05.041] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 04/10/2018] [Accepted: 05/14/2018] [Indexed: 01/23/2023] Open
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24
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Falcone C, Mazzoni C. RNA stability and metabolism in regulated cell death, aging and diseases. FEMS Yeast Res 2018; 18:4978431. [DOI: 10.1093/femsyr/foy050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 04/17/2018] [Indexed: 12/13/2022] Open
Affiliation(s)
- Claudio Falcone
- Pasteur Institute-Cenci Bolognetti Foundation, Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185-Rome, Italy
| | - Cristina Mazzoni
- Pasteur Institute-Cenci Bolognetti Foundation, Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185-Rome, Italy
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25
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Abstract
Processing bodies (P-bodies) are cytoplasmic ribonucleoprotein (RNP) granules primarily composed of translationally repressed mRNAs and proteins related to mRNA decay, suggesting roles in post-transcriptional regulation. P-bodies are conserved in eukaryotic cells and exhibit properties of liquid droplets. However, the function of P-bodies in translational repression and/or mRNA decay remains contentious. Here we review recent advances in our understanding of the molecular composition of P-bodies, the interactions and processes that regulate P-body liquid-liquid phase separation (LLPS), and the cellular localization of mRNA decay machinery, in the context of how these discoveries refine models of P-body function.
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Affiliation(s)
- Yang Luo
- Department of Chemistry , Yale University , New Haven , Connecticut 06520 , United States.,Chemical Biology Institute , Yale University , West Haven , Connecticut 06516 , United States
| | - Zhenkun Na
- Department of Chemistry , Yale University , New Haven , Connecticut 06520 , United States.,Chemical Biology Institute , Yale University , West Haven , Connecticut 06516 , United States
| | - Sarah A Slavoff
- Department of Chemistry , Yale University , New Haven , Connecticut 06520 , United States.,Chemical Biology Institute , Yale University , West Haven , Connecticut 06516 , United States.,Department of Molecular Biophysics and Biochemistry , Yale University , New Haven , Connecticut 06529 , United States
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26
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Tenekeci U, Poppe M, Beuerlein K, Buro C, Müller H, Weiser H, Kettner-Buhrow D, Porada K, Newel D, Xu M, Chen ZJ, Busch J, Schmitz ML, Kracht M. K63-Ubiquitylation and TRAF6 Pathways Regulate Mammalian P-Body Formation and mRNA Decapping. Mol Cell 2017; 62:943-957. [PMID: 27315556 DOI: 10.1016/j.molcel.2016.05.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 01/22/2016] [Accepted: 05/13/2016] [Indexed: 01/09/2023]
Abstract
Signals and posttranslational modifications regulating the decapping step in mRNA degradation pathways are poorly defined. In this study we reveal the importance of K63-linked ubiquitylation for the assembly of decapping factors, P-body formation, and constitutive decay of instable mRNAs encoding mediators of inflammation by various experimental approaches. K63-branched ubiquitin chains also regulate IL-1-inducible phosphorylation of the P-body component DCP1a. The E3 ligase TRAF6 binds to DCP1a and indirectly regulates DCP1a phosphorylation, expression of decapping factors, and gene-specific mRNA decay. Mutation of six C-terminal lysines of DCP1a suppresses decapping activity and impairs the interaction with the mRNA decay factors DCP2, EDC4, and XRN1, but not EDC3, thus remodeling P-body architecture. The usage of ubiquitin chains for the proper assembly and function of the decay-competent mammalian decapping complex suggests an additional layer of control to allow a coordinated function of decapping activities and mRNA metabolism in higher eukaryotes.
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Affiliation(s)
- Ulas Tenekeci
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Michael Poppe
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Knut Beuerlein
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Christin Buro
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Helmut Müller
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Hendrik Weiser
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Daniela Kettner-Buhrow
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Katharina Porada
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Doris Newel
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Ming Xu
- Department of Molecular Biology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Zhijian J Chen
- Department of Molecular Biology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Julia Busch
- Institute of Biochemistry, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - M Lienhard Schmitz
- Institute of Biochemistry, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Michael Kracht
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany.
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27
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Min KW, Davila S, Zealy RW, Lloyd LT, Lee IY, Lee R, Roh KH, Jung A, Jemielity J, Choi EJ, Chang JH, Yoon JH. eIF4E phosphorylation by MST1 reduces translation of a subset of mRNAs, but increases lncRNA translation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:761-772. [PMID: 28487214 DOI: 10.1016/j.bbagrm.2017.05.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 05/03/2017] [Accepted: 05/05/2017] [Indexed: 10/19/2022]
Abstract
Post-transcriptional gene regulation is an important step in eukaryotic gene expression. The last step to govern production of nascent peptides is during the process of mRNA translation. mRNA translation is controlled by many translation initiation factors that are susceptible to post-translational modifications. Here we report that one of the translation initiation factors, eIF4E, is phosphorylated by Mammalian Ste20-like kinase (MST1). Upon phosphorylation, eIF4E weakly interacts with the 5' CAP to inhibit mRNA translation. Simultaneously, active polyribosome is more associated with long noncoding RNAs (lncRNAs). Moreover, the linc00689-derived micropeptide, STORM (Stress- and TNF-α-activated ORF Micropeptide), is triggered by TNF-α-induced and MST1-mediated eIF4E phosphorylation, which exhibits molecular mimicry of SRP19 and, thus, competes for 7SL RNA. Our findings have uncovered a novel function of MST1 in mRNA and lncRNA translation by direct phosphorylation of eIF4E. This novel signaling pathway will provide new platforms for regulation of mRNA translation via post-translational protein modification.
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Affiliation(s)
- Kyung-Won Min
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Sylvia Davila
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Richard W Zealy
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Lawson T Lloyd
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - In Young Lee
- Laboratory of Cell Death and Human Diseases, Department of Life Sciences, School of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Rumi Lee
- Laboratory of Cell Death and Human Diseases, Department of Life Sciences, School of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Kyung Hye Roh
- Laboratory of Cell Death and Human Diseases, Department of Life Sciences, School of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Ahjin Jung
- Department of Biology Education, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Eui-Ju Choi
- Laboratory of Cell Death and Human Diseases, Department of Life Sciences, School of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Jeong Ho Chang
- Department of Biology Education, Kyungpook National University, Daegu 41566, Republic of Korea.
| | - Je-Hyun Yoon
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA; Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA.
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28
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Kawa D, Testerink C. Regulation of mRNA decay in plant responses to salt and osmotic stress. Cell Mol Life Sci 2016; 74:1165-1176. [PMID: 27677492 PMCID: PMC5346435 DOI: 10.1007/s00018-016-2376-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/09/2016] [Accepted: 09/21/2016] [Indexed: 11/24/2022]
Abstract
Plant acclimation to environmental stresses requires fast signaling to initiate changes in developmental and metabolic responses. Regulation of gene expression by transcription factors and protein kinases acting upstream are important elements of responses to salt and drought. Gene expression can be also controlled at the post-transcriptional level. Recent analyses on mutants in mRNA metabolism factors suggest their contribution to stress signaling. Here we highlight the components of mRNA decay pathways that contribute to responses to osmotic and salt stress. We hypothesize that phosphorylation state of proteins involved in mRNA decapping affect their substrate specificity.
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Affiliation(s)
- Dorota Kawa
- Plant Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Postbus 94215, 1090 GE, Amsterdam, The Netherlands
| | - Christa Testerink
- Plant Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Postbus 94215, 1090 GE, Amsterdam, The Netherlands.
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29
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Shah KH, Varia SN, Cook LA, Herman PK. A Hybrid-Body Containing Constituents of Both P-Bodies and Stress Granules Forms in Response to Hypoosmotic Stress in Saccharomyces cerevisiae. PLoS One 2016; 11:e0158776. [PMID: 27359124 PMCID: PMC4928847 DOI: 10.1371/journal.pone.0158776] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 06/21/2016] [Indexed: 01/09/2023] Open
Abstract
The cytoplasm of the eukaryotic cell is a highly compartmentalized space that contains a variety of ribonucleoprotein (RNP) granules in addition to its complement of membrane-bound organelles. These RNP granules contain specific sets of proteins and mRNAs and form in response to particular environmental and developmental stimuli. Two of the better-characterized of these RNP structures are the stress granule and Processing-body (P-body) that have been conserved from yeast to humans. In this report, we examined the cues regulating stress granule assembly and the relationship between stress granule and P-body foci. These two RNP structures are generally thought to be independent entities in eukaryotic cells. However, we found here that stress granule and P-body proteins were localized to a common or merged granule specifically in response to a hypoosmotic stress. Interestingly, these hybrid-bodies were found to be transient structures that were resolved with time into separate P-body and stress granule foci. In all, these data suggest that the identity of an RNP granule is not absolute and that it can vary depending upon the nature of the induction conditions. Since the activities of a granule are likely influenced by its protein constituency, these observations are consistent with the possibility of RNP granules having distinct functions in different cellular contexts.
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Affiliation(s)
- Khyati H. Shah
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210, United States of America
| | - Sapna N. Varia
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210, United States of America
| | - Laura A. Cook
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210, United States of America
| | - Paul K. Herman
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210, United States of America
- * E-mail:
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30
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Membrane-association of mRNA decapping factors is independent of stress in budding yeast. Sci Rep 2016; 6:25477. [PMID: 27146487 PMCID: PMC4857118 DOI: 10.1038/srep25477] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 04/19/2016] [Indexed: 12/23/2022] Open
Abstract
Recent evidence has suggested that the degradation of mRNA occurs on translating ribosomes or alternatively within RNA granules called P bodies, which are aggregates whose core constituents are mRNA decay proteins and RNA. In this study, we examined the mRNA decapping proteins, Dcp1, Dcp2, and Dhh1, using subcellular fractionation. We found that decapping factors co-sediment in the polysome fraction of a sucrose gradient and do not alter their behaviour with stress, inhibition of translation or inhibition of the P body formation. Importantly, their localisation to the polysome fraction is independent of the RNA, suggesting that these factors may be constitutively localised to the polysome. Conversely, polysomal and post-polysomal sedimentation of the decapping proteins was abolished with the addition of a detergent, which shifts the factors to the non-translating RNP fraction and is consistent with membrane association. Using a membrane flotation assay, we observed the mRNA decapping factors in the lower density fractions at the buoyant density of membrane-associated proteins. These observations provide further evidence that mRNA decapping factors interact with subcellular membranes, and we suggest a model in which the mRNA decapping factors interact with membranes to facilitate regulation of mRNA degradation.
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31
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ATPase-Modulated Stress Granules Contain a Diverse Proteome and Substructure. Cell 2016; 164:487-98. [PMID: 26777405 DOI: 10.1016/j.cell.2015.12.038] [Citation(s) in RCA: 980] [Impact Index Per Article: 122.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 09/29/2015] [Accepted: 12/15/2015] [Indexed: 12/13/2022]
Abstract
Stress granules are mRNA-protein granules that form when translation initiation is limited, and they are related to pathological granules in various neurodegenerative diseases. Super-resolution microscopy reveals stable substructures, referred to as cores, within stress granules that can be purified. Proteomic analysis of stress granule cores reveals a dense network of protein-protein interactions and links between stress granules and human diseases and identifies ATP-dependent helicases and protein remodelers as conserved stress granule components. ATP is required for stress granule assembly and dynamics. Moreover, multiple ATP-driven machines affect stress granules differently, with the CCT complex inhibiting stress granule assembly, while the MCM and RVB complexes promote stress granule persistence. Our observations suggest that stress granules contain a stable core structure surrounded by a dynamic shell with assembly, disassembly, and transitions between the core and shell modulated by numerous protein and RNA remodeling complexes.
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32
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Mitula F, Tajdel M, Cieśla A, Kasprowicz-Maluśki A, Kulik A, Babula-Skowrońska D, Michalak M, Dobrowolska G, Sadowski J, Ludwików A. Arabidopsis ABA-Activated Kinase MAPKKK18 is Regulated by Protein Phosphatase 2C ABI1 and the Ubiquitin-Proteasome Pathway. PLANT & CELL PHYSIOLOGY 2015; 56:2351-67. [PMID: 26443375 PMCID: PMC4675898 DOI: 10.1093/pcp/pcv146] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 09/24/2015] [Indexed: 05/08/2023]
Abstract
Phosphorylation and dephosphorylation events play an important role in the transmission of the ABA signal. Although SnRK2 [sucrose non-fermenting1-related kinase2] protein kinases and group A protein phosphatase type 2C (PP2C)-type phosphatases constitute the core ABA pathway, mitogen-activated protein kinase (MAPK) pathways are also involved in plant response to ABA. However, little is known about the interplay between MAPKs and PP2Cs or SnRK2 in the regulation of ABA pathways. In this study, an effort was made to elucidate the role of MAP kinase kinase kinase18 (MKKK18) in relation to ABA signaling and response. The MKKK18 knockout lines showed more vigorous root growth, decreased abaxial stomatal index and increased stomatal aperture under normal growth conditions, compared with the control wild-type Columbia line. In addition to transcriptional regulation of the MKKK18 promoter by ABA, we demonstrated using in vitro and in vivo kinase assays that the kinase activity of MKKK18 was regulated by ABA. Analysis of the cellular localization of MKKK18 showed that the active kinase was targeted specifically to the nucleus. Notably, we identified abscisic acid insensitive 1 (ABI1) PP2C as a MKKK18-interacting protein, and demonstrated that ABI1 inhibited its activity. Using a cell-free degradation assay, we also established that MKKK18 was unstable and was degraded by the proteasome pathway. The rate of MKKK18 degradation was delayed in the ABI1 knockout line. Overall, we provide evidence that ABI1 regulates the activity and promotes proteasomal degradation of MKKK18.
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Affiliation(s)
- Filip Mitula
- Department of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland
| | - Malgorzata Tajdel
- Department of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland
| | - Agata Cieśla
- Department of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland
| | - Anna Kasprowicz-Maluśki
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland
| | - Anna Kulik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | | | - Michal Michalak
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland
| | - Grazyna Dobrowolska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Jan Sadowski
- Department of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland
| | - Agnieszka Ludwików
- Department of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland
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33
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Yoon JH, Jo MH, White EJF, De S, Hafner M, Zucconi BE, Abdelmohsen K, Martindale JL, Yang X, Wood WH, Shin YM, Song JJ, Tuschl T, Becker KG, Wilson GM, Hohng S, Gorospe M. AUF1 promotes let-7b loading on Argonaute 2. Genes Dev 2015; 29:1599-604. [PMID: 26253535 PMCID: PMC4536308 DOI: 10.1101/gad.263749.115] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Yoon et al. discovered that RBP AU-rich-binding factor 1 (AUF1) promotes let-7b loading onto Argonaute 2 (AGO2), the catalytic component of the RNA-induced silencing complex (RISC). In turn, AGO2–let-7 triggered target mRNA decay. Eukaryotic gene expression is tightly regulated post-transcriptionally by RNA-binding proteins (RBPs) and microRNAs. The RBP AU-rich-binding factor 1 (AUF1) isoform p37 was found to have high affinity for the microRNA let-7b in vitro (Kd = ∼6 nM) in cells. Ribonucleoprotein immunoprecipitation, in vitro association, and single-molecule-binding analyses revealed that AUF1 promoted let-7b loading onto Argonaute 2 (AGO2), the catalytic component of the RNA-induced silencing complex (RISC). In turn, AGO2–let-7 triggered target mRNA decay. Our findings uncover a novel mechanism by which AUF1 binding and transfer of microRNA let-7 to AGO2 facilitates let-7-elicited gene silencing.
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Affiliation(s)
- Je-Hyun Yoon
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Myung Hyun Jo
- Department of Physics and Astronomy, Institute of Applied Physics, National Center for Creative Research Initiatives, Seoul National University, Seoul 151-747, Korea
| | - Elizabeth J F White
- Department of Biochemistry and Molecular Biology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Supriyo De
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases-Intramural Research Program, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Beth E Zucconi
- Department of Biochemistry and Molecular Biology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Jennifer L Martindale
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Xiaoling Yang
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - William H Wood
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Yu Mi Shin
- Cancer Metastasis Control Center, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-338, Korea
| | - Ji-Joon Song
- Cancer Metastasis Control Center, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-338, Korea
| | - Thomas Tuschl
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Rockefeller University, New York, New York 10065, USA
| | - Kevin G Becker
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Gerald M Wilson
- Department of Biochemistry and Molecular Biology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Sungchul Hohng
- Department of Physics and Astronomy, Institute of Applied Physics, National Center for Creative Research Initiatives, Seoul National University, Seoul 151-747, Korea
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
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34
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Large-Scale Analysis of Kinase Signaling in Yeast Pseudohyphal Development Identifies Regulation of Ribonucleoprotein Granules. PLoS Genet 2015; 11:e1005564. [PMID: 26447709 PMCID: PMC4598065 DOI: 10.1371/journal.pgen.1005564] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 09/10/2015] [Indexed: 01/10/2023] Open
Abstract
Yeast pseudohyphal filamentation is a stress-responsive growth transition relevant to processes required for virulence in pathogenic fungi. Pseudohyphal growth is controlled through a regulatory network encompassing conserved MAPK (Ste20p, Ste11p, Ste7p, Kss1p, and Fus3p), protein kinase A (Tpk2p), Elm1p, and Snf1p kinase pathways; however, the scope of these pathways is not fully understood. Here, we implemented quantitative phosphoproteomics to identify each of these signaling networks, generating a kinase-dead mutant in filamentous S. cerevisiae and surveying for differential phosphorylation. By this approach, we identified 439 phosphoproteins dependent upon pseudohyphal growth kinases. We report novel phosphorylation sites in 543 peptides, including phosphorylated residues in Ras2p and Flo8p required for wild-type filamentous growth. Phosphoproteins in these kinase signaling networks were enriched for ribonucleoprotein (RNP) granule components, and we observe co-localization of Kss1p, Fus3p, Ste20p, and Tpk2p with the RNP component Igo1p. These kinases localize in puncta with GFP-visualized mRNA, and KSS1 is required for wild-type levels of mRNA localization in RNPs. Kss1p pathway activity is reduced in lsm1Δ/Δ and pat1Δ/Δ strains, and these genes encoding P-body proteins are epistatic to STE7. The P-body protein Dhh1p is also required for hyphal development in Candida albicans. Collectively, this study presents a wealth of data identifying the yeast phosphoproteome in pseudohyphal growth and regulatory interrelationships between pseudohyphal growth kinases and RNPs. Eukaryotic cells affect precise changes in shape and growth in response to environmental and nutritional stress, enabling cell survival and wild-type function. The single-celled budding yeast provides a striking example, undergoing a set of changes under conditions of nitrogen or glucose limitation resulting in the formation of extended cellular chains or filaments. Related filamentous growth transitions are required for virulence in pathogenic fungi and have been studied extensively; however, the full scope of signaling underlying the filamentous growth transition remains to be determined. Here, we used a combination of genetics and proteomics to identify proteins that undergo phosphorylation dependent upon kinases required for filamentous growth. Within this protein set, we identified novel sites of phosphorylation in the yeast proteome and extensive phosphorylation of mRNA-protein complexes regulating mRNA decay and translation. The data indicate an interrelationship between filamentous growth and these ubiquitously conserved sites of RNA regulation: the RNA-protein complexes are required for the filamentous growth transition, and a well studied filamentous growth signaling kinase is required for wild-type numbers of RNA-protein complexes. This interdependence is previously unappreciated, highlighting an additional level of translational control underlying this complex growth transition.
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35
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Corcoran JA, McCormick C. Viral activation of stress-regulated Rho-GTPase signaling pathway disrupts sites of mRNA degradation to influence cellular gene expression. Small GTPases 2015; 6:178-85. [PMID: 26480288 PMCID: PMC4905259 DOI: 10.1080/21541248.2015.1093068] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 09/07/2015] [Accepted: 09/08/2015] [Indexed: 01/09/2023] Open
Abstract
Viruses are useful tools that often reveal previously unrecognized levels of control within a cell. By studying the oncogenic Kaposi's sarcoma-associated herpesvirus (KSHV), we discovered a new signaling axis in endothelial cells (ECs) that links actin cytoskeleton dynamics to post-transcriptional control of gene expression. Translational repression and rapid decay of mRNAs containing AU-rich elements (AREs) occurs in cytoplasmic RNA granules known as processing bodies (PBs). Rho-GTPase activity influences PB dynamics but mechanistic details remain obscure. We have previously shown that the KSHV Kaposin B protein blocks the degradation of ARE-mRNAs that encode potent cytokines and angiogenic factors, at least in part by preventing PB formation. Moreover, Kaposin B is sufficient to cause marked alterations in endothelial cell physiology including the formation of long parallel actin stress fibers and accelerated migration and angiogenic phenotypes. All of these phenotypes depend on Kaposin B-mediated activation of a non-canonical signaling pathway comprising the stress-inducible kinase MK2, hsp27, p115RhoGEF and RhoA. Accelerated endothelial cell migration and angiogenesis depends on the subsequent activation of the RhoA-dependent kinase ROCK, but PB disruption is ROCK-independent. In this Commentary, we discuss implications of the activation of this signaling axis, and propose mechanistic links between RhoA activation and PB dynamics.
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Affiliation(s)
- Jennifer A Corcoran
- Department of Microbiology and Immunology; Dalhousie University; Halifax NS, Canada
| | - Craig McCormick
- Department of Microbiology and Immunology; Dalhousie University; Halifax NS, Canada
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36
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Cytoplasmic mRNA turnover and ageing. Mech Ageing Dev 2015; 152:32-42. [PMID: 26432921 PMCID: PMC4710634 DOI: 10.1016/j.mad.2015.09.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 09/17/2015] [Accepted: 09/27/2015] [Indexed: 12/12/2022]
Abstract
We address the cytoplasmic mRNA decay processes that determine the mRNAs half-life. We briefly describe the major, evolutionary conserved, ageing pathways and mechanisms. We summarize critical findings that link mRNA turnover and ageing modulators.
Messenger RNA (mRNA) turnover that determines the lifetime of cytoplasmic mRNAs is a means to control gene expression under both normal and stress conditions, whereas its impact on ageing and age-related disorders has just become evident. Gene expression control is achieved at the level of the mRNA clearance as well as mRNA stability and accessibility to other molecules. All these processes are regulated by cis-acting motifs and trans-acting factors that determine the rates of translation and degradation of transcripts. Specific messenger RNA granules that harbor the mRNA decay machinery or various factors, involved in translational repression and transient storage of mRNAs, are also part of the mRNA fate regulation. Their assembly and function can be modulated to promote stress resistance to adverse conditions and over time affect the ageing process and the lifespan of the organism. Here, we provide insights into the complex relationships of ageing modulators and mRNA turnover mechanisms.
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Bilanchone V, Clemens K, Kaake R, Dawson AR, Matheos D, Nagashima K, Sitlani P, Patterson K, Chang I, Huang L, Sandmeyer S. Ty3 Retrotransposon Hijacks Mating Yeast RNA Processing Bodies to Infect New Genomes. PLoS Genet 2015; 11:e1005528. [PMID: 26421679 PMCID: PMC4589538 DOI: 10.1371/journal.pgen.1005528] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 08/24/2015] [Indexed: 01/15/2023] Open
Abstract
Retrotransposition of the budding yeast long terminal repeat retrotransposon Ty3 is activated during mating. In this study, proteins that associate with Ty3 Gag3 capsid protein during virus-like particle (VLP) assembly were identified by mass spectrometry and screened for roles in mating-stimulated retrotransposition. Components of RNA processing bodies including DEAD box helicases Dhh1/DDX6 and Ded1/DDX3, Sm-like protein Lsm1, decapping protein Dcp2, and 5' to 3' exonuclease Xrn1 were among the proteins identified. These proteins associated with Ty3 proteins and RNA, and were required for formation of Ty3 VLP retrosome assembly factories and for retrotransposition. Specifically, Dhh1/DDX6 was required for normal levels of Ty3 genomic RNA, and Lsm1 and Xrn1 were required for association of Ty3 protein and RNA into retrosomes. This role for components of RNA processing bodies in promoting VLP assembly and retrotransposition during mating in a yeast that lacks RNA interference, contrasts with roles proposed for orthologous components in animal germ cell ribonucleoprotein granules in turnover and epigenetic suppression of retrotransposon RNAs.
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Affiliation(s)
- Virginia Bilanchone
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Kristina Clemens
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Robyn Kaake
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, California, United States of America
| | - Anthony R. Dawson
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Dina Matheos
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Kunio Nagashima
- Electron Microscope Laboratory, NCI-Frederick, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Parth Sitlani
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Kurt Patterson
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Ivan Chang
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, California, United States of America
| | - Suzanne Sandmeyer
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California, United States of America
- * E-mail:
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Abstract
Messenger ribonucleoprotein (mRNP) granules are dynamic, self-assembling structures that harbor non-translating mRNAs bound by various proteins that regulate mRNA translation, localization, and turnover. Their importance in gene expression regulation is far reaching, ranging from precise spatial-temporal control of mRNAs that drive developmental programs in oocytes and embryos, to similarly exquisite control of mRNAs in neurons that underpin synaptic plasticity, and thus, memory formation. Analysis of mRNP granules in their various contexts has revealed common themes of assembly, disassembly, and modes of mRNA regulation, yet new studies continue to reveal unexpected and important findings, such as links between aberrant mRNP granule assembly and neurodegenerative disease. Continued study of these enigmatic structures thus promises fascinating new insights into cellular function, and may also suggest novel therapeutic strategies in various disease states.
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Affiliation(s)
- J Ross Buchan
- a Department of Molecular and Cellular Biology ; University of Arizona ; Tucson , AZ USA
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Yamashita A, Shichino Y, Yamamoto M. The long non-coding RNA world in yeasts. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:147-54. [PMID: 26265144 DOI: 10.1016/j.bbagrm.2015.08.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/29/2015] [Accepted: 08/06/2015] [Indexed: 12/26/2022]
Abstract
In recent years, it has become evident that eukaryotic genomes are pervasively transcribed and produce numerous non-coding transcripts, including long non-coding RNAs (lncRNAs). Although research of such genomic enigmas is in the early stages, a growing number of lncRNAs have been characterized and found to be principal actors in a variety of biological processes rather than merely representing transcriptional noise. Here, we review recent findings on lncRNAs in yeast systems. We especially focus on lncRNA-mediated cellular regulations to respond to environmental changes in the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Akira Yamashita
- Laboratory of Cell Responses, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan; Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan.
| | - Yuichi Shichino
- Laboratory of Cell Responses, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Masayuki Yamamoto
- Laboratory of Cell Responses, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan; Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
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A conserved mechanism of TOR-dependent RCK-mediated mRNA degradation regulates autophagy. Nat Cell Biol 2015; 17:930-942. [PMID: 26098573 PMCID: PMC4528364 DOI: 10.1038/ncb3189] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 05/14/2015] [Indexed: 12/17/2022]
Abstract
Autophagy is an essential eukaryotic pathway requiring tight regulation to maintain homeostasis and preclude disease. Using yeast and mammalian cells, we report a conserved mechanism of autophagy regulation by RNA helicase RCK family members in association with the decapping enzyme Dcp2. Under nutrient-replete conditions, Dcp2 undergoes TOR-dependent phosphorylation and associates with RCK members to form a complex with autophagy-related (ATG) mRNA transcripts, leading to decapping, degradation and autophagy suppression. Simultaneous with the induction of ATG mRNA synthesis, starvation reverses the process, facilitating ATG mRNA accumulation and autophagy induction. This conserved post-transcriptional mechanism modulates fungal virulence and the mammalian inflammasome, the latter providing mechanistic insight into autoimmunity reported in a patient with a PIK3CD/p110δ gain-of-function mutation. We propose a dynamic model wherein RCK family members, in conjunction with Dcp2, function in controlling ATG mRNA stability to govern autophagy, which in turn modulates vital cellular processes affecting inflammation and microbial pathogenesis.
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Raju KK, Natarajan S, Kumar NS, Kumar DA, NM R. Role of cytoplasmic deadenylation and mRNA decay factors in yeast apoptosis. FEMS Yeast Res 2015; 15:fou006. [DOI: 10.1093/femsyr/fou006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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42
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Roux ME, Rasmussen MW, Palma K, Lolle S, Regué ÀM, Bethke G, Glazebrook J, Zhang W, Sieburth L, Larsen MR, Mundy J, Petersen M. The mRNA decay factor PAT1 functions in a pathway including MAP kinase 4 and immune receptor SUMM2. EMBO J 2015; 34:593-608. [PMID: 25603932 DOI: 10.15252/embj.201488645] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Multi-layered defense responses are activated in plants upon recognition of invading pathogens. Transmembrane receptors recognize conserved pathogen-associated molecular patterns (PAMPs) and activate MAP kinase cascades, which regulate changes in gene expression to produce appropriate immune responses. For example, Arabidopsis MAP kinase 4 (MPK4) regulates the expression of a subset of defense genes via at least one WRKY transcription factor. We report here that MPK4 is found in complexes in vivo with PAT1, a component of the mRNA decapping machinery. PAT1 is also phosphorylated by MPK4 and, upon flagellin PAMP treatment, PAT1 accumulates and localizes to cytoplasmic processing (P) bodies which are sites for mRNA decay. Pat1 mutants exhibit dwarfism and de-repressed immunity dependent on the immune receptor SUMM2. Since mRNA decapping is a critical step in mRNA turnover, linking MPK4 to mRNA decay via PAT1 provides another mechanism by which MPK4 may rapidly instigate immune responses.
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Affiliation(s)
- Milena Edna Roux
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Signe Lolle
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Àngels Mateu Regué
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Gerit Bethke
- Department of Plant Biology, University of Minnesota, St. Paul, MN, USA
| | - Jane Glazebrook
- Department of Plant Biology, University of Minnesota, St. Paul, MN, USA
| | - Weiping Zhang
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Leslie Sieburth
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Martin R Larsen
- University of Southern Denmark Institute for Biochemistry and Molecular Biology, Odense, Denmark
| | - John Mundy
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Morten Petersen
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
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43
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Scaffold function of long non-coding RNA HOTAIR in protein ubiquitination. Nat Commun 2014; 4:2939. [PMID: 24326307 DOI: 10.1038/ncomms3939] [Citation(s) in RCA: 333] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 11/14/2013] [Indexed: 02/06/2023] Open
Abstract
Although mammalian long non-coding (lnc)RNAs are best known for modulating transcription, their post-transcriptional influence on mRNA splicing, stability and translation is emerging. Here we report a post-translational function for the lncRNA HOTAIR as an inducer of ubiquitin-mediated proteolysis. HOTAIR associates with E3 ubiquitin ligases bearing RNA-binding domains, Dzip3 and Mex3b, as well as with their respective ubiquitination substrates, Ataxin-1 and Snurportin-1. In this manner, HOTAIR facilitates the ubiquitination of Ataxin-1 by Dzip3 and Snurportin-1 by Mex3b in cells and in vitro, and accelerates their degradation. HOTAIR levels are highly upregulated in senescent cells, causing rapid decay of targets Ataxin-1 and Snurportin-1, and preventing premature senescence. These results uncover a role for a lncRNA, HOTAIR, as a platform for protein ubiquitination.
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Stecker KE, Minkoff BB, Sussman MR. Phosphoproteomic Analyses Reveal Early Signaling Events in the Osmotic Stress Response. PLANT PHYSIOLOGY 2014; 165:1171-1187. [PMID: 24808101 PMCID: PMC4081330 DOI: 10.1104/pp.114.238816] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/29/2014] [Indexed: 05/18/2023]
Abstract
Elucidating how plants sense and respond to water loss is important for identifying genetic and chemical interventions that may help sustain crop yields in water-limiting environments. Currently, the molecular mechanisms involved in the initial perception and response to dehydration are not well understood. Modern mass spectrometric methods for quantifying changes in the phosphoproteome provide an opportunity to identify key phosphorylation events involved in this process. Here, we have used both untargeted and targeted isotope-assisted mass spectrometric methods of phosphopeptide quantitation to characterize proteins in Arabidopsis (Arabidopsis thaliana) whose degree of phosphorylation is rapidly altered by hyperosmotic treatment. Thus, protein phosphorylation events responsive to 5 min of 0.3 m mannitol treatment were first identified using 15N metabolic labeling and untargeted mass spectrometry with a high-resolution ion-trap instrument. The results from these discovery experiments were then validated using targeted Selected Reaction Monitoring mass spectrometry with a triple quadrupole. Targeted Selected Reaction Monitoring experiments were conducted with plants treated under nine different environmental perturbations to determine whether the phosphorylation changes were specific for osmosignaling or involved cross talk with other signaling pathways. The results indicate that regulatory proteins such as members of the mitogen-activated protein kinase family are specifically phosphorylated in response to osmotic stress. Proteins involved in 5' messenger RNA decapping and phosphatidylinositol 3,5-bisphosphate synthesis were also identified as targets of dehydration-induced phosphoregulation. The results of these experiments demonstrate the utility of targeted phosphoproteomic analysis in understanding protein regulation networks and provide new insight into cellular processes involved in the osmotic stress response.
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Affiliation(s)
- Kelly E Stecker
- Department of Biochemistry and Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706
| | - Benjamin B Minkoff
- Department of Biochemistry and Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706
| | - Michael R Sussman
- Department of Biochemistry and Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706
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Weidner J, Wang C, Prescianotto-Baschong C, Estrada AF, Spang A. The polysome-associated proteins Scp160 and Bfr1 prevent P body formation under normal growth conditions. J Cell Sci 2014; 127:1992-2004. [PMID: 24569876 DOI: 10.1242/jcs.142083] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Numerous mRNAs are degraded in processing bodies (P bodies) in Saccharomyces cerevisiae. In logarithmically growing cells, only 0-1 P bodies per cell are detectable. However, the number and appearance of P bodies change once the cell encounters stress. Here, we show that the polysome-associated mRNA-binding protein Scp160 interacts with P body components, such as the decapping protein Dcp2 and the scaffold protein Pat1, presumably, on polysomes. Loss of either Scp160 or its interaction partner Bfr1 caused the formation of Dcp2-positive structures. These Dcp2-positive foci contained mRNA, because their formation was inhibited by the presence of cycloheximide. In addition, Scp160 was required for proper P body formation because only a subset of bona fide P body components could assemble into the Dcp2-positive foci in Δscp160 cells. In either Δbfr1 or Δscp160 cells, P body formation was uncoupled from translational attenuation as the polysome profile remained unchanged. Collectively, our data suggest that Bfr1 and Scp160 prevent P body formation under normal growth conditions.
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Affiliation(s)
- Julie Weidner
- Growth & Development, Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
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47
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Jonas S, Izaurralde E. The role of disordered protein regions in the assembly of decapping complexes and RNP granules. Genes Dev 2014; 27:2628-41. [PMID: 24352420 PMCID: PMC3877753 DOI: 10.1101/gad.227843.113] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Removal of the 5′ cap structure is a critical step in mRNA turnover, yet key questions regarding the assembly and regulation of decapping complexes remain unanswered. This review provides comprehensive insight into the structural and biochemical properties of decapping factors. Jonas and Izaurralde highlight the plasticity of the decapping network and cover recent advances that reveal how short linear motifs (SliMs) in disordered regions help maintain interactions between decapping network members. The removal of the 5′ cap structure by the decapping enzyme DCP2 inhibits translation and generally commits the mRNA to irreversible 5′-to-3′ exonucleolytic degradation by XRN1. DCP2 catalytic activity is stimulated by DCP1, and these proteins form the conserved core of the decapping complex. Additional decapping factors orchestrate the recruitment and activity of this complex in vivo. These factors include enhancer of decapping 3 (EDC3), EDC4, like Sm14A (LSm14A), Pat, the LSm1–7 complex, and the RNA helicase DDX6. Decapping factors are often modular and feature folded domains flanked or connected by low-complexity disordered regions. Recent studies have made important advances in understanding how these disordered regions contribute to the assembly of decapping complexes and promote phase transitions that drive RNP granule formation. These studies have also revealed that the decapping network is governed by interactions mediated by short linear motifs (SLiMs) in these disordered regions. Consequently, the network has rapidly evolved, and although decapping factors are conserved, individual interactions between orthologs have been rewired during evolution. The plasticity of the network facilitates the acquisition of additional subunits or domains in pre-existing subunits, enhances opportunities for regulating mRNA degradation, and eventually leads to the emergence of novel functions.
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Affiliation(s)
- Stefanie Jonas
- Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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48
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Whi3, an S. cerevisiae RNA-binding protein, is a component of stress granules that regulates levels of its target mRNAs. PLoS One 2013; 8:e84060. [PMID: 24386330 PMCID: PMC3873981 DOI: 10.1371/journal.pone.0084060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 11/11/2013] [Indexed: 01/31/2023] Open
Abstract
RNA binding proteins (RBPs) are vital to the regulation of mRNA transcripts, and can alter mRNA localization, degradation, translation, and storage. Whi3 was originally identified in a screen for small cell size mutants, and has since been characterized as an RBP. The identification of Whi3-interacting mRNAs involved in mediating cellular responses to stress suggested that Whi3 might be involved in stress-responsive RNA processing. We show that Whi3 localizes to stress granules in response to glucose deprivation or heat shock. The kinetics and pattern of Whi3 localization in response to a range of temperatures were subtly but distinctly different from those of known components of RNA processing granules. Deletion of Whi3 resulted in an increase in the relative abundance of Whi3 target RNAs, either in the presence or absence of heat shock. Increased levels of the CLN3 mRNA in whi3Δ cells may explain their decreased cell size. Another mRNA target of Whi3 encodes the zinc-responsive transcription factor Zap1, suggesting a role for Whi3 in response to zinc stress. Indeed, we found that whi3Δ cells have enhanced sensitivity to zinc toxicity. Together our results suggest an expanded model for Whi3 function: in addition to its role as a regulator of the cell cycle, Whi3 may have a role in stress-dependent RNA processing and responses to a variety of stress conditions.
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Yoon JH, Abdelmohsen K, Srikantan S, Guo R, Yang X, Martindale JL, Gorospe M. Tyrosine phosphorylation of HuR by JAK3 triggers dissociation and degradation of HuR target mRNAs. Nucleic Acids Res 2013; 42:1196-208. [PMID: 24106086 PMCID: PMC3902907 DOI: 10.1093/nar/gkt903] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In response to stress conditions, many mammalian mRNAs accumulate in stress granules (SGs) together with numerous RNA-binding proteins that control mRNA turnover and translation. However, the signaling cascades that modulate the presence of ribonucleoprotein (RNP) complexes in SGs are poorly understood. Here, we investigated the localization of human antigen R (HuR), an mRNA-stabilizing RNA-binding protein, in SGs following exposure to the stress agent arsenite. Unexpectedly, the mobilization of HuR to SGs was prevented through the activation of Janus kinase 3 (JAK3) by the vitamin K3 analog menadione. JAK3 phosphorylated HuR at tyrosine 200, in turn inhibiting HuR localization in SGs, reducing HuR interaction with targets SIRT1 and VHL mRNAs, and accelerating target mRNA decay. Our findings indicate that HuR is tyrosine-phosphorylated by JAK3, and link this modification to HuR subcytoplasmic localization and to the fate of HuR target mRNAs.
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Affiliation(s)
- Je-Hyun Yoon
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
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Hopkins KC, McLane LM, Maqbool T, Panda D, Gordesky-Gold B, Cherry S. A genome-wide RNAi screen reveals that mRNA decapping restricts bunyaviral replication by limiting the pools of Dcp2-accessible targets for cap-snatching. Genes Dev 2013; 27:1511-25. [PMID: 23824541 DOI: 10.1101/gad.215384.113] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Bunyaviruses are an emerging group of medically important viruses, many of which are transmitted from insects to mammals. To identify host factors that impact infection, we performed a genome-wide RNAi screen in Drosophila and identified 131 genes that impacted infection of the mosquito-transmitted bunyavirus Rift Valley fever virus (RVFV). Dcp2, the catalytic component of the mRNA decapping machinery, and two decapping activators, DDX6 and LSM7, were antiviral against disparate bunyaviruses in both insect cells and adult flies. Bunyaviruses 5' cap their mRNAs by "cap-snatching" the 5' ends of poorly defined host mRNAs. We found that RVFV cap-snatches the 5' ends of Dcp2 targeted mRNAs, including cell cycle-related genes. Loss of Dcp2 allows increased viral transcription without impacting viral mRNA stability, while ectopic expression of Dcp2 impedes viral transcription. Furthermore, arresting cells in late S/early G2 led to increased Dcp2 mRNA targets and increased RVFV replication. Therefore, RVFV competes for the Dcp2-accessible mRNA pool, which is dynamically regulated and can present a bottleneck for viral replication.
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