1
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Li T, Chao TC, Tsai KL. Structures and compositional dynamics of Mediator in transcription regulation. Curr Opin Struct Biol 2024; 88:102892. [PMID: 39067114 DOI: 10.1016/j.sbi.2024.102892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/30/2024] [Accepted: 07/05/2024] [Indexed: 07/30/2024]
Abstract
The eukaryotic Mediator, comprising a large Core (cMED) and a dissociable CDK8 kinase module (CKM), functions as a critical coregulator during RNA polymerase II (RNAPII) transcription. cMED recruits RNAPII and facilitates the assembly of the pre-initiation complex (PIC) at promoters. In contrast, CKM prevents RNAPII binding to cMED while simultaneously exerting positive or negative influence on gene transcription through its kinase function. Recent structural studies on cMED and CKM have revealed their intricate architectures and subunit interactions. Here, we explore these structures, providing a comprehensive insight into Mediator (cMED-CKM) architecture and its potential mechanism in regulating RNAPII transcription. Additionally, we discuss the remaining puzzles that require further investigation to fully understand how cMED coordinates with CKM to regulate transcription in various events.
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Affiliation(s)
- Tao Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston TX, USA
| | - Ti-Chun Chao
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston TX, USA
| | - Kuang-Lei Tsai
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston TX, USA.
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2
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Wu G, Lian R, Li M, Jin L, Jia T, Wang L, Gan L, Zhao S, Liang R, Dong Y. Novel homozygous missense variants in MED27 associated with neurodevelopmental disorder: Clinical and pathogenetic research. Heliyon 2024; 10:e37258. [PMID: 39296199 PMCID: PMC11409145 DOI: 10.1016/j.heliyon.2024.e37258] [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: 02/22/2024] [Revised: 08/04/2024] [Accepted: 08/29/2024] [Indexed: 09/21/2024] Open
Abstract
Background Neurodevelopmental disorder with spasticity, cataracts, and cerebellar hypoplasia (NEDSCAC), induced by MED27 gene, is an autosomal recessive rare disorder characterized by widespread developmental delay with varying degrees of intellectual impairment. Other symptoms include limb spasticity, cataracts, and cerebellar hypoplasia. So far there have been limited reports on NEDSCAC. Methods In this study, we conducted genetic testing on a child presenting with developmental delay as the primary clinical feature. The genetic test results indicated the presence of novel homozygous missense variants c.74G > A, p.(Arg25His) in the MED27 gene. In vitro functional validation experiments, including plasmid construction and cell transfection, Western blotting, and molecular dynamics structural modeling, were performed on the MED27 Arg25His variant. Results The results demonstrated a significant reduction in protein expression of MED27 Arg25His and indicated may weaken the interaction force between the MED27 subunit and MED14 subunit. Conclusions This study expands our understanding of MED27 gene variants and their associated clinical phenotypes. Additionally, it contributes to the investigation of the potential pathogenesis of NEDSCAC caused by MED27 gene variants.
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Affiliation(s)
- Gongao Wu
- Department of Pediatrics, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Ruofei Lian
- Department of Pediatrics, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Mengchun Li
- Department of Pediatrics, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Liang Jin
- Department of Pediatrics, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Tianming Jia
- Department of Pediatrics, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Lijun Wang
- Department of Pediatrics, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Ling Gan
- Department of Pediatrics, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Shichao Zhao
- Department of Pediatrics, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Ruirui Liang
- Department of Pediatrics, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Yan Dong
- Department of Pediatrics, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
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3
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Zhao H, Li J, Xiang Y, Malik S, Vartak SV, Veronezi GMB, Young N, Riney M, Kalchschmidt J, Conte A, Jung SK, Ramachandran S, Roeder RG, Shi Y, Casellas R, Asturias FJ. An IDR-dependent mechanism for nuclear receptor control of Mediator interaction with RNA polymerase II. Mol Cell 2024; 84:2648-2664.e10. [PMID: 38955181 PMCID: PMC11283359 DOI: 10.1016/j.molcel.2024.06.006] [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: 06/28/2023] [Revised: 02/29/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024]
Abstract
The essential Mediator (MED) coactivator complex plays a well-understood role in regulation of basal transcription in all eukaryotes, but the mechanism underlying its role in activator-dependent transcription remains unknown. We investigated modulation of metazoan MED interaction with RNA polymerase II (RNA Pol II) by antagonistic effects of the MED26 subunit and the CDK8 kinase module (CKM). Biochemical analysis of CKM-MED showed that the CKM blocks binding of the RNA Pol II carboxy-terminal domain (CTD), preventing RNA Pol II interaction. This restriction is eliminated by nuclear receptor (NR) binding to CKM-MED, which enables CTD binding in a MED26-dependent manner. Cryoelectron microscopy (cryo-EM) and crosslinking-mass spectrometry (XL-MS) revealed that the structural basis for modulation of CTD interaction with MED relates to a large intrinsically disordered region (IDR) in CKM subunit MED13 that blocks MED26 and CTD interaction with MED but is repositioned upon NR binding. Hence, NRs can control transcription initiation by priming CKM-MED for MED26-dependent RNA Pol II interaction.
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Affiliation(s)
- Haiyan Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | - Jiaqin Li
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | - Yufei Xiang
- Center of Protein Engineering and Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sohail Malik
- Laboratory of Biochemistry and Molecular Biology, Rockefeller University, New York, NY 10065, USA
| | | | - Giovana M B Veronezi
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | - Natalie Young
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | - McKayla Riney
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | | | - Andrea Conte
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Seol Kyoung Jung
- Biodata Mining and Discovery Section, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Srinivas Ramachandran
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, Rockefeller University, New York, NY 10065, USA
| | - Yi Shi
- Center of Protein Engineering and Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Francisco J Asturias
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA.
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Freytes SN, Gobbini ML, Cerdán PD. The Plant Mediator Complex in the Initiation of Transcription by RNA Polymerase II. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:211-237. [PMID: 38277699 DOI: 10.1146/annurev-arplant-070623-114005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
Thirty years have passed since the discovery of the Mediator complex in yeast. We are witnessing breakthroughs and advances that have led to high-resolution structural models of yeast and mammalian Mediators in the preinitiation complex, showing how it is assembled and how it positions the RNA polymerase II and its C-terminal domain (CTD) to facilitate the CTD phosphorylation that initiates transcription. This information may be also used to guide future plant research on the mechanisms of Mediator transcriptional control. Here, we review what we know about the subunit composition and structure of plant Mediators, the roles of the individual subunits and the genetic analyses that pioneered Mediator research, and how transcription factors recruit Mediators to regulatory regions adjoining promoters. What emerges from the research is a Mediator that regulates transcription activity and recruits hormonal signaling modules and histone-modifying activities to set up an off or on transcriptional state that recruits general transcription factors for preinitiation complex assembly.
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Affiliation(s)
| | | | - Pablo D Cerdán
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina; , ,
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
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5
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Voutsadakis IA. Mediator kinase module proteins, genetic alterations and expression of super-enhancer regulated genes in colorectal cancer. Pharmacol Rep 2024; 76:535-556. [PMID: 38602606 DOI: 10.1007/s43440-024-00589-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 04/12/2024]
Abstract
BACKGROUND Genetic alterations are well characterized as contributors to the pathogenesis of cancers. Epigenetic abnormalities can lead to perturbations of the expression of genes in cancer cells without structural defects. Deregulation of proteins of the transcription machinery may result in perturbations of target genes. Mediator, a multiprotein component of the transcription machinery facilitates the function of RNA polymerase II, which transcribes most human genes. A part of the mediator with kinase activity, called the Mediator kinase module shows genetic alterations in a sub-set of colorectal cancers. METHODS Data from publicly available genomic series of colorectal cancer patients were examined to determine alterations of Mediator kinase module component genes, including MED12, MED12L, MED13, MED13L, CDK8, CDK19, and CCNC. The prevalence of alterations in genomically defined colorectal cancer sub-sets was also interrogated. The effect of Mediator kinase module member gene expression on colorectal cancer relapse-free survival was investigated. RESULTS Mutations in genes of the Mediator kinase module were present in a small percentage of colorectal cancers, ranging between 2 to 10% for MED12 and MED13 and alternative units MED12L and MED13L and below 2% for kinases CDK8 and CDK19 and cyclin C. Amplifications of the CDK8 gene were observed in 3% to 5% of colorectal cancers. The highest prevalence of mutations was observed in MSI cancers and the equivalent CMS1 group, with other genomic groups showing much lower frequency. An association of higher expression of MED12 with inferior relapse-free survival was observed. In contrast, higher expression of cyclin C was associated with improved survival. Colorectal cancer cell lines with CDK8 amplifications displayed sensitivity to several small molecule inhibitors of the KRAS/PI3K pathway but not to BET inhibitors. CONCLUSION The Mediator kinase module is deregulated in a sub-set of colorectal cancers with differences observed in genomically defined groups. These variations may result in differences in sensitivity to targeted therapies and may have to be taken into consideration as such therapies are developed.
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Affiliation(s)
- Ioannis A Voutsadakis
- Algoma District Cancer Program, Sault Area Hospital, Sault Ste Marie, ON, P6B 0A8, Canada.
- Division of Clinical Sciences, Section of Internal Medicine, Northern Ontario School of Medicine, 750 Great Northern Road, Sudbury, ON, Canada.
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Blomberg J, Tasselius V, Vergara A, Karamat F, Imran QM, Strand Å, Rosvall M, Björklund S. Pseudomonas syringae infectivity correlates to altered transcript and metabolite levels of Arabidopsis mediator mutants. Sci Rep 2024; 14:6771. [PMID: 38514763 PMCID: PMC10958028 DOI: 10.1038/s41598-024-57192-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/15/2024] [Indexed: 03/23/2024] Open
Abstract
Rapid metabolic responses to pathogens are essential for plant survival and depend on numerous transcription factors. Mediator is the major transcriptional co-regulator for integration and transmission of signals from transcriptional regulators to RNA polymerase II. Using four Arabidopsis Mediator mutants, med16, med18, med25 and cdk8, we studied how differences in regulation of their transcript and metabolite levels correlate to their responses to Pseudomonas syringae infection. We found that med16 and cdk8 were susceptible, while med25 showed increased resistance. Glucosinolate, phytoalexin and carbohydrate levels were reduced already before infection in med16 and cdk8, but increased in med25, which also displayed increased benzenoids levels. Early after infection, wild type plants showed reduced glucosinolate and nucleoside levels, but increases in amino acids, benzenoids, oxylipins and the phytoalexin camalexin. The Mediator mutants showed altered levels of these metabolites and in regulation of genes encoding key enzymes for their metabolism. At later stage, mutants displayed defective levels of specific amino acids, carbohydrates, lipids and jasmonates which correlated to their infection response phenotypes. Our results reveal that MED16, MED25 and CDK8 are required for a proper, coordinated transcriptional response of genes which encode enzymes involved in important metabolic pathways for Arabidopsis responses to Pseudomonas syringae infections.
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Affiliation(s)
- Jeanette Blomberg
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87, Umeå, Sweden
| | - Viktor Tasselius
- Department of Physics, Umeå University, 901 87, Umeå, Sweden
- Biostatistics, School of Public Health and Community Medicine, Gothenburg University, P.O. Box 463, 405 30, Gothenburg, Sweden
| | | | - Fazeelat Karamat
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87, Umeå, Sweden
| | - Qari Muhammad Imran
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87, Umeå, Sweden
| | - Åsa Strand
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 901 87, Umeå, Sweden
| | - Martin Rosvall
- Department of Physics, Umeå University, 901 87, Umeå, Sweden
| | - Stefan Björklund
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87, Umeå, Sweden.
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7
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Crawford T, Siebler L, Sulkowska A, Nowack B, Jiang L, Pan Y, Lämke J, Kappel C, Bäurle I. The Mediator kinase module enhances polymerase activity to regulate transcriptional memory after heat stress in Arabidopsis. EMBO J 2024; 43:437-461. [PMID: 38228917 PMCID: PMC10897291 DOI: 10.1038/s44318-023-00024-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 01/18/2024] Open
Abstract
Plants are often exposed to recurring adverse environmental conditions in the wild. Acclimation to high temperatures entails transcriptional responses, which prime plants to better withstand subsequent stress events. Heat stress (HS)-induced transcriptional memory results in more efficient re-induction of transcription upon recurrence of heat stress. Here, we identified CDK8 and MED12, two subunits of the kinase module of the transcription co-regulator complex, Mediator, as promoters of heat stress memory and associated histone modifications in Arabidopsis. CDK8 is recruited to heat-stress memory genes by HEAT SHOCK TRANSCRIPTION FACTOR A2 (HSFA2). Like HSFA2, CDK8 is largely dispensable for the initial gene induction upon HS, and its function in transcriptional memory is thus independent of primary gene activation. In addition to the promoter and transcriptional start region of target genes, CDK8 also binds their 3'-region, where it may promote elongation, termination, or rapid re-initiation of RNA polymerase II (Pol II) complexes during transcriptional memory bursts. Our work presents a complex role for the Mediator kinase module during transcriptional memory in multicellular eukaryotes, through interactions with transcription factors, chromatin modifications, and promotion of Pol II efficiency.
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Affiliation(s)
- Tim Crawford
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Lara Siebler
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - Bryan Nowack
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Li Jiang
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Yufeng Pan
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Jörn Lämke
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Isabel Bäurle
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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8
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Hu Q, Wu Y, Hong T, Wu D, Wang L. OsMED16, a tail subunit of Mediator complex, interacts with OsE2Fa to synergistically regulate rice leaf development and blast resistance. Int J Biol Macromol 2023; 253:126728. [PMID: 37678689 DOI: 10.1016/j.ijbiomac.2023.126728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/20/2023] [Accepted: 09/03/2023] [Indexed: 09/09/2023]
Abstract
Mediator, a universal eukaryotic coactivator, is a multiprotein complex to transduce information from the DNA-bound transcription factors to the RNA polymerase II transcriptional machinery. In this study, the biofunctions of a rice mediator subunit OsMED16 in leaf development and blast resistance were characterized. OsMED16 encodes a putative protein of 1170 amino acids, which is 393 bp shorted than the version in Rice Genome Annotation Project databases. Overexpression of OsMED16 plants exhibited wider leaves with larger and more numerous cells in lateral axis, and enhanced resistance to M. oryzae with hyperaccumulated salicylic acid. Further analysis revealed that OsMED16 interacts with OsE2Fa in nuclei, and the complex could directly regulate the transcriptional levels of several genes involved in cell cycle regulation and SA mediated blast resistance, such as OsCC52A1, OsCDKA1, OsCDKB2;2, OsICS1 and OsWRKY45. Altogether, this study proved that OsMED16 is a positive regulator of rice leaf development and blast resistance, and providing new insights into the crosstalk between cell cycle regulation and immunity.
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Affiliation(s)
- Qin Hu
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi University, Daxue East Road 100, Nanning 530004, China; College of Agriculture, Guangxi University, Daxue East Road 100, Nanning 530004, China.
| | - Yanfei Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Youyi Avenue 368, Wuhan 430062, China
| | - Tianshu Hong
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi University, Daxue East Road 100, Nanning 530004, China; College of Agriculture, Guangxi University, Daxue East Road 100, Nanning 530004, China
| | - Deng Wu
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi University, Daxue East Road 100, Nanning 530004, China; College of Agriculture, Guangxi University, Daxue East Road 100, Nanning 530004, China
| | - Lulu Wang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi University, Daxue East Road 100, Nanning 530004, China; College of Agriculture, Guangxi University, Daxue East Road 100, Nanning 530004, China
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Malik N, Basu U, Srivastava R, Daware A, Ranjan R, Sharma A, Thakro V, Mohanty JK, Jha UC, Tripathi S, Tyagi AK, Parida SK. Natural alleles of Mediator subunit genes modulate plant height in chickpea. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1271-1292. [PMID: 37671896 DOI: 10.1111/tpj.16423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/04/2023] [Indexed: 09/07/2023]
Abstract
SUMMARYPlant height (PH) is an important plant architectural trait targeted during Green Revolution to enhance crop yields. Identification of genes and natural alleles governing plant height without compromising agronomic performance can fill the lacuna of knowledge connecting ideal plant architecture with maximum achievable yield in chickpea. Through coherent strategy involving genome‐wide association study, QTL/fine mapping, map‐based cloning, molecular haplotyping, and downstream functional genomics, the current study identified two Mediator subunit genes namely, CaMED23 and CaMED5b and their derived natural alleles/haplotypes underlying the major QTLs and trans‐acting eQTLs regulating plant height in chickpea. Differential accumulation of haplotype‐specific transcripts of these two Mediator genes in corresponding haplotype‐introgressed near‐isogenic lines (NILs) correlates negatively with the plant height trait. Quantitative as well as qualitative estimation based on histology, scanning electron microscopy, and histochemical assay unraveled the reduced lengths and cell sizes of internodes along with compromised lignin levels in dwarf/semi‐dwarf chickpea NILs introgressed with superior CaMED23 and CaMED5b gene haplotypes. This observation, supported by global transcriptome profiling‐based diminished expression of various phenylpropanoid pathway genes upstream of lignin biosynthesis in dwarf/semi‐dwarf NILs, essentially links plant height with lignin accumulation. The identified molecular signatures in the Mediator subunit genes can be efficiently utilized to develop desirable dwarf/semi‐dwarf‐type chickpea cultivars without affecting their yield per plant via modulating lignin/phenylpropanoid biosynthesis.
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Affiliation(s)
- Naveen Malik
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, 303002, India
| | - Udita Basu
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rishi Srivastava
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Anurag Daware
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rajeev Ranjan
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Akash Sharma
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Virevol Thakro
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Jitendra K Mohanty
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Uday Chand Jha
- Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India
| | | | - Akhilesh K Tyagi
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Swarup K Parida
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
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Zhou Z, Liu J, Zhang J, Yan H, Yi T, Shim WB. Characterization of Fusarium verticillioides Med1 LxxLL Motif Involved in Fumonisin Biosynthesis. Toxins (Basel) 2023; 15:652. [PMID: 37999515 PMCID: PMC10675092 DOI: 10.3390/toxins15110652] [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: 09/27/2023] [Revised: 10/31/2023] [Accepted: 11/10/2023] [Indexed: 11/25/2023] Open
Abstract
The Med1 transcriptional coactivator is a crucial component of the Mediator middle complex, which regulates the expression of specific genes involved in cell development, differentiation, reproduction, and homeostasis. The Med1 LxxLL motif, a five-amino-acid peptide sequence, is essential for Med1-mediated gene expression. Our previous study revealed that the disruption of the Med1 subunit leads to a significant increase in fumonisin B1 (FB1) production in the maize pathogen Fusarium verticillioides. However, our understanding of how Med1 regulates FB1 biosynthesis in F. verticillioides, particularly through the Med1 LxxLL motifs, remains limited. To characterize the role of LxxLL motifs, we generated a series of Med1 LxxLL deletion and amino acid substitution mutants. These mutants exhibited impaired mycelial growth and conidia germination while demonstrating enhanced conidia production and virulence. Similar to the Med1 deletion mutant, Med1 LxxLL motif mutants also exhibited increased FB1 biosynthesis in F. verticillioides. Proteomic profiling revealed that the Med1 LxxLL motif regulated the biosynthesis of several key substances that affected FB1 production, including starch and carotenoid. Subsequent studies demonstrated that the production of amylopectin, which is strongly linked to FB1 biosynthesis, was significantly increased in Med1 LxxLL motif mutants. In addition, the disruption of carotenoid metabolic genes decreased carotenoid content, thus stimulating FB1 biosynthesis in F. verticillioides. Taken together, our results provide valuable insights into how the Med1 LxxLL motif regulates FB1 biosynthesis in the mycotoxigenic fungus F. verticillioides.
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Affiliation(s)
- Zehua Zhou
- Hunan Provincial Key Laboratory for Biology and Control of Plant Pests, Hunan Agricultural University, Changsha 410128, China; (Z.Z.); (J.L.)
| | - Jie Liu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Pests, Hunan Agricultural University, Changsha 410128, China; (Z.Z.); (J.L.)
| | - Jie Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China;
| | - Huijuan Yan
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA;
| | - Tuyong Yi
- Hunan Provincial Key Laboratory for Biology and Control of Plant Pests, Hunan Agricultural University, Changsha 410128, China; (Z.Z.); (J.L.)
| | - Won Bo Shim
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
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11
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Malik S, Roeder RG. Regulation of the RNA polymerase II pre-initiation complex by its associated coactivators. Nat Rev Genet 2023; 24:767-782. [PMID: 37532915 PMCID: PMC11088444 DOI: 10.1038/s41576-023-00630-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 08/04/2023]
Abstract
The RNA polymerase II (Pol II) pre-initiation complex (PIC) is a critical node in eukaryotic transcription regulation, and its formation is the major rate-limiting step in transcriptional activation. Diverse cellular signals borne by transcriptional activators converge on this large, multiprotein assembly and are transduced via intermediary factors termed coactivators. Cryogenic electron microscopy, multi-omics and single-molecule approaches have recently offered unprecedented insights into both the structure and cellular functions of the PIC and two key PIC-associated coactivators, Mediator and TFIID. Here, we review advances in our understanding of how Mediator and TFIID interact with activators and affect PIC formation and function. We also discuss how their functions are influenced by their chromatin environment and selected cofactors. We consider how, through its multifarious interactions and functionalities, a Mediator-containing and TFIID-containing PIC can yield an integrated signal processing system with the flexibility to determine the unique temporal and spatial expression pattern of a given gene.
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Affiliation(s)
- Sohail Malik
- Laboratory of Biochemistry & Molecular Biology, The Rockefeller University, New York, NY, USA.
| | - Robert G Roeder
- Laboratory of Biochemistry & Molecular Biology, The Rockefeller University, New York, NY, USA
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12
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Teng C, Zhang C, Guo F, Song L, Fang Y. Advances in the Study of the Transcriptional Regulation Mechanism of Plant miRNAs. Life (Basel) 2023; 13:1917. [PMID: 37763320 PMCID: PMC10533097 DOI: 10.3390/life13091917] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
MicroRNAs (miRNA) are a class of endogenous, non-coding, small RNAs with about 22 nucleotides (nt), that are widespread in plants and are involved in various biological processes, such as development, flowering phase transition, hormone signal transduction, and stress response. The transcriptional regulation of miRNAs is an important process of miRNA gene regulation, and it is essential for miRNA biosynthesis and function. Like mRNAs, miRNAs are transcribed by RNA polymerase II, and these transcription processes are regulated by various transcription factors and other proteins. Consequently, the upstream genes regulating miRNA transcription, their specific expression, and the regulating mechanism were reviewed to provide more information for further research on the miRNA regulatory mechanism and help to further understand the regulatory networks of plant miRNAs.
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Affiliation(s)
| | | | | | | | - Yanni Fang
- College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China; (C.T.); (C.Z.); (F.G.)
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13
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Casasa S, Katsougia E, Ragsdale EJ. A Mediator subunit imparts robustness to a polyphenism decision. Proc Natl Acad Sci U S A 2023; 120:e2308816120. [PMID: 37527340 PMCID: PMC10410750 DOI: 10.1073/pnas.2308816120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 06/21/2023] [Indexed: 08/03/2023] Open
Abstract
Polyphenism is a type of developmental plasticity that translates continuous environmental variability into discontinuous phenotypes. Such discontinuity likely requires a switch between alternative gene-regulatory networks, a principle that has been borne out by mechanisms found to promote morph-specific gene expression. However, whether robustness is required to execute a polyphenism decision has awaited testing at the molecular level. Here, we used a nematode model for polyphenism, Pristionchus pacificus, to identify the molecular regulatory factors that ensure the development of alternative forms. This species has a dimorphism in its adult feeding structures, specifically teeth, which are a morphological novelty that allows predation on other nematodes. Through a forward genetic screen, we determined that a duplicate homolog of the Mediator subunit MDT-15/MED15, P. pacificus MDT-15.1, is necessary for the polyphenism and the robustness of the resulting phenotypes. This transcriptional coregulator, which has a conserved role in metabolic responses to nutritional stress, coordinates these processes with its effects on this diet-induced polyphenism. Moreover, this MED15 homolog genetically interacts with two nuclear receptors, NHR-1 and NHR-40, to achieve dimorphism: Single and double mutants for these three factors result in morphologies that together produce a continuum of forms between the extremes of the polyphenism. In summary, we have identified a molecular regulator that confers discontinuity to a morphological polyphenism, while also identifying a role for MED15 as a plasticity effector.
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Affiliation(s)
- Sofia Casasa
- Department of Biology, Indiana University, Bloomington, IN47405
| | - Eleni Katsougia
- Department of Biology, Indiana University, Bloomington, IN47405
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14
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The TFIIS N-terminal domain (TND): a transcription assembly module at the interface of order and disorder. Biochem Soc Trans 2023; 51:125-135. [PMID: 36651856 PMCID: PMC9987994 DOI: 10.1042/bst20220342] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/22/2022] [Accepted: 01/03/2023] [Indexed: 01/19/2023]
Abstract
Interaction scaffolds that selectively recognize disordered protein strongly shape protein interactomes. An important scaffold of this type that contributes to transcription is the TFIIS N-terminal domain (TND). The TND is a five-helical bundle that has no known enzymatic activity, but instead selectively reads intrinsically disordered sequences of other proteins. Here, we review the structural and functional properties of TNDs and their cognate disordered ligands known as TND-interacting motifs (TIMs). TNDs or TIMs are found in prominent members of the transcription machinery, including TFIIS, super elongation complex, SWI/SNF, Mediator, IWS1, SPT6, PP1-PNUTS phosphatase, elongin, H3K36me3 readers, the transcription factor MYC, and others. We also review how the TND interactome contributes to the regulation of transcription. Because the TND is the most significantly enriched fold among transcription elongation regulators, TND- and TIM-driven interactions have widespread roles in the regulation of many transcriptional processes.
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15
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Gorbea Colón JJ, Palao L, Chen SF, Kim HJ, Snyder L, Chang YW, Tsai KL, Murakami K. Structural basis of a transcription pre-initiation complex on a divergent promoter. Mol Cell 2023; 83:574-588.e11. [PMID: 36731470 PMCID: PMC10162435 DOI: 10.1016/j.molcel.2023.01.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 11/28/2022] [Accepted: 01/06/2023] [Indexed: 02/04/2023]
Abstract
Most eukaryotic promoter regions are divergently transcribed. As the RNA polymerase II pre-initiation complex (PIC) is intrinsically asymmetric and responsible for transcription in a single direction, it is unknown how divergent transcription arises. Here, the Saccharomyces cerevisiae Mediator complexed with a PIC (Med-PIC) was assembled on a divergent promoter and analyzed by cryoelectron microscopy. The structure reveals two distinct Med-PICs forming a dimer through the Mediator tail module, induced by a homodimeric activator protein localized near the dimerization interface. The tail dimer is associated with ∼80-bp upstream DNA, such that two flanking core promoter regions are positioned and oriented in a suitable form for PIC assembly in opposite directions. Also, cryoelectron tomography visualized the progress of the PIC assembly on the two core promoter regions, providing direct evidence for the role of the Med-PIC dimer in divergent transcription.
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Affiliation(s)
- Jose J Gorbea Colón
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leon Palao
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shin-Fu Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Hee Jong Kim
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Laura Snyder
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Kuang-Lei Tsai
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| | - Kenji Murakami
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Center for Genome Integrity, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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16
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Lambert É, Puwakdandawa K, Tao YF, Robert F. From structure to molecular condensates: emerging mechanisms for Mediator function. FEBS J 2023; 290:286-309. [PMID: 34698446 DOI: 10.1111/febs.16250] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/15/2021] [Accepted: 10/25/2021] [Indexed: 02/05/2023]
Abstract
Mediator is a large modular protein assembly whose function as a coactivator of transcription is conserved in all eukaryotes. The Mediator complex can integrate and relay signals from gene-specific activators bound at enhancers to activate the general transcription machinery located at promoters. It has thus been described as a bridge between these elements during initiation of transcription. Here, we review recent studies on Mediator relating to its structure, gene specificity and general requirement, roles in chromatin architecture as well as novel concepts involving phase separation and transcriptional bursting. We revisit the mechanism of action of Mediator and ultimately put forward models for its mode of action in gene activation.
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Affiliation(s)
- Élie Lambert
- Institut de recherches cliniques de Montréal, Canada
| | | | - Yi Fei Tao
- Institut de recherches cliniques de Montréal, Canada
| | - François Robert
- Institut de recherches cliniques de Montréal, Canada.,Département de Médecine, Faculté de Médecine, Université de Montréal, Canada
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17
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Jullien D, Guillou E, Bernat-Fabre S, Payet A, Bourbon HMG, Boube M. Inducible degradation of the Drosophila Mediator subunit Med19 reveals its role in regulating developmental but not constitutively-expressed genes. PLoS One 2022; 17:e0275613. [PMID: 36445897 PMCID: PMC9707739 DOI: 10.1371/journal.pone.0275613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/20/2022] [Indexed: 11/30/2022] Open
Abstract
The multi-subunit Mediator complex plays a critical role in gene expression by bridging enhancer-bound transcription factors and the RNA polymerase II machinery. Although experimental case studies suggest differential roles of Mediator subunits, a comprehensive view of the specific set of genes regulated by individual subunits in a developing tissue is still missing. Here we address this fundamental question by focusing on the Med19 subunit and using the Drosophila wing imaginal disc as a developmental model. By coupling auxin-inducible degradation of endogenous Med19 in vivo with RNA-seq, we got access to the early consequences of Med19 elimination on gene expression. Differential gene expression analysis reveals that Med19 is not globally required for mRNA transcription but specifically regulates positively or negatively less than a quarter of the expressed genes. By crossing our transcriptomic data with those of Drosophila gene expression profile database, we found that Med19-dependent genes are highly enriched with spatially-regulated genes while the expression of most constitutively expressed genes is not affected upon Med19 loss. Whereas globally downregulation does not exceed upregulation, we identified a functional class of genes encoding spatially-regulated transcription factors, and more generally developmental regulators, responding unidirectionally to Med19 loss with an expression collapse. Moreover, we show in vivo that the Notch-responsive wingless and the E(spl)-C genes require Med19 for their expression. Combined with experimental evidences suggesting that Med19 could function as a direct transcriptional effector of Notch signaling, our data support a model in which Med19 plays a critical role in the transcriptional activation of developmental genes in response to cell signaling pathways.
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Affiliation(s)
- Denis Jullien
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit UMR 5077, Federal University of Toulouse, Toulouse, France
- * E-mail: (MB); (DJ)
| | - Emmanuelle Guillou
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit UMR 5077, Federal University of Toulouse, Toulouse, France
| | - Sandra Bernat-Fabre
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit UMR 5077, Federal University of Toulouse, Toulouse, France
| | - Adeline Payet
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit UMR 5077, Federal University of Toulouse, Toulouse, France
| | - Henri-Marc G. Bourbon
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit UMR 5077, Federal University of Toulouse, Toulouse, France
| | - Muriel Boube
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit UMR 5077, Federal University of Toulouse, Toulouse, France
- RESTORE Research Center, Université de Toulouse, INSERM 1301, CNRS 5070, EFS, ENVT, Toulouse, France
- * E-mail: (MB); (DJ)
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18
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Schubert OT, Bloom JS, Sadhu MJ, Kruglyak L. Genome-wide base editor screen identifies regulators of protein abundance in yeast. eLife 2022; 11:e79525. [PMID: 36326816 PMCID: PMC9633064 DOI: 10.7554/elife.79525] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 09/23/2022] [Indexed: 11/07/2022] Open
Abstract
Proteins are key molecular players in a cell, and their abundance is extensively regulated not just at the level of gene expression but also post-transcriptionally. Here, we describe a genetic screen in yeast that enables systematic characterization of how protein abundance regulation is encoded in the genome. The screen combines a CRISPR/Cas9 base editor to introduce point mutations with fluorescent tagging of endogenous proteins to facilitate a flow-cytometric readout. We first benchmarked base editor performance in yeast with individual gRNAs as well as in positive and negative selection screens. We then examined the effects of 16,452 genetic perturbations on the abundance of eleven proteins representing a variety of cellular functions. We uncovered hundreds of regulatory relationships, including a novel link between the GAPDH isoenzymes Tdh1/2/3 and the Ras/PKA pathway. Many of the identified regulators are specific to one of the eleven proteins, but we also found genes that, upon perturbation, affected the abundance of most of the tested proteins. While the more specific regulators usually act transcriptionally, broad regulators often have roles in protein translation. Overall, our novel screening approach provides unprecedented insights into the components, scale and connectedness of the protein regulatory network.
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Affiliation(s)
- Olga T Schubert
- Department of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Department of Biological Chemistry, University of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical Institute, University of California, Los AngelesLos AngelesUnited States
- Institute for Quantitative and Computational Biology, University of California, Los AngelesLos AngelesUnited States
- Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH)ZürichSwitzerland
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag)DübendorfSwitzerland
| | - Joshua S Bloom
- Department of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Department of Biological Chemistry, University of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical Institute, University of California, Los AngelesLos AngelesUnited States
- Institute for Quantitative and Computational Biology, University of California, Los AngelesLos AngelesUnited States
| | - Meru J Sadhu
- Department of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Department of Biological Chemistry, University of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical Institute, University of California, Los AngelesLos AngelesUnited States
- Institute for Quantitative and Computational Biology, University of California, Los AngelesLos AngelesUnited States
| | - Leonid Kruglyak
- Department of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Department of Biological Chemistry, University of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical Institute, University of California, Los AngelesLos AngelesUnited States
- Institute for Quantitative and Computational Biology, University of California, Los AngelesLos AngelesUnited States
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19
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Richter WF, Nayak S, Iwasa J, Taatjes DJ. The Mediator complex as a master regulator of transcription by RNA polymerase II. Nat Rev Mol Cell Biol 2022; 23:732-749. [PMID: 35725906 PMCID: PMC9207880 DOI: 10.1038/s41580-022-00498-3] [Citation(s) in RCA: 82] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2022] [Indexed: 02/08/2023]
Abstract
The Mediator complex, which in humans is 1.4 MDa in size and includes 26 subunits, controls many aspects of RNA polymerase II (Pol II) function. Apart from its size, a defining feature of Mediator is its intrinsic disorder and conformational flexibility, which contributes to its ability to undergo phase separation and to interact with a myriad of regulatory factors. In this Review, we discuss Mediator structure and function, with emphasis on recent cryogenic electron microscopy data of the 4.0-MDa transcription preinitiation complex. We further discuss how Mediator and sequence-specific DNA-binding transcription factors enable enhancer-dependent regulation of Pol II function at distal gene promoters, through the formation of molecular condensates (or transcription hubs) and chromatin loops. Mediator regulation of Pol II reinitiation is also discussed, in the context of transcription bursting. We propose a working model for Mediator function that combines experimental results and theoretical considerations related to enhancer-promoter interactions, which reconciles contradictory data regarding whether enhancer-promoter communication is direct or indirect. We conclude with a discussion of Mediator's potential as a therapeutic target and of future research directions.
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Affiliation(s)
- William F Richter
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Shraddha Nayak
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Janet Iwasa
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, CO, USA.
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20
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Nayak S, Taatjes DJ. SnapShot: Mediator complex structure. Cell 2022; 185:3458-3458.e1. [PMID: 36055203 PMCID: PMC10686218 DOI: 10.1016/j.cell.2022.07.011] [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] [Indexed: 11/20/2022]
Abstract
The Mediator complex controls RNA polymerase II transcription genome-wide. In humans, Mediator consists of 26 subunits; furthermore, a four-subunit "Mediator kinase module" can reversibly associate with the complex. Mediator structure is generally conserved from yeast to humans, although the human complex is larger, more structurally disordered, and contains metazoan-specific subunits. To view this SnapShot, open or download the PDF.
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Affiliation(s)
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, CO USA
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21
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Zhou Z, Yan H, Kim MS, Shim WB. Distinct Function of Mediator Subunits in Fungal Development, Stress Response, and Secondary Metabolism in Maize Pathogen Fusarium verticillioides. PHYTOPATHOLOGY 2022; 112:1730-1738. [PMID: 35271780 DOI: 10.1094/phyto-12-21-0495-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Mediator is a nucleus-localized, multisubunit protein complex highly conserved across eukaryotes. It interacts with RNA polymerase II transcription machinery as well as various transcription factors to regulate gene expression. However, systematic characterization of the Mediator complex has not been performed in filamentous fungi. In our study, the goal was to investigate key biological functions of Mediator subunits in a mycotoxigenic plant pathogen Fusarium verticillioides. Although there is some level of divergence in the constituent subunits, the overall structure was conserved between Saccharomyces cerevisiae and F. verticillioides. We generated 11 Mediator subunit deletion mutants and characterized vegetative growth, conidia formation, environmental stress response, carbon and fatty acid use, virulence, and fumonisin B1 (FB1) biosynthesis. Each Mediator subunit deletion mutant showed deficiencies in at least three of the phenotypes tested, suggesting that each subunit has different principal functions in F. verticillioides development, metabolism, and virulence. The deletion of FvMed1 led to increased FB1 production, and we confirmed that FvMed1 is transported from the nucleus to the cytoplasm under fumonisin-producing conditions. Taken together, our study characterized various important functional roles for Mediator subunits in F. verticillioides and suggests that select subunits can perform unique cytoplasmic functions independent of the core Mediator in fungal nucleus.
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Affiliation(s)
- Zehua Zhou
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, U.S.A
- Hunan Agricultural University, College of Plant Protection & Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Plant Pests, Furong District, Changsha, Hunan 410128, China
| | - Huijuan Yan
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, U.S.A
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94143, U.S.A
| | - Man S Kim
- Clinical Research Institute, College of Medicine, Kyung Hee University Hospital at Gangdong, Seoul, South Korea
| | - Won Bo Shim
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, U.S.A
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22
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Morse RH. Function and dynamics of the Mediator complex: novel insights and new frontiers. Transcription 2022; 13:39-52. [PMID: 35708525 PMCID: PMC9467533 DOI: 10.1080/21541264.2022.2085502] [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] [Indexed: 11/04/2022] Open
Abstract
The Mediator complex was discovered in the early 1990s as a biochemically fractionated factor from yeast extracts that was necessary for activator-stimulated transcriptional activation to be observed in in vitro transcription assays. The structure of this large, multi-protein complex is now understood in great detail, and novel genetic approaches have provided rich insights into its dynamics during transcriptional activation and the mechanism by which it facilitates activated transcription. Here I review recent findings and unanswered questions regarding Mediator dynamics, the roles of individual subunits, and differences between its function in yeast and metazoan cells.
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Affiliation(s)
- Randall H Morse
- Wadsworth Center, New York State Department of Health, Albany, NY, United States.,Department of Biomedical Sciences, University at Albany School of Public Health, Albany, NY, United States
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23
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Eigenhuis KN, Somsen HB, van den Berg DLC. Transcription Pause and Escape in Neurodevelopmental Disorders. Front Neurosci 2022; 16:846272. [PMID: 35615272 PMCID: PMC9125161 DOI: 10.3389/fnins.2022.846272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
Transcription pause-release is an important, highly regulated step in the control of gene expression. Modulated by various factors, it enables signal integration and fine-tuning of transcriptional responses. Mutations in regulators of pause-release have been identified in a range of neurodevelopmental disorders that have several common features affecting multiple organ systems. This review summarizes current knowledge on this novel subclass of disorders, including an overview of clinical features, mechanistic details, and insight into the relevant neurodevelopmental processes.
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24
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Iyer U, Park JE, Sze SK, Bozdech Z, Featherstone M. Mediator Complex of the Malaria Parasite Plasmodium falciparum Associates with Evolutionarily Novel Subunits. ACS OMEGA 2022; 7:14867-14874. [PMID: 35557691 PMCID: PMC9088918 DOI: 10.1021/acsomega.2c00368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/31/2022] [Indexed: 06/15/2023]
Abstract
The eukaryotic Mediator is a large and conserved multisubunit protein complex that directly contacts RNA polymerase II and impinges on multiple aspects of gene expression. The genome of the human malaria parasite Plasmodium falciparum has been predicted to encode several Mediator subunits. We provide physical evidence for the presence of a Mediator complex in P. falciparum by using coimmunoprecipitation and mass spectrometry to identify interaction partners of the highly conserved Mediator subunit PfMed31. We identify 11 of 14 predicted Mediator subunits and the products of two uncharacterized genes, PF3D7_0526800 and PF3D7_1363600, which are strongly associated with PfMed31. As expected, several additional interaction partners have known roles in the transcriptional control of gene expression and mRNA processing. Intriguingly, multiple interaction partners are implicated in endoplasmic reticulum function and the ER stress (ERS) response, suggesting crosstalk between the ERS response and the transcriptional machinery. Our results establish for the first time the physical presence of the Mediator complex within P. falciparum and strongly suggest that it plays both conserved and unique roles in the control of gene expression. Data are available via ProteomeXchange with the identifier PXD027640.
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25
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Pan J, Kwon JJ, Talamas JA, Borah AA, Vazquez F, Boehm JS, Tsherniak A, Zitnik M, McFarland JM, Hahn WC. Sparse dictionary learning recovers pleiotropy from human cell fitness screens. Cell Syst 2022; 13:286-303.e10. [PMID: 35085500 PMCID: PMC9035054 DOI: 10.1016/j.cels.2021.12.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/30/2021] [Accepted: 12/21/2021] [Indexed: 12/28/2022]
Abstract
In high-throughput functional genomic screens, each gene product is commonly assumed to exhibit a singular biological function within a defined protein complex or pathway. In practice, a single gene perturbation may induce multiple cascading functional outcomes, a genetic principle known as pleiotropy. Here, we model pleiotropy in fitness screen collections by representing each gene perturbation as the sum of multiple perturbations of biological functions, each harboring independent fitness effects inferred empirically from the data. Our approach (Webster) recovered pleiotropic functions for DNA damage proteins from genotoxic fitness screens, untangled distinct signaling pathways upstream of shared effector proteins from cancer cell fitness screens, and predicted the stoichiometry of an unknown protein complex subunit from fitness data alone. Modeling compound sensitivity profiles in terms of genetic functions recovered compound mechanisms of action. Our approach establishes a sparse approximation mechanism for unraveling complex genetic architectures underlying high-dimensional gene perturbation readouts.
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Affiliation(s)
- Joshua Pan
- Dana-Farber Cancer Institute, Department of Medical Oncology, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Jason J Kwon
- Dana-Farber Cancer Institute, Department of Medical Oncology, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Jessica A Talamas
- Dana-Farber Cancer Institute, Department of Medical Oncology, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Ashir A Borah
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Jesse S Boehm
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aviad Tsherniak
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Marinka Zitnik
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Department of Biomedical Informatics, Boston, MA 02215, USA; Harvard University, Data Science Initiative, Cambridge, MA 02138, USA
| | | | - William C Hahn
- Dana-Farber Cancer Institute, Department of Medical Oncology, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA; Brigham and Women's Hospital and Harvard Medical School, Department of Medicine, Boston, MA 02215, USA.
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26
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Farnung L, Vos SM. Assembly of RNA polymerase II transcription initiation complexes. Curr Opin Struct Biol 2022; 73:102335. [PMID: 35183822 PMCID: PMC9339144 DOI: 10.1016/j.sbi.2022.102335] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 12/28/2021] [Accepted: 01/04/2022] [Indexed: 11/03/2022]
Abstract
The first step of eukaryotic gene expression is the assembly of RNA polymerase II and general transcription factors on promoter DNA. This highly regulated process involves ∼80 different proteins that together form the preinitiation complex (PIC). Decades of work have gone into understanding PIC assembly using biochemical and structural approaches. These efforts have yielded significant but partial descriptions of PIC assembly. Over the past few years, cryo-electron microscopy has provided the first high-resolution structures of the near-complete mammalian PIC assembly. These structures have revealed that PIC assembly is a highly dynamic process. This review will summarize recent structural findings and discuss their implications for understanding cell type-specific gene expression.
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Affiliation(s)
- Lucas Farnung
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, 240 Longwood Ave., Boston, MA, 02115, USA. https://twitter.com/@LucasFarnung
| | - Seychelle M Vos
- Massachusetts Institute of Technology, Department of Biology, 31 Ames St., Cambridge, MA, 02142, USA.
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27
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Sooraj D, Sun C, Doan A, Garama DJ, Dannappel MV, Zhu D, Chua HK, Mahara S, Wan Hassan WA, Tay YK, Guanizo A, Croagh D, Prodanovic Z, Gough DJ, Wan C, Firestein R. MED12 and BRD4 cooperate to sustain cancer growth upon loss of mediator kinase. Mol Cell 2022; 82:123-139.e7. [PMID: 34910943 DOI: 10.1016/j.molcel.2021.11.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 08/27/2021] [Accepted: 11/13/2021] [Indexed: 11/23/2022]
Abstract
Mediator kinases (CDK8/19) are transcriptional regulators broadly implicated in cancer. Despite their central role in fine-tuning gene-expression programs, we find complete loss of CDK8/19 is tolerated in colorectal cancer (CRC) cells. Using orthogonal functional genomic and pharmacological screens, we identify BET protein inhibition as a distinct vulnerability in CDK8/19-depleted cells. Combined CDK8/19 and BET inhibition led to synergistic growth retardation in human and mouse models of CRC. Strikingly, depletion of CDK8/19 in these cells led to global repression of RNA polymerase II (Pol II) promoter occupancy and transcription. Concurrently, loss of Mediator kinase led to a profound increase in MED12 and BRD4 co-occupancy at enhancer elements and increased dependence on BET proteins for the transcriptional output of cell-essential genes. In total, this work demonstrates a synthetic lethal interaction between Mediator kinase and BET proteins and exposes a therapeutic vulnerability that can be targeted using combination therapies.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Animals
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Binding Sites
- Cell Cycle Proteins/antagonists & inhibitors
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Proliferation/drug effects
- Colorectal Neoplasms/drug therapy
- Colorectal Neoplasms/enzymology
- Colorectal Neoplasms/genetics
- Cyclin-Dependent Kinase 8/genetics
- Cyclin-Dependent Kinase 8/metabolism
- Cyclin-Dependent Kinases/genetics
- Cyclin-Dependent Kinases/metabolism
- Enhancer Elements, Genetic
- Female
- Gene Expression Regulation, Neoplastic
- HCT116 Cells
- Humans
- Male
- Mediator Complex/antagonists & inhibitors
- Mediator Complex/genetics
- Mediator Complex/metabolism
- Mice, Inbred BALB C
- Mice, Knockout
- Mice, Nude
- Nerve Tissue Proteins/antagonists & inhibitors
- Nerve Tissue Proteins/genetics
- Nerve Tissue Proteins/metabolism
- Nuclear Proteins/antagonists & inhibitors
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Protein Kinase Inhibitors/pharmacology
- Receptors, Cell Surface/antagonists & inhibitors
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/metabolism
- Signal Transduction
- Transcription Factors/antagonists & inhibitors
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcription, Genetic
- Tumor Burden
- Xenograft Model Antitumor Assays
- Mice
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Affiliation(s)
- Dhanya Sooraj
- Hudson Institute of Medical Research, Clayton, VIC, Australia; Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Claire Sun
- Hudson Institute of Medical Research, Clayton, VIC, Australia; Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Anh Doan
- Hudson Institute of Medical Research, Clayton, VIC, Australia; Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Daniel J Garama
- Hudson Institute of Medical Research, Clayton, VIC, Australia; Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Marius V Dannappel
- Hudson Institute of Medical Research, Clayton, VIC, Australia; Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Danxi Zhu
- Hudson Institute of Medical Research, Clayton, VIC, Australia; Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Hui K Chua
- Hudson Institute of Medical Research, Clayton, VIC, Australia; Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Sylvia Mahara
- Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Wan Amir Wan Hassan
- School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Yeng Kwang Tay
- School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Aleks Guanizo
- Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Daniel Croagh
- School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Zdenka Prodanovic
- Department of Pathology, Monash Medical Centre, Clayton, VIC, Australia
| | - Daniel J Gough
- Hudson Institute of Medical Research, Clayton, VIC, Australia; Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Chunhua Wan
- Hudson Institute of Medical Research, Clayton, VIC, Australia; Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Ron Firestein
- Hudson Institute of Medical Research, Clayton, VIC, Australia; Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia.
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28
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Tang M, Li B, Zhou X, Bolt T, Li JJ, Cruz N, Gaudinier A, Ngo R, Clark‐Wiest C, Kliebenstein DJ, Brady SM. A genome-scale TF-DNA interaction network of transcriptional regulation of Arabidopsis primary and specialized metabolism. Mol Syst Biol 2021; 17:e10625. [PMID: 34816587 PMCID: PMC8611409 DOI: 10.15252/msb.202110625] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 12/13/2022] Open
Abstract
Plant metabolism is more complex relative to individual microbes. In single-celled microbes, transcriptional regulation by single transcription factors (TFs) is sufficient to shift primary metabolism. Corresponding genome-level transcriptional regulatory maps of metabolism reveal the underlying design principles responsible for these shifts as a model in which master regulators largely coordinate specific metabolic pathways. Plant primary and specialized metabolism occur within innumerable cell types, and their reactions shift depending on internal and external cues. Given the importance of plants and their metabolites in providing humanity with food, fiber, and medicine, we set out to develop a genome-scale transcriptional regulatory map of Arabidopsis metabolic genes. A comprehensive set of protein-DNA interactions between Arabidopsis thaliana TFs and gene promoters in primary and specialized metabolic pathways were mapped. To demonstrate the utility of this resource, we identified and functionally validated regulators of the tricarboxylic acid (TCA) cycle. The resulting network suggests that plant metabolic design principles are distinct from those of microbes. Instead, metabolism appears to be transcriptionally coordinated via developmental- and stress-conditional processes that can coordinate across primary and specialized metabolism. These data represent the most comprehensive resource of interactions between TFs and metabolic genes in plants.
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Affiliation(s)
- Michelle Tang
- Department of Plant Biology and Genome CenterUniversity of California, DavisDavisCAUSA
- Department of Plant SciencesUniversity of California, DavisDavisCAUSA
- Plant Biology Graduate GroupUniversity of California, DavisDavisCAUSA
| | - Baohua Li
- Department of Plant SciencesUniversity of California, DavisDavisCAUSA
| | - Xue Zhou
- Department of Plant SciencesUniversity of California, DavisDavisCAUSA
| | - Tayah Bolt
- Department of Plant SciencesUniversity of California, DavisDavisCAUSA
| | - Jia Jie Li
- Department of Plant SciencesUniversity of California, DavisDavisCAUSA
| | - Neiman Cruz
- Department of Plant Biology and Genome CenterUniversity of California, DavisDavisCAUSA
| | - Allison Gaudinier
- Department of Plant Biology and Genome CenterUniversity of California, DavisDavisCAUSA
- Plant Biology Graduate GroupUniversity of California, DavisDavisCAUSA
| | - Richard Ngo
- Department of Plant Biology and Genome CenterUniversity of California, DavisDavisCAUSA
- Department of Plant SciencesUniversity of California, DavisDavisCAUSA
| | - Caitlin Clark‐Wiest
- Department of Plant Biology and Genome CenterUniversity of California, DavisDavisCAUSA
- Department of Plant SciencesUniversity of California, DavisDavisCAUSA
| | - Daniel J Kliebenstein
- Department of Plant SciencesUniversity of California, DavisDavisCAUSA
- DynaMo Center of ExcellenceUniversity of CopenhagenFrederiksberg CDenmark
| | - Siobhan M Brady
- Department of Plant Biology and Genome CenterUniversity of California, DavisDavisCAUSA
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29
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Tan C, Zhu S, Chen Z, Liu C, Li YE, Zhu M, Zhang Z, Zhang Z, Zhang L, Gu Y, Liang Z, Boyer TG, Ouyang K, Evans SM, Fang X. Mediator complex proximal Tail subunit MED30 is critical for Mediator core stability and cardiomyocyte transcriptional network. PLoS Genet 2021; 17:e1009785. [PMID: 34506481 PMCID: PMC8432849 DOI: 10.1371/journal.pgen.1009785] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/18/2021] [Indexed: 01/28/2023] Open
Abstract
Dysregulation of cardiac transcription programs has been identified in patients and families with heart failure, as well as those with morphological and functional forms of congenital heart defects. Mediator is a multi-subunit complex that plays a central role in transcription initiation by integrating regulatory signals from gene-specific transcriptional activators to RNA polymerase II (Pol II). Recently, Mediator subunit 30 (MED30), a metazoan specific Mediator subunit, has been associated with Langer-Giedion syndrome (LGS) Type II and Cornelia de Lange syndrome-4 (CDLS4), characterized by several abnormalities including congenital heart defects. A point mutation in MED30 has been identified in mouse and is associated with mitochondrial cardiomyopathy. Very recent structural analyses of Mediator revealed that MED30 localizes to the proximal Tail, anchoring Head and Tail modules, thus potentially influencing stability of the Mediator core. However, in vivo cellular and physiological roles of MED30 in maintaining Mediator core integrity remain to be tested. Here, we report that deletion of MED30 in embryonic or adult cardiomyocytes caused rapid development of cardiac defects and lethality. Importantly, cardiomyocyte specific ablation of MED30 destabilized Mediator core subunits, while the kinase module was preserved, demonstrating an essential role of MED30 in stability of the overall Mediator complex. RNAseq analyses of constitutive cardiomyocyte specific Med30 knockout (cKO) embryonic hearts and inducible cardiomyocyte specific Med30 knockout (icKO) adult cardiomyocytes further revealed critical transcription networks in cardiomyocytes controlled by Mediator. Taken together, our results demonstrated that MED30 is essential for Mediator stability and transcriptional networks in both developing and adult cardiomyocytes. Our results affirm the key role of proximal Tail modular subunits in maintaining core Mediator stability in vivo.
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Affiliation(s)
- Changming Tan
- Department of Medicine, University of California, San Diego, California, United States of America
- Department of Cardiovascular Surgery, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Siting Zhu
- Department of Medicine, University of California, San Diego, California, United States of America
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, School of Chemical Biology and Biotechnology, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Zee Chen
- Department of Medicine, University of California, San Diego, California, United States of America
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, School of Chemical Biology and Biotechnology, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Canzhao Liu
- Department of Medicine, University of California, San Diego, California, United States of America
| | - Yang E. Li
- Department of Medicine, University of California, San Diego, California, United States of America
| | - Mason Zhu
- Department of Medicine, University of California, San Diego, California, United States of America
| | - Zhiyuan Zhang
- Department of Medicine, University of California, San Diego, California, United States of America
- Department of Cardiovascular Surgery, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhiwei Zhang
- Department of Medicine, University of California, San Diego, California, United States of America
- Department of Cardiovascular Surgery, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lunfeng Zhang
- Department of Medicine, University of California, San Diego, California, United States of America
| | - Yusu Gu
- Department of Medicine, University of California, San Diego, California, United States of America
| | - Zhengyu Liang
- Department of Medicine, University of California, San Diego, California, United States of America
| | - Thomas G. Boyer
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas, United States of America
| | - Kunfu Ouyang
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, School of Chemical Biology and Biotechnology, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Sylvia M. Evans
- Department of Medicine, University of California, San Diego, California, United States of America
- Department of Pharmacology, University of California, San Diego, California, United States of America
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, United States of America
| | - Xi Fang
- Department of Medicine, University of California, San Diego, California, United States of America
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30
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Hu H, Tang Y, Wu J, Chen F, Yang Y, Pan X, Dong X, Jin X, Liu S, Du X. Brassica napus Mediator Subunit16 Induces BnMED25- and BnWRKY33-Activated Defense Signaling to Confer Sclerotinia sclerotiorum Resistance. FRONTIERS IN PLANT SCIENCE 2021; 12:663536. [PMID: 34489988 PMCID: PMC8417128 DOI: 10.3389/fpls.2021.663536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/31/2021] [Indexed: 06/13/2023]
Abstract
The plant mediator is a highly conserved protein complex that interacts with transcription factors (TFs) and RNA polymerase II (RNAP II) to relay regulatory information during transcription. Plant immune response is one of the biological processes that is orchestrated by this regulatory mechanism. Brassica napus, an important oil crop, is severely attacked by a devastating disease Sclerotinia stem rot. Here, we explored broad-spectrum disease resistant roles of B. napus mediator subunit 16 (BnMED16) and its host defense mechanism against fugal pathogen Sclerotinia sclerotiorum. We found that BnMED16 expression was significantly increased by S. sclerotiorum infection, and its homologous overexpression resulted in rapid and comprehensive defense responses from the beginning to the end. This affected signal transduction with multiple channels including pathogen recognition, intracellular Ca2+ concentration, reactive oxygen species (ROS) accumulation and clearance, and activation of mitogen-activated protein kinase (MAPK) signaling cascades initially. Subsequently, pathogen-/defense-related genes and hormone-responsive pathways were highly activated, which resulted in enhanced cell wall and secretion of defense proteases. Furthermore, the biochemical analysis showed that BnMED16 interacts with BnMED25 and BnWRKY33. Additionally, BnMED25 also interacts with TFs BnMYC2, BnCOI1, and BnEIN3 of the JA/ET signal transduction pathway. Taken together, we proposed a hypothetical model that BnMED16 confers S. sclerotiorum resistance by enhancing BnMED25-mediated JA/ET defense pathways and BnWRKY33-activated defense signaling in B. napus. The BnMED16 overexpressing lines with enhanced broad-spectrum disease resistance could be useful for breeding Sclerotinia-resistant oilseed rape varieties, as well as serving as basis for further strategy development in resistance breeding.
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Affiliation(s)
- Huizhen Hu
- Southwest Research Center for Landscape Architecture Engineering, State Forestry and Grassland Administration, Yunnan Province Engineering Research Center for Functional Flower Resources and Industrialization, College of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming, China
| | - Yiwei Tang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
| | - Jian Wu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Feizhi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
| | - Yidan Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
| | - Xuancheng Pan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
| | - Xiang Dong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
| | - Xianda Jin
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
| | - Sheng Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Xuezhu Du
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
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31
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Stanek TJ, Gennaro VJ, Tracewell MA, Di Marcantonio D, Pauley KL, Butt S, McNair C, Wang F, Kossenkov AV, Knudsen KE, Butt T, Sykes SM, McMahon SB. The SAGA complex regulates early steps in transcription via its deubiquitylase module subunit USP22. EMBO J 2021; 40:e102509. [PMID: 34155658 PMCID: PMC8365265 DOI: 10.15252/embj.2019102509] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 04/10/2021] [Accepted: 04/26/2021] [Indexed: 12/12/2022] Open
Abstract
The SAGA coactivator complex is essential for eukaryotic transcription and comprises four distinct modules, one of which contains the ubiquitin hydrolase USP22. In yeast, the USP22 ortholog deubiquitylates H2B, resulting in Pol II Ser2 phosphorylation and subsequent transcriptional elongation. In contrast to this H2B-associated role in transcription, we report here that human USP22 contributes to the early stages of stimulus-responsive transcription, where USP22 is required for pre-initiation complex (PIC) stability. Specifically, USP22 maintains long-range enhancer-promoter contacts and controls loading of Mediator tail and general transcription factors (GTFs) onto promoters, with Mediator core recruitment being USP22-independent. In addition, we identify Mediator tail subunits MED16 and MED24 and the Pol II subunit RBP1 as potential non-histone substrates of USP22. Overall, these findings define a role for human SAGA within the earliest steps of transcription.
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Affiliation(s)
- Timothy J Stanek
- Department of Biochemistry and Molecular BiologySidney Kimmel Medical CollegeThomas Jefferson UniversityPhiladelphiaPAUSA
| | - Victoria J Gennaro
- Department of Biochemistry and Molecular BiologySidney Kimmel Medical CollegeThomas Jefferson UniversityPhiladelphiaPAUSA
| | - Mason A Tracewell
- Department of Biochemistry and Molecular BiologySidney Kimmel Medical CollegeThomas Jefferson UniversityPhiladelphiaPAUSA
| | | | - Kristen L Pauley
- Department of Biochemistry and Molecular BiologySidney Kimmel Medical CollegeThomas Jefferson UniversityPhiladelphiaPAUSA
| | - Sabrina Butt
- Department of Biochemistry and Molecular BiologySidney Kimmel Medical CollegeThomas Jefferson UniversityPhiladelphiaPAUSA
| | - Christopher McNair
- Department of Cancer BiologySidney Kimmel Medical College and Sidney Kimmel Cancer CenterThomas Jefferson UniversityPhiladelphiaPAUSA
| | | | | | - Karen E Knudsen
- Department of Cancer BiologySidney Kimmel Medical College and Sidney Kimmel Cancer CenterThomas Jefferson UniversityPhiladelphiaPAUSA
| | | | - Stephen M Sykes
- Blood Cell Development and Function ProgramFox Chase Cancer CenterPhiladelphiaPAUSA
| | - Steven B McMahon
- Department of Biochemistry and Molecular BiologySidney Kimmel Medical CollegeThomas Jefferson UniversityPhiladelphiaPAUSA
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32
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Cevher MA. Reconstitution of Pol II (G) responsive form of the human Mediator complex. Turk J Biol 2021; 45:253-261. [PMID: 34377050 PMCID: PMC8313941 DOI: 10.3906/biy-2009-12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 04/16/2021] [Indexed: 01/15/2023] Open
Abstract
RNA polymerase II (Pol II) is a 12 subunit protein complex from yeast to human that is required for gene expression. Gdown1 containing Pol II [Pol II (G)] is a special form of Pol II that is catalytically inactive and heavily depends on the 30-subunit Mediator complex for its activator and basal dependent function in vitro. Here we report for the first time, the identification and the generation of a 15-subunit human Mediator complex via the novel multibac baculovirus expression system that is fully responsive to Pol II (G). Our results show complete recovery of Pol II (G) dependent transcription both with full 30-subunit Mediator and also with 15-subunit recombinant Mediator that we synthesized. Moreover, we also show that the recombinant Mediator interacts with Pol II (G) as well. These results enlighten us towards understanding how a certain population of Pol II that is involved in selected gene regulation is activated by Mediator complex.
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Affiliation(s)
- Murat Alper Cevher
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara Turkey.,Visiting Assistant Professor, Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York USA
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33
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Chen X, Yin X, Li J, Wu Z, Qi Y, Wang X, Liu W, Xu Y. Structures of the human Mediator and Mediator-bound preinitiation complex. Science 2021; 372:science.abg0635. [DOI: 10.1126/science.abg0635] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/15/2021] [Accepted: 04/27/2021] [Indexed: 12/18/2022]
Abstract
The 1.3-megadalton transcription factor IID (TFIID) is required for preinitiation complex (PIC) assembly and RNA polymerase II (Pol II)–mediated transcription initiation on almost all genes. The 26-subunit Mediator stimulates transcription and cyclin-dependent kinase 7 (CDK7)–mediated phosphorylation of the Pol II C-terminal domain (CTD). We determined the structures of human Mediator in the Tail module–extended (at near-atomic resolution) and Tail-bent conformations and structures of TFIID-based PIC-Mediator (76 polypeptides, ~4.1 megadaltons) in four distinct conformations. PIC-Mediator assembly induces concerted reorganization (Head-tilting and Middle-down) of Mediator and creates a Head-Middle sandwich, which stabilizes two CTD segments and brings CTD to CDK7 for phosphorylation; this suggests a CTD-gating mechanism favorable for phosphorylation. The TFIID-based PIC architecture modulates Mediator organization and TFIIH stabilization, underscoring the importance of TFIID in orchestrating PIC-Mediator assembly.
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Affiliation(s)
- Xizi Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Xiaotong Yin
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Jiabei Li
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Zihan Wu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yilun Qi
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Xinxin Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Weida Liu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
- International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
- Human Phenome Institute, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
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34
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Weidle UH, Brinkmann U, Auslaender S. microRNAs and Corresponding Targets Involved in Metastasis of Colorectal Cancer in Preclinical In Vivo Models. Cancer Genomics Proteomics 2021; 17:453-468. [PMID: 32859626 DOI: 10.21873/cgp.20204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/08/2020] [Accepted: 07/17/2020] [Indexed: 12/27/2022] Open
Abstract
The high death toll of colorectal cancer patients is due to metastatic disease which is difficult to treat. The liver is the preferred site of metastasis, followed by the lungs and peritoneum. In order to identify new targets and new modalities of intervention we surveyed the literature for microRNAs (miRs) which modulate metastasis of colorectal cancer in preclinical in vivo models. We identified 12 up-regulated and 19 down-regulated miRs corresponding to the latter criterium. The vast majority (n=16) of identified miRs are involved in modulation of epithelial-mesenchymal transition (EMT). Other categories of metastasis-related miRs exhibit tumor- and metastasis-suppressing functions, modulation of signaling pathways, transmembrane receptors and a class of miRs, which interfere with targets which do not fit into these categories. Finally, we discuss the principles of miR inhibition and reconstitution of function, prospective clinical evaluation of with miR-related agents in the context of clinical evaluation in metastasis relevant settings.
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Affiliation(s)
- Ulrich H Weidle
- Large Molecule Research, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Penzberg, Germany
| | - Ulrich Brinkmann
- Large Molecule Research, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Penzberg, Germany
| | - Simon Auslaender
- Large Molecule Research, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Penzberg, Germany
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35
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Structure of the human Mediator–RNA polymerase II pre-initiation complex. Nature 2021; 594:129-133. [DOI: 10.1038/s41586-021-03555-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/14/2021] [Indexed: 12/25/2022]
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Ito K, Schneeberger M, Gerber A, Jishage M, Marchildon F, Maganti AV, Cohen P, Friedman JM, Roeder RG. Critical roles of transcriptional coactivator MED1 in the formation and function of mouse adipose tissues. Genes Dev 2021; 35:729-748. [PMID: 33888560 PMCID: PMC8091968 DOI: 10.1101/gad.346791.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 03/16/2021] [Indexed: 01/12/2023]
Abstract
In this study, Ito et al. sought to understand the precise roles of MED1, and its various domains, at various stages of adipogenesis and in adipose tissue. Using multiple genetic approaches to assess requirements for MED1 in adipocyte formation and function in mice, they show that MED1 is indeed essential for the differentiation and/or function of both brown and white adipocytes, as its absence in these cells leads to, respectively, defective brown fat function and lipodystrophy. The MED1 subunit has been shown to mediate ligand-dependent binding of the Mediator coactivator complex to multiple nuclear receptors, including the adipogenic PPARγ, and to play an essential role in ectopic PPARγ-induced adipogenesis of mouse embryonic fibroblasts. However, the precise roles of MED1, and its various domains, at various stages of adipogenesis and in adipose tissue have been unclear. Here, after establishing requirements for MED1, including specific domains, for differentiation of 3T3L1 cells and both primary white and brown preadipocytes, we used multiple genetic approaches to assess requirements for MED1 in adipocyte formation, maintenance, and function in mice. We show that MED1 is indeed essential for the differentiation and/or function of both brown and white adipocytes, as its absence in these cells leads to, respectively, defective brown fat function and lipodystrophy. This work establishes MED1 as an essential transcriptional coactivator that ensures homeostatic functions of adipocytes.
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Affiliation(s)
- Keiichi Ito
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York 10065, USA
| | - Marc Schneeberger
- Laboratory of Molecular Genetics, The Rockefeller University, New York, New York 10065, USA
| | - Alan Gerber
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York 10065, USA
| | - Miki Jishage
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York 10065, USA
| | - Francois Marchildon
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, New York 10065, USA
| | - Aarthi V Maganti
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, New York 10065, USA
| | - Paul Cohen
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, New York 10065, USA
| | - Jeffrey M Friedman
- Laboratory of Molecular Genetics, The Rockefeller University, New York, New York 10065, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York 10065, USA
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Abdella R, Talyzina A, Chen S, Inouye CJ, Tjian R, He Y. Structure of the human Mediator-bound transcription preinitiation complex. Science 2021; 372:52-56. [PMID: 33707221 PMCID: PMC8117670 DOI: 10.1126/science.abg3074] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/03/2021] [Indexed: 12/24/2022]
Abstract
Eukaryotic transcription requires the assembly of a multisubunit preinitiation complex (PIC) composed of RNA polymerase II (Pol II) and the general transcription factors. The coactivator Mediator is recruited by transcription factors, facilitates the assembly of the PIC, and stimulates phosphorylation of the Pol II C-terminal domain (CTD) by the TFIIH subunit CDK7. Here, we present the cryo-electron microscopy structure of the human Mediator-bound PIC at a resolution below 4 angstroms. Transcription factor binding sites within Mediator are primarily flexibly tethered to the tail module. CDK7 is stabilized by multiple contacts with Mediator. Two binding sites exist for the Pol II CTD, one between the head and middle modules of Mediator and the other in the active site of CDK7, providing structural evidence for Pol II CTD phosphorylation within the Mediator-bound PIC.
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Affiliation(s)
- R Abdella
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - A Talyzina
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - S Chen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - C J Inouye
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA, USA
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - R Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA, USA
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Y He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, Chicago, IL, USA
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38
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Guo P, Chong L, Wu F, Hsu CC, Li C, Zhu JK, Zhu Y. Mediator tail module subunits MED16 and MED25 differentially regulate abscisic acid signaling in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:802-815. [PMID: 33369119 DOI: 10.1111/jipb.13062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/19/2020] [Indexed: 05/06/2023]
Abstract
MED25 has been implicated as a negative regulator of the abscisic acid (ABA) signaling pathway. However, it is unclear whether other Mediator subunits could associate with MED25 to participate in the ABA response. Here, we used affinity purification followed by mass spectrometry to uncover Mediator subunits that associate with MED25 in transgenic plants. We found that at least 26 Mediator subunits, belonging to the head, middle, tail, and CDK8 kinase modules, were co-purified with MED25 in vivo. Interestingly, the tail module subunit MED16 was identified to associate with MED25 under both mock and ABA treatments. We further showed that the disruption of MED16 led to reduced ABA sensitivity compared to the wild type. Transcriptomic analysis revealed that the expression of several ABA-responsive genes was significantly lower in med16 than those in wild type. Furthermore, we discovered that MED16 may possibly compete with MED25 to interact with the key transcription factor ABA INSENSITIVE 5 (ABI5) to positively regulate ABA signaling. Consistently, med16 and med25 mutants displayed opposite phenotypes in ABA response, cuticle permeability, and differential ABI5-mediated EM1 and EM6 expression. Together, our data indicate that MED16 and MED25 differentially regulate ABA signaling by antagonistically affecting ABI5-mediated transcription in Arabidopsis.
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Affiliation(s)
- Pengcheng Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Leelyn Chong
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Fangming Wu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Chuan-Chih Hsu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529
| | - Chuanyou Li
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, Shanghai, 200032, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Yingfang Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475001, China
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39
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Tourigny JP, Schumacher K, Saleh MM, Devys D, Zentner GE. Architectural Mediator subunits are differentially essential for global transcription in Saccharomyces cerevisiae. Genetics 2021; 217:iyaa042. [PMID: 33789343 PMCID: PMC8045717 DOI: 10.1093/genetics/iyaa042] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 12/16/2020] [Indexed: 12/18/2022] Open
Abstract
Mediator is a modular coactivator complex involved in the transcription of the majority of RNA polymerase II-regulated genes. However, the degrees to which individual core subunits of Mediator contribute to its activity have been unclear. Here, we investigate the contribution of two essential architectural subunits of Mediator to transcription in Saccharomyces cerevisiae. We show that acute depletion of the main complex scaffold Med14 or the head module nucleator Med17 is lethal and results in global transcriptional downregulation, though Med17 removal has a markedly greater negative effect. Consistent with this, Med17 depletion impairs preinitiation complex (PIC) assembly to a greater extent than Med14 removal. Co-depletion of Med14 and Med17 reduced transcription and TFIIB promoter occupancy similarly to Med17 ablation alone, indicating that the contributions of Med14 and Med17 to Mediator function are not additive. We propose that, while the structural integrity of complete Mediator and the head module are both important for PIC assembly and transcription, the head module plays a greater role in this process and is thus the key functional module of Mediator in this regard.
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Affiliation(s)
- Jason P Tourigny
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Kenny Schumacher
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- UMR7104, Centre National de la Recherche Scientifique, 67404 Illkirch, France
- U964, Institut National de la Santé et de la Recherche Médicale, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Moustafa M Saleh
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Didier Devys
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- UMR7104, Centre National de la Recherche Scientifique, 67404 Illkirch, France
- U964, Institut National de la Santé et de la Recherche Médicale, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Gabriel E Zentner
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN 46202, USA
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40
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Zhao H, Young N, Kalchschmidt J, Lieberman J, El Khattabi L, Casellas R, Asturias FJ. Structure of mammalian Mediator complex reveals Tail module architecture and interaction with a conserved core. Nat Commun 2021; 12:1355. [PMID: 33649303 PMCID: PMC7921410 DOI: 10.1038/s41467-021-21601-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 02/01/2021] [Indexed: 01/04/2023] Open
Abstract
The Mediator complex plays an essential and multi-faceted role in regulation of RNA polymerase II transcription in all eukaryotes. Structural analysis of yeast Mediator has provided an understanding of the conserved core of the complex and its interaction with RNA polymerase II but failed to reveal the structure of the Tail module that contains most subunits targeted by activators and repressors. Here we present a molecular model of mammalian (Mus musculus) Mediator, derived from a 4.0 Å resolution cryo-EM map of the complex. The mammalian Mediator structure reveals that the previously unresolved Tail module, which includes a number of metazoan specific subunits, interacts extensively with core Mediator and has the potential to influence its conformation and interactions.
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Affiliation(s)
- Haiyan Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO, USA
| | - Natalie Young
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO, USA
| | | | | | - Laila El Khattabi
- Institut Cochin Laboratoire de Cytogénétique Constitutionnelle Pré et Post Natale, Paris, France
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD, USA.,Center for Cancer Research, NCI, NIH, Bethesda, MD, USA
| | - Francisco J Asturias
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO, USA.
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41
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Zhang H, Chen DH, Mattoo RUH, Bushnell DA, Wang Y, Yuan C, Wang L, Wang C, Davis RE, Nie Y, Kornberg RD. Mediator structure and conformation change. Mol Cell 2021; 81:1781-1788.e4. [PMID: 33571424 DOI: 10.1016/j.molcel.2021.01.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/29/2020] [Accepted: 01/19/2021] [Indexed: 01/22/2023]
Abstract
Mediator is a universal adaptor for transcription control. It serves as an interface between gene-specific activator or repressor proteins and the general RNA polymerase II (pol II) transcription machinery. Previous structural studies revealed a relatively small part of Mediator and none of the gene activator-binding regions. We have determined the cryo-EM structure of the Mediator at near-atomic resolution. The structure reveals almost all amino acid residues in ordered regions, including the major targets of activator proteins, the Tail module, and the Med1 subunit of the Middle module. Comparison of Mediator structures with and without pol II reveals conformational changes that propagate across the entire Mediator, from Head to Tail, coupling activator- and pol II-interacting regions.
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Affiliation(s)
- Heqiao Zhang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dong-Hua Chen
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rayees U H Mattoo
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David A Bushnell
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yannan Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
| | - Chao Yuan
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
| | - Lin Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
| | - Chunnian Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
| | - Ralph E Davis
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yan Nie
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China.
| | - Roger D Kornberg
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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42
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Agrawal R, Jiří F, Thakur JK. The kinase module of the Mediator complex: an important signalling processor for the development and survival of plants. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:224-240. [PMID: 32945869 DOI: 10.1093/jxb/eraa439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 09/16/2020] [Indexed: 05/06/2023]
Abstract
Mediator, a multisubunit protein complex, is a signal processor that conveys regulatory information from transcription factors to RNA polymerase II and therefore plays an important role in the regulation of gene expression. This megadalton complex comprises four modules, namely, the head, middle, tail, and kinase modules. The first three modules form the core part of the complex, whereas association of the kinase module is facultative. The kinase module is able to alter the function of Mediator and has been established as a major transcriptional regulator of numerous developmental and biochemical processes. The kinase module consists of MED12, MED13, CycC, and kinase CDK8. Upon association with Mediator, the kinase module can alter its structure and function dramatically. In the past decade, research has established that the kinase module is very important for plant growth and development, and in the fight against biotic and abiotic challenges. However, there has been no comprehensive review discussing these findings in detail and depth. In this review, we survey the regulation of kinase module subunits and highlight their many functions in plants. Coordination between the subunits to process different signals for optimum plant growth and development is also discussed.
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Affiliation(s)
- Rekha Agrawal
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Fajkus Jiří
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jitendra K Thakur
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
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43
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Straub J, Venigalla S, Newman JJ. Mediator's Kinase Module: A Modular Regulator of Cell Fate. Stem Cells Dev 2020; 29:1535-1551. [PMID: 33161841 DOI: 10.1089/scd.2020.0164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Selective gene expression is crucial in maintaining the self-renewing and multipotent properties of stem cells. Mediator is a large, evolutionarily conserved, multi-subunit protein complex that modulates gene expression by relaying signals from cell type-specific transcription factors to RNA polymerase II. In humans, this complex consists of 30 subunits arranged in four modules. One critical module of the Mediator complex is the kinase module consisting of four subunits: MED12, MED13, CDK8, and CCNC. The kinase module exists in variable association with the 26-subunit Mediator core and affects transcription through phosphorylation of transcription factors and by controlling Mediator structure and function. Many studies have shown the kinase module to be a key player in the maintenance of stem cells that is distinct from a general role in transcription. Genetic studies have revealed that dysregulation of this kinase subunit contributes to the development of many human diseases. In this review, we discuss the importance of the Mediator kinase module by examining how this module functions with the more recently identified transcriptional super-enhancers, how changes in the kinase module and its activity can lead to the development of human disease, and the role of this unique module in directing and maintaining cell state. As we look to use stem cells to understand human development and treat human disease through both cell-based therapies and tissue engineering, we need to remain aware of the on-going research and address critical gaps in knowledge related to the molecular mechanisms that control cell fate.
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Affiliation(s)
- Joseph Straub
- School of Biological Sciences, Louisiana Tech University, Ruston, Louisiana, USA
| | - Sree Venigalla
- School of Biological Sciences, Louisiana Tech University, Ruston, Louisiana, USA
| | - Jamie J Newman
- School of Biological Sciences, Louisiana Tech University, Ruston, Louisiana, USA
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Zhu Y, Huang P, Guo P, Chong L, Yu G, Sun X, Hu T, Li Y, Hsu CC, Tang K, Zhou Y, Zhao C, Gao W, Tao WA, Mengiste T, Zhu JK. CDK8 is associated with RAP2.6 and SnRK2.6 and positively modulates abscisic acid signaling and drought response in Arabidopsis. THE NEW PHYTOLOGIST 2020; 228:1573-1590. [PMID: 32619295 DOI: 10.1111/nph.16787] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 06/20/2020] [Indexed: 06/11/2023]
Abstract
CDK8 is a key subunit of Mediator complex, a large multiprotein complex that is a fundamental part of the conserved eukaryotic transcriptional machinery. However, the biological functions of CDK8 in plant abiotic stress responses remain largely unexplored. Here, we demonstrated CDK8 as a critical regulator in the abscisic acid (ABA) signaling and drought response pathways in Arabidopsis. Compared to wild-type, cdk8 mutants showed reduced sensitivity to ABA, impaired stomatal apertures and hypersensitivity to drought stress. Transcriptomic and chromatin immunoprecipitation analysis revealed that CDK8 positively regulates the transcription of several ABA-responsive genes, probably through promoting the recruitment of RNA polymerase II to their promoters. We discovered that both CDK8 and SnRK2.6 interact physically with an ERF/AP2 transcription factor RAP2.6, which can directly bind to the promoters of RD29A and COLD-REGULATED 15A (COR15A) with GCC or DRE elements, thereby promoting their expression. Importantly, we also showed that CDK8 is essential for the ABA-induced expression of RAP2.6 and RAP2.6-mediated upregulation of ABA-responsive genes, indicating that CDK8 could link the SnRK2.6-mediated ABA signaling to RNA polymerase II to promote immediate transcriptional response to ABA and drought signals. Overall, our data provide new insights into the roles of CDK8 in modulating ABA signaling and drought responses.
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Affiliation(s)
- Yingfang Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Pengcheng Huang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Pengcheng Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Leelyn Chong
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Gaobo Yu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163711, China
| | - Xiaoli Sun
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163711, China
| | - Tao Hu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Yuan Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Chuan-Chih Hsu
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Kai Tang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yun Zhou
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Chunzhao Zhao
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Wei Gao
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Jian-Kang Zhu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
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45
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Cui W, Marcho C, Wang Y, Degani R, Golan M, Tremblay KD, Rivera-Pérez JA, Mager J. MED20 is essential for early embryogenesis and regulates NANOG expression. Reproduction 2020; 157:215-222. [PMID: 30571656 DOI: 10.1530/rep-18-0508] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 12/17/2018] [Indexed: 12/15/2022]
Abstract
Mediator is an evolutionarily conserved multi-subunit complex, bridging transcriptional activators and repressors to the general RNA polymerase II (Pol II) initiation machinery. Though the Mediator complex is crucial for the transcription of almost all Pol II promoters in eukaryotic organisms, the phenotypes of individual Mediator subunit mutants are each distinct. Here, we report for the first time, the essential role of subunit MED20 in early mammalian embryo development. Although Med20 mutant mouse embryos exhibit normal morphology at E3.5 blastocyst stage, they cannot be recovered at early post-gastrulation stages. Outgrowth assays show that mutant blastocysts cannot hatch from the zona pellucida, indicating impaired blastocyst function. Assessments of cell death and cell lineage specification reveal that apoptosis, inner cell mass, trophectoderm and primitive endoderm markers are normal in mutant blastocysts. However, the epiblast marker NANOG is ectopically expressed in the trophectoderm of Med20 mutants, indicative of defects in trophoblast specification. These results suggest that MED20 specifically, and the Mediator complex in general, are essential for the earliest steps of mammalian development and cell lineage specification.
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Affiliation(s)
- Wei Cui
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts, USA.,Animal Models Core Facility, Institute for Applied Life Sciences (IALS), University of Massachusetts, Amherst, Massachusetts, USA
| | - Chelsea Marcho
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts, USA
| | - Yongsheng Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Rinat Degani
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts, USA
| | - Morgane Golan
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts, USA
| | - Kimberly D Tremblay
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts, USA
| | - Jaime A Rivera-Pérez
- Division of Genes and Development, Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jesse Mager
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts, USA
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46
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Immarigeon C, Bernat-Fabre S, Guillou E, Verger A, Prince E, Benmedjahed MA, Payet A, Couralet M, Monte D, Villeret V, Bourbon HM, Boube M. Mediator complex subunit Med19 binds directly GATA transcription factors and is required with Med1 for GATA-driven gene regulation in vivo. J Biol Chem 2020; 295:13617-13629. [PMID: 32737196 DOI: 10.1074/jbc.ra120.013728] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/21/2020] [Indexed: 02/02/2023] Open
Abstract
The evolutionarily conserved multiprotein Mediator complex (MED) serves as an interface between DNA-bound transcription factors (TFs) and the RNA Pol II machinery. It has been proposed that each TF interacts with a dedicated MED subunit to induce specific transcriptional responses. But are these binary partnerships sufficient to mediate TF functions? We have previously established that the Med1 Mediator subunit serves as a cofactor of GATA TFs in Drosophila, as shown in mammals. Here, we observe mutant phenotype similarities between another subunit, Med19, and the Drosophila GATA TF Pannier (Pnr), suggesting functional interaction. We further show that Med19 physically interacts with the Drosophila GATA TFs, Pnr and Serpent (Srp), in vivo and in vitro through their conserved C-zinc finger domains. Moreover, Med19 loss of function experiments in vivo or in cellulo indicate that it is required for Pnr- and Srp-dependent gene expression, suggesting general GATA cofactor functions. Interestingly, Med19 but not Med1 is critical for the regulation of all tested GATA target genes, implying shared or differential use of MED subunits by GATAs depending on the target gene. Lastly, we show a direct interaction between Med19 and Med1 by GST pulldown experiments indicating privileged contacts between these two subunits of the MED middle module. Together, these findings identify Med19/Med1 as a composite GATA TF interface and suggest that binary MED subunit-TF partnerships are probably oversimplified models. We propose several mechanisms to account for the transcriptional regulation of GATA-targeted genes.
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Affiliation(s)
- Clément Immarigeon
- Centre de Biologie Integrative CBD, UMR5547 CNRS/UPS, Université de Toulouse, Toulouse Cedex, France
| | - Sandra Bernat-Fabre
- Centre de Biologie Integrative CBD, UMR5547 CNRS/UPS, Université de Toulouse, Toulouse Cedex, France
| | - Emmanuelle Guillou
- Centre de Biologie Integrative CBD, UMR5547 CNRS/UPS, Université de Toulouse, Toulouse Cedex, France
| | - Alexis Verger
- Inserm, CHU Lille, Institut Pasteur de Lille, CNRS ERL 9002 Integrative Structural Biology, Université Lille, Lille, France
| | - Elodie Prince
- Centre de Biologie Integrative CBD, UMR5547 CNRS/UPS, Université de Toulouse, Toulouse Cedex, France
| | - Mohamed A Benmedjahed
- Centre de Biologie Integrative CBD, UMR5547 CNRS/UPS, Université de Toulouse, Toulouse Cedex, France
| | - Adeline Payet
- Centre de Biologie Integrative CBD, UMR5547 CNRS/UPS, Université de Toulouse, Toulouse Cedex, France
| | - Marie Couralet
- Centre de Biologie Integrative CBD, UMR5547 CNRS/UPS, Université de Toulouse, Toulouse Cedex, France
| | - Didier Monte
- Inserm, CHU Lille, Institut Pasteur de Lille, CNRS ERL 9002 Integrative Structural Biology, Université Lille, Lille, France
| | - Vincent Villeret
- Inserm, CHU Lille, Institut Pasteur de Lille, CNRS ERL 9002 Integrative Structural Biology, Université Lille, Lille, France
| | - Henri-Marc Bourbon
- Centre de Biologie Integrative CBD, UMR5547 CNRS/UPS, Université de Toulouse, Toulouse Cedex, France
| | - Muriel Boube
- Centre de Biologie Integrative CBD, UMR5547 CNRS/UPS, Université de Toulouse, Toulouse Cedex, France.
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Tessier TM, MacNeil KM, Mymryk JS. Piggybacking on Classical Import and Other Non-Classical Mechanisms of Nuclear Import Appear Highly Prevalent within the Human Proteome. BIOLOGY 2020; 9:biology9080188. [PMID: 32718019 PMCID: PMC7463951 DOI: 10.3390/biology9080188] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 12/23/2022]
Abstract
One of the most conserved cellular pathways among eukaryotes is the extensively studied classical protein nuclear import pathway mediated by importin-α. Classical nuclear localization signals (cNLSs) are recognized by importin-α and are highly predictable due to their abundance of basic amino acids. However, various studies in model organisms have repeatedly demonstrated that only a fraction of nuclear proteins contain identifiable cNLSs, including those that directly interact with importin-α. Using data from the Human Protein Atlas and the Human Reference Interactome, and proteomic data from BioID/protein-proximity labeling studies using multiple human importin-α proteins, we determine that nearly 50% of the human nuclear proteome does not have a predictable cNLS. Surprisingly, between 25% and 50% of previously identified human importin-α cargoes do not have predictable cNLS. Analysis of importin-α cargo without a cNLS identified an alternative basic rich motif that does not resemble a cNLS. Furthermore, several previously suspected piggybacking proteins were identified, such as those belonging to the RNA polymerase II and transcription factor II D complexes. Additionally, many components of the mediator complex interact with at least one importin-α, yet do not have a predictable cNLS, suggesting that many of the subunits may enter the nucleus through an importin-α-dependent piggybacking mechanism.
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Affiliation(s)
- Tanner M. Tessier
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6A 3K7, Canada; (T.M.T.); (K.M.M.)
| | - Katelyn M. MacNeil
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6A 3K7, Canada; (T.M.T.); (K.M.M.)
| | - Joe S. Mymryk
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6A 3K7, Canada; (T.M.T.); (K.M.M.)
- Department of Otolaryngology, Head & Neck Surgery, The University of Western Ontario, London, ON N6A 3K7, Canada
- Department of Oncology, The University of Western Ontario, London, ON N6A 3K7, Canada
- London Regional Cancer Program, Lawson Health Research Institute, London, ON N6A 5W9, Canada
- Correspondence: ; Tel.: +1-519-685-8600 (ext. 53012)
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Abstract
RNA polymerase II (Pol II) transcribes all protein-coding genes and many noncoding RNAs in eukaryotic genomes. Although Pol II is a complex, 12-subunit enzyme, it lacks the ability to initiate transcription and cannot consistently transcribe through long DNA sequences. To execute these essential functions, an array of proteins and protein complexes interact with Pol II to regulate its activity. In this review, we detail the structure and mechanism of over a dozen factors that govern Pol II initiation (e.g., TFIID, TFIIH, and Mediator), pausing, and elongation (e.g., DSIF, NELF, PAF, and P-TEFb). The structural basis for Pol II transcription regulation has advanced rapidly in the past decade, largely due to technological innovations in cryoelectron microscopy. Here, we summarize a wealth of structural and functional data that have enabled a deeper understanding of Pol II transcription mechanisms; we also highlight mechanistic questions that remain unanswered or controversial.
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Affiliation(s)
- Allison C Schier
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80303, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80303, USA
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Crawford T, Karamat F, Lehotai N, Rentoft M, Blomberg J, Strand Å, Björklund S. Specific functions for Mediator complex subunits from different modules in the transcriptional response of Arabidopsis thaliana to abiotic stress. Sci Rep 2020; 10:5073. [PMID: 32193425 PMCID: PMC7081235 DOI: 10.1038/s41598-020-61758-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 02/26/2020] [Indexed: 11/22/2022] Open
Abstract
Adverse environmental conditions are detrimental to plant growth and development. Acclimation to abiotic stress conditions involves activation of signaling pathways which often results in changes in gene expression via networks of transcription factors (TFs). Mediator is a highly conserved co-regulator complex and an essential component of the transcriptional machinery in eukaryotes. Some Mediator subunits have been implicated in stress-responsive signaling pathways; however, much remains unknown regarding the role of plant Mediator in abiotic stress responses. Here, we use RNA-seq to analyze the transcriptional response of Arabidopsis thaliana to heat, cold and salt stress conditions. We identify a set of common abiotic stress regulons and describe the sequential and combinatorial nature of TFs involved in their transcriptional regulation. Furthermore, we identify stress-specific roles for the Mediator subunits MED9, MED16, MED18 and CDK8, and putative TFs connecting them to different stress signaling pathways. Our data also indicate different modes of action for subunits or modules of Mediator at the same gene loci, including a co-repressor function for MED16 prior to stress. These results illuminate a poorly understood but important player in the transcriptional response of plants to abiotic stress and identify target genes and mechanisms as a prelude to further biochemical characterization.
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Affiliation(s)
- Tim Crawford
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, 901 87, Sweden
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Fazeelat Karamat
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, 901 87, Sweden
| | - Nóra Lehotai
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, 901 87, Sweden
| | - Matilda Rentoft
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, 901 87, Sweden
| | - Jeanette Blomberg
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, 901 87, Sweden
| | - Åsa Strand
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, 901 87, Sweden
| | - Stefan Björklund
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, 901 87, Sweden.
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Gallagher JE, Ser SL, Ayers MC, Nassif C, Pupo A. The Polymorphic PolyQ Tail Protein of the Mediator Complex, Med15, Regulates the Variable Response to Diverse Stresses. Int J Mol Sci 2020; 21:ijms21051894. [PMID: 32164312 PMCID: PMC7094212 DOI: 10.3390/ijms21051894] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 01/01/2023] Open
Abstract
The Mediator is composed of multiple subunits conserved from yeast to humans and plays a central role in transcription. The tail components are not required for basal transcription but are required for responses to different stresses. While some stresses are familiar, such as heat, desiccation, and starvation, others are exotic, yet yeast can elicit a successful stress response. 4-Methylcyclohexane methanol (MCHM) is a hydrotrope that induces growth arrest in yeast. We found that a naturally occurring variation in the Med15 allele, a component of the Mediator tail, altered the stress response to many chemicals in addition to MCHM. Med15 contains two polyglutamine repeats (polyQ) of variable lengths that change the gene expression of diverse pathways. The Med15 protein existed in multiple isoforms and its stability was dependent on Ydj1, a protein chaperone. The protein level of Med15 with longer polyQ tracts was lower and turned over faster than the allele with shorter polyQ repeats. MCHM sensitivity via variation of Med15 was regulated by Snf1 in a Myc-tag-dependent manner. Tagging Med15 with Myc altered its function in response to stress. Genetic variation in transcriptional regulators magnified genetic differences in response to environmental changes. These polymorphic control genes were master variators.
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