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Pérez-Ortín JE, Jordán-Pla A, Zhang Y, Moreno-García J, Bassot C, Barba-Aliaga M, de Campos-Mata L, Choder M, Díez J, Piazza I, Pelechano V, García-Martínez J. Comparison of Xrn1 and Rat1 5' → 3' exoribonucleases in budding yeast supports the specific role of Xrn1 in cotranslational mRNA decay. Yeast 2024. [PMID: 38874348 DOI: 10.1002/yea.3968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 05/24/2024] [Accepted: 05/30/2024] [Indexed: 06/15/2024] Open
Abstract
The yeast Saccharomyces cerevisiae and most eukaryotes carry two 5' → 3' exoribonuclease paralogs. In yeast, they are called Xrn1, which shuttles between the nucleus and the cytoplasm, and executes major cytoplasmic messenger RNA (mRNA) decay, and Rat1, which carries a strong nuclear localization sequence (NLS) and localizes to the nucleus. Xrn1 is 30% identical to Rat1 but has an extra ~500 amino acids C-terminal extension. In the cytoplasm, Xrn1 can degrade decapped mRNAs during the last round of translation by ribosomes, a process referred to as "cotranslational mRNA decay." The division of labor between the two enzymes is still enigmatic and serves as a paradigm for the subfunctionalization of many other paralogs. Here we show that Rat1 is capable of functioning in cytoplasmic mRNA decay, provided that Rat1 remains cytoplasmic due to its NLS disruption (cRat1). This indicates that the physical segregation of the two paralogs plays roles in their specific functions. However, reversing segregation is not sufficient to fully complement the Xrn1 function. Specifically, cRat1 can partially restore the cell volume, mRNA stability, the proliferation rate, and 5' → 3' decay alterations that characterize xrn1Δ cells. Nevertheless, cotranslational decay is only slightly complemented by cRat1. The use of the AlphaFold prediction for cRat1 and its subsequent docking with the ribosome complex and the sequence conservation between cRat1 and Xrn1 suggest that the tight interaction with the ribosome observed for Xrn1 is not maintained in cRat1. Adding the Xrn1 C-terminal domain to Rat1 does not improve phenotypes, which indicates that lack of the C-terminal is not responsible for partial complementation. Overall, during evolution, it appears that the two paralogs have acquired specific characteristics to make functional partitioning beneficial.
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Affiliation(s)
- José E Pérez-Ortín
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, Burjassot, Spain
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Antonio Jordán-Pla
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, Burjassot, Spain
| | - Yujie Zhang
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Jorge Moreno-García
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, Burjassot, Spain
| | - Claudio Bassot
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC Berlin), Berlin, Germany
| | - Marina Barba-Aliaga
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, Burjassot, Spain
| | - Leire de Campos-Mata
- Virology Unit, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Mordechai Choder
- Department of Molecular Microbiology, Technion-Israel Institute of Technology, Rappaport Faculty of Medicine, Haifa, Israel
| | - Juana Díez
- Virology Unit, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Ilaria Piazza
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC Berlin), Berlin, Germany
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - José García-Martínez
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, Burjassot, Spain
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Liu H, Marayati BF, de la Cerda D, Lemezis BM, Gao J, Song Q, Chen M, Reid KZ. The Cross-Regulation Between Set1, Clr4, and Lsd1/2 in Schizosaccharomyces pombe. PLoS Genet 2024; 20:e1011107. [PMID: 38181050 PMCID: PMC10795994 DOI: 10.1371/journal.pgen.1011107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 01/18/2024] [Accepted: 12/12/2023] [Indexed: 01/07/2024] Open
Abstract
Eukaryotic chromatin is organized into either silenced heterochromatin or relaxed euchromatin regions, which controls the accessibility of transcriptional machinery and thus regulates gene expression. In fission yeast, Schizosaccharomyces pombe, Set1 is the sole H3K4 methyltransferase and is mainly enriched at the promoters of actively transcribed genes. In contrast, Clr4 methyltransferase initiates H3K9 methylation, which has long been regarded as a hallmark of heterochromatic silencing. Lsd1 and Lsd2 are two highly conserved H3K4 and H3K9 demethylases. As these histone-modifying enzymes perform critical roles in maintaining histone methylation patterns and, consequently, gene expression profiles, cross-regulations among these enzymes are part of the complex regulatory networks. Thus, elucidating the mechanisms that govern their signaling and mutual regulations remains crucial. Here, we demonstrated that C-terminal truncation mutants, lsd1-ΔHMG and lsd2-ΔC, do not compromise the integrity of the Lsd1/2 complex but impair their chromatin-binding capacity at the promoter region of target genomic loci. We identified protein-protein interactions between Lsd1/2 and Raf2 or Swd2, which are the subunits of the Clr4 complex (CLRC) and Set1-associated complex (COMPASS), respectively. We showed that Clr4 and Set1 modulate the protein levels of Lsd1 and Lsd2 in opposite ways through the ubiquitin-proteasome-dependent pathway. During heat stress, the protein levels of Lsd1 and Lsd2 are upregulated in a Set1-dependent manner. The increase in protein levels is crucial for differential gene expression under stress conditions. Together, our results support a cross-regulatory model by which Set1 and Clr4 methyltransferases control the protein levels of Lsd1/2 demethylases to shape the dynamic chromatin landscape.
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Affiliation(s)
- Haoran Liu
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Bahjat Fadi Marayati
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - David de la Cerda
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Brendan Matthew Lemezis
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Jieyu Gao
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Qianqian Song
- Department of Health Outcomes and Biomedical Informatics, University of Florida, Gainesville, Florida, United States of America
| | - Minghan Chen
- Department of Computer Science, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Ke Zhang Reid
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
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García-Martínez J, Singh A, Medina D, Chávez S, Pérez-Ortín JE. Enhanced gene regulation by cooperation between mRNA decay and gene transcription. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194910. [PMID: 36731791 PMCID: PMC10663100 DOI: 10.1016/j.bbagrm.2023.194910] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/31/2023]
Abstract
It has become increasingly clear in the last few years that gene expression in eukaryotes is not a linear process from mRNA synthesis in the nucleus to translation and degradation in the cytoplasm, but works as a circular one where the mRNA level is controlled by crosstalk between nuclear transcription and cytoplasmic decay pathways. One of the consequences of this crosstalk is the approximately constant level of mRNA. This is called mRNA buffering and happens when transcription and mRNA degradation act at compensatory rates. However, if transcription and mRNA degradation act additively, enhanced gene expression regulation occurs. In this work, we analyzed new and previously published genomic datasets obtained for several yeast mutants related to either transcription or mRNA decay that are not known to play any role in the other process. We show that some, which were presumed only transcription factors (Sfp1) or only decay factors (Puf3, Upf2/3), may represent examples of RNA-binding proteins (RBPs) that make specific crosstalk to enhance the control of the mRNA levels of their target genes by combining additive effects on transcription and mRNA stability. These results were mathematically modeled to see the effects of RBPs when they have positive or negative effects on mRNA synthesis and decay rates. We found that RBPs can be an efficient way to buffer or enhance gene expression responses depending on their respective effects on transcription and mRNA stability.
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Affiliation(s)
- José García-Martínez
- Instituto de Biotecnología y Biomedicina (Biotecmed), Facultad de Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE 19716, USA
| | - Daniel Medina
- Instituto de Biotecnología y Biomedicina (Biotecmed), Facultad de Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain
| | - Sebastián Chávez
- Departamento de Genética, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, 41013 Seville, Spain; Dirección de Evaluación y Acreditación, Agencia Andaluza del Conocimiento, Doña Berenguela s/n, planta 3ª C.P. 14006, Córdoba, Spain
| | - José E Pérez-Ortín
- Instituto de Biotecnología y Biomedicina (Biotecmed), Facultad de Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain.
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Zarreen F, Karim MJ, Chakraborty S. The diverse roles of histone 2B monoubiquitination in the life of plants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3854-3865. [PMID: 35348666 DOI: 10.1093/jxb/erac120] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Covalent modification of histones is an important tool for gene transcriptional control in eukaryotes, which coordinates growth, development, and adaptation to environmental changes. In recent years, an important role for monoubiquitination of histone 2B (H2B) has emerged in plants, where it is associated with transcriptional activation. In this review, we discuss the dynamics of the H2B monoubiquitination system in plants and its role in regulating developmental processes including flowering, circadian rhythm, photomorphogenesis, and the response to abiotic and biotic stress including drought, salinity, and fungal, bacterial, and viral pathogens. Furthermore, we highlight the crosstalk between H2B monoubiquitination and other histone modifications which fine-tunes transcription and ensures developmental plasticity. Finally, we put into perspective how this versatile regulatory mechanism can be developed as a useful tool for crop improvement.
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Affiliation(s)
- Fauzia Zarreen
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Mir Jishan Karim
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Supriya Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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5
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Nuclear mRNA Export and Aging. Int J Mol Sci 2022; 23:ijms23105451. [PMID: 35628261 PMCID: PMC9142925 DOI: 10.3390/ijms23105451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 02/04/2023] Open
Abstract
The relationship between transcription and aging is one that has been studied intensively and experimentally with diverse attempts. However, the impact of the nuclear mRNA export on the aging process following its transcription is still poorly understood, although the nuclear events after transcription are coupled closely with the transcription pathway because the essential factors required for mRNA transport, namely TREX, TREX-2, and nuclear pore complex (NPC), physically and functionally interact with various transcription factors, including the activator/repressor and pre-mRNA processing factors. Dysregulation of the mediating factors for mRNA export from the nucleus generally leads to the aberrant accumulation of nuclear mRNA and further impairment in the vegetative growth and normal lifespan and the pathogenesis of neurodegenerative diseases. The optimal stoichiometry and density of NPC are destroyed during the process of cellular aging, and their damage triggers a defect of function in the nuclear permeability barrier. This review describes recent findings regarding the role of the nuclear mRNA export in cellular aging and age-related neurodegenerative disorders.
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Zhao M, Han M, Liang L, Song Q, Li X, Du Y, Hu D, Cheng Y, Wang QK, Ke T. Mog1 deficiency promotes cardiac contractile dysfunction and isoproterenol-induced arrhythmias associated with cardiac fibrosis and Cx43 remodeling. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166429. [PMID: 35533905 DOI: 10.1016/j.bbadis.2022.166429] [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: 02/08/2022] [Revised: 04/21/2022] [Accepted: 05/02/2022] [Indexed: 10/18/2022]
Abstract
Our earlier studies identified MOG1 as a Nav1.5-binding protein that promotes Nav1.5 intracellular trafficking to plasma membranes. Genetic studies have identified MOG1 variants responsible for cardiac arrhythmias. However, the physiological functions of MOG1 in vivo remain incompletely characterized. In this study, we generated Mog1 knockout (Mog1-/-) mice. Mog1-/- mice did not develop spontaneous arrhythmias at the baseline, but exhibited a prolongation of QRS duration. Mog1-/- mice treated with isoproterenol (ISO), but not with flecainide, exhibited an increased risk of arrhythmias and even sudden death. Mog1-/- mice had normal cardiac morphology, however, LV systolic dysfunction was identified and associated with an increase in ventricular fibrosis. Whole-cell patch-clamping and Western blotting analysis clearly demonstrated the normal cardiac expression and function of Nav1.5 in Mog1-/- mice. Further RNA-seq and iTRAQ analysis identified critical pathways and genes, including extracellular matrix (Mmp2), gap junction (Gja1), and mitochondrial components that were dysregulated in Mog1-/- mice. RT-qPCR, Western blotting, and immunofluorescence assays revealed reduced cardiac expression of Gja1 in Mog1-/- mice. Dye transfer assays confirmed impairment of gap-junction function; Cx43 gap-junction enhancer ZP123 decreased arrhythmia inducibility in ISO-treated Mog1-/- mice. Transmission electron microscopy analysis revealed abnormal sarcomere ultrastructure and altered mitochondrial morphology in Mog1-/- mice. Mitochondrial dynamics was found to be disturbed, and associated with a trend toward increased mitochondrial fusion in Mog1-/- mice. Meanwhile, the level of ATP supply was increased in the hearts of Mog1-/- mice. These results indicate that MOG1 plays an important role in cardiac electrophysiology and cardiac contractile function.
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Affiliation(s)
- Miao Zhao
- Center for Human Genome Research, The Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Cardio-X Institute, Huazhong University of Science and Technology, Wuhan, 430074, Hubei Province, PR China
| | - Meng Han
- Hubei Provincial Key Laboratory of Occurrence and Intervention of Kidney Diseases, Medical College, Hubei Polytechnic University, Huangshi, Hubei Province, PR China
| | - Lina Liang
- Center for Human Genome Research, The Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Cardio-X Institute, Huazhong University of Science and Technology, Wuhan, 430074, Hubei Province, PR China
| | - Qixue Song
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 518055 Shenzhen, PR China
| | - Xia Li
- Center for Human Genome Research, The Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Cardio-X Institute, Huazhong University of Science and Technology, Wuhan, 430074, Hubei Province, PR China
| | - Yimei Du
- Research Center of Ion Channelopathy, Institute of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, PR China
| | - Dongping Hu
- Center for Human Genome Research, The Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Cardio-X Institute, Huazhong University of Science and Technology, Wuhan, 430074, Hubei Province, PR China
| | - Yu Cheng
- Center for Human Genome Research, The Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Cardio-X Institute, Huazhong University of Science and Technology, Wuhan, 430074, Hubei Province, PR China
| | - Qing K Wang
- Center for Human Genome Research, The Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Cardio-X Institute, Huazhong University of Science and Technology, Wuhan, 430074, Hubei Province, PR China.
| | - Tie Ke
- Center for Human Genome Research, The Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Cardio-X Institute, Huazhong University of Science and Technology, Wuhan, 430074, Hubei Province, PR China.
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7
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Gou D, Zhou J, Song Q, Wang Z, Bai X, Zhang Y, Zuo M, Wang F, Chen A, Yousaf M, Yang Z, Peng H, Li K, Xie W, Tang J, Yao Y, Han M, Ke T, Chen Q, Xu C, Wang Q. Mog1 knockout causes cardiac hypertrophy and heart failure by downregulating tbx5-cryab-hspb2 signalling in zebrafish. Acta Physiol (Oxf) 2021; 231:e13567. [PMID: 33032360 DOI: 10.1111/apha.13567] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 09/09/2020] [Accepted: 09/29/2020] [Indexed: 12/19/2022]
Abstract
AIMS MOG1 is a small protein that can bind to small GTPase RAN and regulate transport of RNA and proteins between the cytoplasm and nucleus. However, the in vivo physiological role of mog1 in the heart needs to be fully defined. METHODS Mog1 knockout zebrafish was generated by TALEN. Echocardiography, histological analysis, and electrocardiograms were used to examine cardiac structure and function. RNA sequencing and real-time RT-PCR were used to elucidate the molecular mechanism and to analyse the gene expression. Isoproterenol was used to induce cardiac hypertrophy. Whole-mount in situ hybridization was used to observe cardiac morphogenesis. RESULTS Mog1 knockout zebrafish developed cardiac hypertrophy and heart failure (enlarged pericardium, increased nppa and nppb expression and ventricular wall thickness, and reduced ejection fraction), which was aggravated by isoproterenol. RNAseq and KEGG pathway analyses revealed the effect of mog1 knockout on the pathways of cardiac hypertrophy, dilatation and contraction. Mechanistic studies revealed that mog1 knockout decreased expression of tbx5, which reduced expression of cryab and hspb2, resulting in cardiac hypertrophy and heart failure. Overexpression of cryab, hspb2 and tbx5 rescued the cardiac oedema phenotype of mog1 KO zebrafish. Telemetry electrocardiogram monitoring showed QRS and QTc prolongation and a reduced heart rate in mog1 knockout zebrafish, which was associated with reduced scn1b expression. Moreover, mog1 knockout resulted in abnormal cardiac looping during embryogenesis because of the reduced expression of nkx2.5, gata4 and hand2. CONCLUSION Our data identified an important molecular determinant for cardiac hypertrophy and heart failure, and rhythm maintenance of the heart.
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Affiliation(s)
- Dongzhi Gou
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Juan Zhou
- School of Basic Medicine Gannan Medical University Ganzhou P. R. China
| | - Qixue Song
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Zhijie Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Xuemei Bai
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Yidan Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Mengxia Zuo
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Fan Wang
- Department of Cardiovascular and Metabolic Sciences Lerner Research Institute Department of Cardiovascular Medicine Cleveland Clinic Cleveland OH USA
- Department of Molecular Medicine Cleveland Clinic Lerner College of Medicine of CaseWestern Reserve University Cleveland OH USA
| | - Ailan Chen
- Department of Cardiology Guangzhou Medical University Guangzhou P. R. China
| | - Muhammad Yousaf
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Zhongcheng Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Huixing Peng
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Ke Li
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Wen Xie
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Jingluo Tang
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Yufeng Yao
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Meng Han
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Tie Ke
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Qiuyun Chen
- Department of Cardiovascular and Metabolic Sciences Lerner Research Institute Department of Cardiovascular Medicine Cleveland Clinic Cleveland OH USA
- Department of Molecular Medicine Cleveland Clinic Lerner College of Medicine of CaseWestern Reserve University Cleveland OH USA
| | - Chengqi Xu
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Qing Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
- Department of Cardiovascular and Metabolic Sciences Lerner Research Institute Department of Cardiovascular Medicine Cleveland Clinic Cleveland OH USA
- Department of Molecular Medicine Cleveland Clinic Lerner College of Medicine of CaseWestern Reserve University Cleveland OH USA
- Department of Genetics and Genome Science Case Western Reserve University School of Medicine Cleveland OH USA
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Xie L. Mog1 to tbx5-cryab/hspb2: A novel signalling network potentiates heart failure? Acta Physiol (Oxf) 2021; 231:e13593. [PMID: 33280261 DOI: 10.1111/apha.13593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Linglin Xie
- Department of Nutrition Texas A&M University College Station TX USA
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9
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Functional analysis of an essential Ran-binding protein gene, CpRbp1, from the chestnut blight fungus Cryphonectria parasitica using heterokaryon rescue. Sci Rep 2020; 10:8111. [PMID: 32415177 PMCID: PMC7229160 DOI: 10.1038/s41598-020-65036-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 04/24/2020] [Indexed: 12/11/2022] Open
Abstract
A Ran binding protein (RanBP) homolog, CpRbp1, from Cryphonectria parasitica, has been identified as a protein that is affected by hypovirus infection or tannic acid supplementation. In this study, functional analyses of CpRbp1 were performed by constructing a knockout mutant and analyzing the resulting heterokaryon. Transformation-mediated gene replacement resulted in two putative CpRbp1-null mutants and genotype analyses identified these two mutants as heterokaryotic transformants consisting of two types of nuclei, one with the wild-type CpRbp1 allele and another with the CpRbp1-null mutant allele. Although stable mycelial growth of the heterokaryotic transformant was observed on selective medium containing hygromycin B, neither germination nor growth of the resulting conidia, which were single-cell monokaryotic progeny, was observed on the medium. In trans complementation of heterokaryons using a full-length wild-type allele of the CpRbp1 gene resulted in complemented transformants. These transformants sporulated single-cell monokaryotic conidia that were able to grow on media selective for replacing and/or complementing markers. These results clearly indicate that CpRbp1 is an essential gene, and heterokaryons allowed the fungus to maintain lethal CpRbp1-null mutant nuclei. Moreover, in trans complementation of heterokaryons using chimeric structures of the CpRbp1 gene allowed for analysis of its functional domains, which was previously hampered due to the lethality of the gene. In addition, in trans complementation using heterologous RanBP genes from Aspergillus nidulans was successful, suggesting that the function of RanBP is conserved during evolution. Furthermore, in trans complementation allowed for functional analyses of lethal orthologs. This study demonstrates that our fungal heterokaryon system can be applied effectively to determine whether a gene of interest is essential, perform functional analyses of a lethal gene, and analyze corresponding heterologous genes.
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10
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Nuño-Cabanes C, Ugidos M, Tarazona S, Martín-Expósito M, Ferrer A, Rodríguez-Navarro S, Conesa A. A multi-omics dataset of heat-shock response in the yeast RNA binding protein Mip6. Sci Data 2020; 7:69. [PMID: 32109230 PMCID: PMC7046740 DOI: 10.1038/s41597-020-0412-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/10/2020] [Indexed: 11/25/2022] Open
Abstract
Gene expression is a biological process regulated at different molecular levels, including chromatin accessibility, transcription, and RNA maturation and transport. In addition, these regulatory mechanisms have strong links with cellular metabolism. Here we present a multi-omics dataset that captures different aspects of this multi-layered process in yeast. We obtained RNA-seq, metabolomics, and H4K12ac ChIP-seq data for wild-type and mip6Δ strains during a heat-shock time course. Mip6 is an RNA-binding protein that contributes to RNA export during environmental stress and is informative of the contribution of post-transcriptional regulation to control cellular adaptations to environmental changes. The experiment was performed in quadruplicate, and the different omics measurements were obtained from the same biological samples, which facilitates the integration and analysis of data using covariance-based methods. We validate our dataset by showing that ChIP-seq, RNA-seq and metabolomics signals recapitulate existing knowledge about the response of ribosomal genes and the contribution of trehalose metabolism to heat stress. Raw data, processed data and preprocessing scripts are made available.
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Grants
- PROMETEO/2016/093 Regional Government of Valencia | Conselleria d'Educació, Investigació, Cultura i Esport (Conselleria d'Educació, Investigació, Cultura i Esport de la Generalitat Valenciana)
- PROMETEO/2016/093 Regional Government of Valencia | Conselleria d'Educació, Investigació, Cultura i Esport (Conselleria d'Educació, Investigació, Cultura i Esport de la Generalitat Valenciana)
- PROMETEO/2016/093 Regional Government of Valencia | Conselleria d'Educació, Investigació, Cultura i Esport (Conselleria d'Educació, Investigació, Cultura i Esport de la Generalitat Valenciana)
- PROMETEO/2016/093 Regional Government of Valencia | Conselleria d'Educació, Investigació, Cultura i Esport (Conselleria d'Educació, Investigació, Cultura i Esport de la Generalitat Valenciana)
- PROMETEO/2016/093 Regional Government of Valencia | Conselleria d'Educació, Investigació, Cultura i Esport (Conselleria d'Educació, Investigació, Cultura i Esport de la Generalitat Valenciana)
- Regional Government of Valencia | Conselleria d'Educació, Investigació, Cultura i Esport (Conselleria d'Educació, Investigació, Cultura i Esport de la Generalitat Valenciana)
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Affiliation(s)
- Carme Nuño-Cabanes
- Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia (CSIC). Jaume Roig, 11, E-46010, Valencia, Spain
- Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe, Eduardo Primo-Yúfera, E-46012, Valencia, Spain
| | - Manuel Ugidos
- Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia (CSIC). Jaume Roig, 11, E-46010, Valencia, Spain
- Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe, Eduardo Primo-Yúfera, E-46012, Valencia, Spain
| | - Sonia Tarazona
- Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València (UPV), Valencia, Spain
| | - Manuel Martín-Expósito
- Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia (CSIC). Jaume Roig, 11, E-46010, Valencia, Spain
| | - Alberto Ferrer
- Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València (UPV), Valencia, Spain
| | - Susana Rodríguez-Navarro
- Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia (CSIC). Jaume Roig, 11, E-46010, Valencia, Spain.
- Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe, Eduardo Primo-Yúfera, E-46012, Valencia, Spain.
| | - Ana Conesa
- Microbiology and Cell Science Department, University of Florida, Gainesville, Florida, USA.
- Institute for Food and Agricultural Reserach, University of Florida, Gainesville, Florida, USA.
- Genetics Institute, University of Florida, Gainesville, Florida, USA.
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11
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Muellner J, Schmidt KH. Yeast Genome Maintenance by the Multifunctional PIF1 DNA Helicase Family. Genes (Basel) 2020; 11:genes11020224. [PMID: 32093266 PMCID: PMC7073672 DOI: 10.3390/genes11020224] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 12/04/2022] Open
Abstract
The two PIF1 family helicases in Saccharomyces cerevisiae, Rrm3, and ScPif1, associate with thousands of sites throughout the genome where they perform overlapping and distinct roles in telomere length maintenance, replication through non-histone proteins and G4 structures, lagging strand replication, replication fork convergence, the repair of DNA double-strand break ends, and transposable element mobility. ScPif1 and its fission yeast homolog Pfh1 also localize to mitochondria where they protect mitochondrial genome integrity. In addition to yeast serving as a model system for the rapid functional evaluation of human Pif1 variants, yeast cells lacking Rrm3 have proven useful for elucidating the cellular response to replication fork pausing at endogenous sites. Here, we review the increasingly important cellular functions of the yeast PIF1 helicases in maintaining genome integrity, and highlight recent advances in our understanding of their roles in facilitating fork progression through replisome barriers, their functional interactions with DNA repair, and replication stress response pathways.
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Affiliation(s)
- Julius Muellner
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA;
- Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Kristina H. Schmidt
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA;
- Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
- Correspondence:
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12
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Martín-Expósito M, Gas ME, Mohamad N, Nuño-Cabanes C, Tejada-Colón A, Pascual-García P, de la Fuente L, Chaves-Arquero B, Merran J, Corden J, Conesa A, Pérez-Cañadillas JM, Bravo J, Rodríguez-Navarro S. Mip6 binds directly to the Mex67 UBA domain to maintain low levels of Msn2/4 stress-dependent mRNAs. EMBO Rep 2019; 20:e47964. [PMID: 31680439 DOI: 10.15252/embr.201947964] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 08/30/2019] [Accepted: 09/11/2019] [Indexed: 11/09/2022] Open
Abstract
RNA-binding proteins (RBPs) participate in all steps of gene expression, underscoring their potential as regulators of RNA homeostasis. We structurally and functionally characterize Mip6, a four-RNA recognition motif (RRM)-containing RBP, as a functional and physical interactor of the export factor Mex67. Mip6-RRM4 directly interacts with the ubiquitin-associated (UBA) domain of Mex67 through a loop containing tryptophan 442. Mip6 shuttles between the nucleus and the cytoplasm in a Mex67-dependent manner and concentrates in cytoplasmic foci under stress. Photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation experiments show preferential binding of Mip6 to mRNAs regulated by the stress-response Msn2/4 transcription factors. Consistent with this binding, MIP6 deletion affects their export and expression levels. Additionally, Mip6 interacts physically and/or functionally with proteins with a role in mRNA metabolism and transcription such as Rrp6, Xrn1, Sgf73, and Rpb1. These results reveal a novel role for Mip6 in the homeostasis of Msn2/4-dependent transcripts through its direct interaction with the Mex67 UBA domain.
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Affiliation(s)
- Manuel Martín-Expósito
- Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia (CSIC), Valencia, Spain.,Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Maria-Eugenia Gas
- Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Nada Mohamad
- Signal Transduction Laboratory, Instituto de Biomedicina de Valencia (CSIC), Valencia, Spain
| | - Carme Nuño-Cabanes
- Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia (CSIC), Valencia, Spain.,Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Ana Tejada-Colón
- Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia (CSIC), Valencia, Spain
| | - Pau Pascual-García
- Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Lorena de la Fuente
- Genomics of Gene Expression Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Belén Chaves-Arquero
- Department of Biological Physical Chemistry, Institute of Physical-Chemistry "Rocasolano" (CSIC), Madrid, Spain
| | - Jonathan Merran
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jeffry Corden
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ana Conesa
- Genetics Institute, University of Florida, Gainesville, FL, USA.,Microbiology and Cell Science Department, Institute for Food and Agricultural Research, University of Florida, Gainesville, FL, USA
| | | | - Jerónimo Bravo
- Signal Transduction Laboratory, Instituto de Biomedicina de Valencia (CSIC), Valencia, Spain
| | - Susana Rodríguez-Navarro
- Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia (CSIC), Valencia, Spain.,Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
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