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Li T, Tang HC, Tsai KL. Unveiling the noncanonical activation mechanism of CDKs: insights from recent structural studies. Front Mol Biosci 2023; 10:1290631. [PMID: 38028546 PMCID: PMC10666765 DOI: 10.3389/fmolb.2023.1290631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
The Cyclin-dependent kinases (CDKs) play crucial roles in a range of essential cellular processes. While the classical two-step activation mechanism is generally applicable to cell cycle-related CDKs, both CDK7 and CDK8, involved in transcriptional regulation, adopt distinct mechanisms for kinase activation. In both cases, binding to their respective cyclin partners results in only partial activity, while their full activation requires the presence of an additional subunit. Recent structural studies of these two noncanonical kinases have provided unprecedented insights into their activation mechanisms, enabling us to understand how the third subunit coordinates the T-loop stabilization and enhances kinase activity. In this review, we summarize the structure and function of CDK7 and CDK8 within their respective functional complexes, while also describing their noncanonical activation mechanisms. These insights open new avenues for targeted drug discovery and potential therapeutic interventions in various diseases related to CDK7 and CDK8.
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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, United States
| | - Hui-Chi Tang
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Kuang-Lei Tsai
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
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2
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Pluta AJ, Studniarek C, Murphy S, Norbury CJ. Cyclin-dependent kinases: Masters of the eukaryotic universe. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1816. [PMID: 37718413 PMCID: PMC10909489 DOI: 10.1002/wrna.1816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/21/2023] [Accepted: 08/03/2023] [Indexed: 09/19/2023]
Abstract
A family of structurally related cyclin-dependent protein kinases (CDKs) drives many aspects of eukaryotic cell function. Much of the literature in this area has considered individual members of this family to act primarily either as regulators of the cell cycle, the context in which CDKs were first discovered, or as regulators of transcription. Until recently, CDK7 was the only clear example of a CDK that functions in both processes. However, new data points to several "cell-cycle" CDKs having important roles in transcription and some "transcriptional" CDKs having cell cycle-related targets. For example, novel functions in transcription have been demonstrated for the archetypal cell cycle regulator CDK1. The increasing evidence of the overlap between these two CDK types suggests that they might play a critical role in coordinating the two processes. Here we review the canonical functions of cell-cycle and transcriptional CDKs, and provide an update on how these kinases collaborate to perform important cellular functions. We also provide a brief overview of how dysregulation of CDKs contributes to carcinogenesis, and possible treatment avenues. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Processing > 3' End Processing RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
| | | | - Shona Murphy
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
| | - Chris J. Norbury
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
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3
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Zhai Z, Blanford JK, Cai Y, Sun J, Liu H, Shi H, Schwender J, Shanklin J. CYCLIN-DEPENDENT KINASE 8 positively regulates oil synthesis by activating WRINKLED1 transcription. THE NEW PHYTOLOGIST 2023; 238:724-736. [PMID: 36683527 DOI: 10.1111/nph.18764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/10/2023] [Indexed: 06/17/2023]
Abstract
CYCLIN-DEPENDENT KINASE 8 (CDK8), a component of the kinase module of the Mediator complex in Arabidopsis, is involved in many processes, including flowering, plant defense, drought, and energy stress responses. Here, we investigated cdk8 mutants and CDK8-overexpressing lines to evaluate whether CDK8 also plays a role in regulating lipid synthesis, an energy-demanding anabolism. Quantitative lipid analysis demonstrated significant reductions in lipid synthesis rates and lipid accumulation in developing siliques and seedlings of cdk8, and conversely, elevated lipid contents in wild-type seed overexpressing CDK8. Transactivation assays show that CDK8 is necessary for maximal transactivation of the master seed oil activator WRINKLED1 (WRI1) by the seed maturation transcription factor ABSCISIC ACID INSENSITIVE3, supporting a direct regulatory role of CDK8 in oil synthesis. Thermophoretic studies show GEMINIVIRUS REP INTERACTING KINASE1, an activating kinase of KIN10 (a catalytic subunit of SUCROSE NON-FERMENTING1-RELATED KINASE1), physically interacts with CDK8, resulting in its phosphorylation and degradation in the presence of KIN10. This work defines a mechanism whereby, once activated, KIN10 downregulates WRI1 expression and suppresses lipid synthesis via promoting the degradation of CDK8. The KIN10-CDK8-dependent regulation of lipid synthesis described herein is additional to our previously reported KIN10-dependent phosphorylation and degradation of WRI1.
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Affiliation(s)
- Zhiyang Zhai
- Department of Biology, Brookhaven National Laboratory, Building 463, 50 Bell Ave, Upton, NY, 11973, USA
| | - Jantana K Blanford
- Department of Biology, Brookhaven National Laboratory, Building 463, 50 Bell Ave, Upton, NY, 11973, USA
| | - Yingqi Cai
- Department of Biology, Brookhaven National Laboratory, Building 463, 50 Bell Ave, Upton, NY, 11973, USA
| | - Jing Sun
- Department of Biology, Brookhaven National Laboratory, Building 463, 50 Bell Ave, Upton, NY, 11973, USA
| | - Hui Liu
- Department of Biology, Brookhaven National Laboratory, Building 463, 50 Bell Ave, Upton, NY, 11973, USA
| | - Hai Shi
- Department of Biology, Brookhaven National Laboratory, Building 463, 50 Bell Ave, Upton, NY, 11973, USA
| | - Jorg Schwender
- Department of Biology, Brookhaven National Laboratory, Building 463, 50 Bell Ave, Upton, NY, 11973, USA
| | - John Shanklin
- Department of Biology, Brookhaven National Laboratory, Building 463, 50 Bell Ave, Upton, NY, 11973, USA
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4
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He H, Denecker J, Van Der Kelen K, Willems P, Pottie R, Phua SY, Hannah MA, Vertommen D, Van Breusegem F, Mhamdi A. The Arabidopsis mediator complex subunit 8 regulates oxidative stress responses. THE PLANT CELL 2021; 33:2032-2057. [PMID: 33713138 PMCID: PMC8290281 DOI: 10.1093/plcell/koab079] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/10/2021] [Indexed: 05/13/2023]
Abstract
Signaling events triggered by hydrogen peroxide (H2O2) regulate plant growth and defense by orchestrating a genome-wide transcriptional reprogramming. However, the specific mechanisms that govern H2O2-dependent gene expression are still poorly understood. Here, we identify the Arabidopsis Mediator complex subunit MED8 as a regulator of H2O2 responses. The introduction of the med8 mutation in a constitutive oxidative stress genetic background (catalase-deficient, cat2) was associated with enhanced activation of the salicylic acid pathway and accelerated cell death. Interestingly, med8 seedlings were more tolerant to oxidative stress generated by the herbicide methyl viologen (MV) and exhibited transcriptional hyperactivation of defense signaling, in particular salicylic acid- and jasmonic acid-related pathways. The med8-triggered tolerance to MV was manipulated by the introduction of secondary mutations in salicylic acid and jasmonic acid pathways. In addition, analysis of the Mediator interactome revealed interactions with components involved in mRNA processing and microRNA biogenesis, hence expanding the role of Mediator beyond transcription. Notably, MED8 interacted with the transcriptional regulator NEGATIVE ON TATA-LESS, NOT2, to control the expression of H2O2-inducible genes and stress responses. Our work establishes MED8 as a component regulating oxidative stress responses and demonstrates that it acts as a negative regulator of H2O2-driven activation of defense gene expression.
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Affiliation(s)
- Huaming He
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | - Jordi Denecker
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
- Present address: Illumina Cambridge Ltd, Cambridge, CB21 6DF, UK; Present address: Sciensano, 1050 Brussels, Belgium
| | - Katrien Van Der Kelen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
- Present address: Illumina Cambridge Ltd, Cambridge, CB21 6DF, UK; Present address: Sciensano, 1050 Brussels, Belgium
| | - Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | - Robin Pottie
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | - Su Yin Phua
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | - Matthew A Hannah
- BASF Belgium Coordination Center, Innovation Center Gent, 9052 Gent, Belgium
| | - Didier Vertommen
- de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | - Amna Mhamdi
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
- Author for correspondence: (A.M.)
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5
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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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6
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Osman S, Mohammad E, Lidschreiber M, Stuetzer A, Bazsó FL, Maier KC, Urlaub H, Cramer P. The Cdk8 kinase module regulates interaction of the mediator complex with RNA polymerase II. J Biol Chem 2021; 296:100734. [PMID: 33933450 PMCID: PMC8191332 DOI: 10.1016/j.jbc.2021.100734] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 11/17/2022] Open
Abstract
The Cdk8 kinase module (CKM) is a dissociable part of the coactivator complex mediator, which regulates gene transcription by RNA polymerase II. The CKM has both negative and positive functions in gene transcription that remain poorly understood at the mechanistic level. In order to reconstitute the role of the CKM in transcription initiation, we prepared recombinant CKM from the yeast Saccharomyces cerevisiae. We showed that CKM bound to the core mediator (cMed) complex, sterically inhibiting cMed from binding to the polymerase II preinitiation complex (PIC) in vitro. We further showed that the Cdk8 kinase activity of the CKM weakened CKM-cMed interaction, thereby facilitating dissociation of the CKM and enabling mediator to bind the PIC in order to stimulate transcription initiation. Finally, we report that the kinase activity of Cdk8 is required for gene activation during the stressful condition of heat shock in vivo but not under steady-state growth conditions. Based on these results, we propose a model in which the CKM negatively regulates mediator function at upstream-activating sequences by preventing mediator binding to the PIC at the gene promoter. However, during gene activation in response to stress, the Cdk8 kinase activity of the CKM may release mediator and allow its binding to the PIC, thereby accounting for the positive function of CKM. This may impart improved adaptability to stress by allowing a rapid transcriptional response to environmental changes, and we speculate that a similar mechanism in metazoans may allow the precise timing of developmental transcription programs.
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Affiliation(s)
- Sara Osman
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Eusra Mohammad
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Michael Lidschreiber
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Alexandra Stuetzer
- Bioanalytical Mass Spectrometry Group, Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Bioanalytics Research Group, Institute for Clinical Chemistry, University Medical Center, Göttingen, Germany
| | - Fanni Laura Bazsó
- Bioanalytical Mass Spectrometry Group, Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Bioanalytics Research Group, Institute for Clinical Chemistry, University Medical Center, Göttingen, Germany
| | - Kerstin C Maier
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Bioanalytics Research Group, Institute for Clinical Chemistry, University Medical Center, Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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7
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Stieg DC, Cooper KF, Strich R. The extent of cyclin C promoter occupancy directs changes in stress-dependent transcription. J Biol Chem 2020; 295:16280-16291. [PMID: 32934007 DOI: 10.1074/jbc.ra120.015215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/09/2020] [Indexed: 12/20/2022] Open
Abstract
The Cdk8 kinase module (CKM) is a detachable Mediator subunit composed of cyclin C and one each of paralogs Cdk8/Cdk19, Med12/Med12L, and Med13/Med13L. Our previous RNA-Seq studies demonstrated that cyclin C represses a subset of hydrogen peroxide-induced genes under normal conditions but is involved in activating other loci following stress. Here, we show that cyclin C directs this transcriptional reprograming through changes in its promoter occupancy. Following peroxide stress, cyclin C promoter occupancy increased for genes it activates while decreasing at loci it represses under normal conditions. Promoter occupancy of other CKM components generally mirrored cyclin C, indicating that the CKM moves as a single unit. It has previously been shown that some cyclin C leaves the nucleus following cytotoxic stress to induce mitochondrial fragmentation and apoptosis. We observed that CKM integrity appeared compromised at a subset of repressed promoters, suggesting a source of cyclin C that is targeted for nuclear release. Interestingly, mTOR inhibition induced a new pattern of cyclin C promoter occupancy indicating that this control is fine-tuned to the individual stress. Using inhibitors, we found that Cdk8 kinase activity is not required for CKM movement or repression but was necessary for full gene activation. In conclusion, this study revealed that different stress stimuli elicit specific changes in CKM promoter occupancy correlating to altered transcriptional outputs. Finally, although CKM components were recruited or expelled from promoters as a unit, heterogeneity was observed at individual promoters, suggesting a mechanism to generate gene- and stress-specific responses.
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Affiliation(s)
- David C Stieg
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, New Jersey, USA
| | - Katrina F Cooper
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, New Jersey, USA
| | - Randy Strich
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, New Jersey, USA.
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8
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Abstract
Natural or synthetic genetic modules can lose their function over long-term evolution if the function is costly. How populations can evolve to restore such broken function is poorly understood. To test the reversibility of evolutionary breakdown, we use yeast cell populations with a chromosomally integrated synthetic gene circuit. In previous evolution experiments the gene circuit lost its costly function through various mutations. By exposing such mutant populations to conditions where regaining gene circuit function would be beneficial, we find adaptation scenarios with or without repairing lost gene circuit function. These results are important for drug resistance or future synthetic biology applications where evolutionary loss and regain of function play a significant role. Evolutionary reversibility—the ability to regain a lost function—is an important problem both in evolutionary and synthetic biology, where repairing natural or synthetic systems broken by evolutionary processes may be valuable. Here, we use a synthetic positive-feedback (PF) gene circuit integrated into haploid Saccharomyces cerevisiae cells to test if the population can restore lost PF function. In previous evolution experiments, mutations in a gene eliminated the fitness costs of PF activation. Since PF activation also provides drug resistance, exposing such compromised or broken mutants to both drug and inducer should create selection pressure to regain drug resistance and possibly PF function. Indeed, evolving 7 PF mutant strains in the presence of drug revealed 3 adaptation scenarios through genomic, PF-external mutations that elevate PF basal expression, possibly by affecting transcription, translation, degradation, and other fundamental cellular processes. Nonfunctional mutants gained drug resistance without ever developing high expression, while quasifunctional and dysfunctional PF mutants developed high expression nongenetically, which then diminished, although more slowly for dysfunctional mutants where revertant clones arose. These results highlight how intracellular context, such as the growth rate, can affect regulatory network dynamics and evolutionary dynamics, which has important consequences for understanding the evolution of drug resistance and developing future synthetic biology applications.
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9
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Mao X, Weake VM, Chapple C. Mediator function in plant metabolism revealed by large-scale biology. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5995-6003. [PMID: 31504746 DOI: 10.1093/jxb/erz372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/07/2019] [Indexed: 05/16/2023]
Abstract
Mediator is a multisubunit transcriptional co-regulator that is involved in the regulation of an array of processes including plant metabolism. The pathways regulated by Mediator-dependent processes include those for the synthesis of phenylpropanoids (MED5), cellulose (MED16), lipids (MED15 and CDK8), and the regulation of iron homeostasis (MED16 and MED25). Traditional genetic and biochemical approaches laid the foundation for our understanding of Mediator function, but recent transcriptomic and metabolomic studies have provided deeper insights into how specific subunits cooperate in the regulation of plant metabolism. In this review, we highlight recent developments in the investigation of Mediator and plant metabolism, with particular emphasis on the large-scale biology studies of med mutants.
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Affiliation(s)
- Xiangying Mao
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Vikki M Weake
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - Clint Chapple
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, USA
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10
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Xue D, Guo N, Zhang XL, Zhao JM, Bu YP, Jiang DL, Wang XT, Wang HT, Guan RZ, Xing H. Genome-Wide Analysis Reveals the Role of Mediator Complex in the Soybean- Phytophthora sojae Interaction. Int J Mol Sci 2019; 20:E4570. [PMID: 31540158 PMCID: PMC6770253 DOI: 10.3390/ijms20184570] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/07/2019] [Accepted: 09/09/2019] [Indexed: 02/06/2023] Open
Abstract
The mediator complex is an essential link between transcription factors and RNA polymerase II, and mainly functions in the transduction of diverse signals to genes involved in different pathways. Limited information is available on the role of soybean mediator subunits in growth and development, and their participation in defense response regulation. Here, we performed genome-wide identification of the 95 soybean mediator subunits, which were unevenly localized on the 20 chromosomes and only segmental duplication events were detected. We focused on GmMED16-1, which is highly expressed in the roots, for further functional analysis. Transcription of GmMED16-1 was induced in response to Phytophthora sojae infection. Agrobacterium rhizogenes mediated soybean hairy root transformation was performed for the silencing of the GmMED16-1 gene. Silencing of GmMED16-1 led to an enhanced susceptibility phenotype and increased accumulation of P. sojae biomass in hairy roots of transformants. The transcript levels of NPR1, PR1a, and PR5 in the salicylic acid defense pathway in roots of GmMED16-1-silenced transformants were lower than those of empty-vector transformants. The results provide evidence that GmMED16-1 may participate in the soybean-P. sojae interaction via a salicylic acid-dependent process.
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Affiliation(s)
- Dong Xue
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Na Guo
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiao-Li Zhang
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jin-Ming Zhao
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yuan-Peng Bu
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Dian-Liang Jiang
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Xiao-Ting Wang
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Hai-Tang Wang
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Rong-Zhan Guan
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Han Xing
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
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11
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Mao X, Kim JI, Wheeler MT, Heintzelman AK, Weake VM, Chapple C. Mutation of Mediator subunit CDK8 counteracts the stunted growth and salicylic acid hyperaccumulation phenotypes of an Arabidopsis MED5 mutant. THE NEW PHYTOLOGIST 2019; 223:233-245. [PMID: 30756399 DOI: 10.1111/nph.15741] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 02/08/2019] [Indexed: 05/13/2023]
Abstract
The Mediator complex functions as a hub for transcriptional regulation. MED5, an Arabidopsis Mediator tail subunit, is required for maintaining phenylpropanoid homeostasis. A semidominant mutation (ref4-3) that causes a single amino acid substitution in MED5b functions as a strong suppressor of the pathway, leading to decreased soluble phenylpropanoid accumulation, reduced lignin content and dwarfism. By contrast, loss of MED5 results in increased concentrations of phenylpropanoids. We used a reverse genetic approach to identify suppressors of ref4-3 and found that ref4-3 requires CDK8, a kinase module subunit of Mediator, to repress plant growth. The genetic interaction between MED5 and CDK8 was further characterized using mRNA-sequencing (RNA-seq) and metabolite analysis. Growth inhibition and suppression of phenylpropanoid metabolism can be genetically separated in ref4-3 by elimination of CDK8 kinase activity; however, the stunted growth of ref4-3 is not dependent on the phosphorylation event introduced by the G383S mutation. In addition, rather than perturbation of lignin biosynthesis, misregulation of DJC66, a gene encoding a DNAJ protein, is involved in the dwarfism of the med5 mutants. Together, our study reveals genetic interactions between Mediator tail and kinase module subunits and enhances our understanding of dwarfing in phenylpropanoid pathway mutants.
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Affiliation(s)
- Xiangying Mao
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Jeong Im Kim
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Mitchell T Wheeler
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Anne K Heintzelman
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
- Northwest Missouri State University, Maryville, MO, 64468, USA
| | - Vikki M Weake
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA
| | - Clint Chapple
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
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12
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Twenty years of Mediator complex structural studies. Biochem Soc Trans 2019; 47:399-410. [PMID: 30733343 PMCID: PMC6393861 DOI: 10.1042/bst20180608] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/14/2019] [Accepted: 01/16/2019] [Indexed: 11/18/2022]
Abstract
Mediator is a large multiprotein complex conserved in all eukaryotes that plays an essential role in transcriptional regulation. Mediator comprises 25 subunits in yeast and 30 subunits in humans that form three main modules and a separable four-subunit kinase module. For nearly 20 years, because of its size and complexity, Mediator has posed a formidable challenge to structural biologists. The first two-dimensional electron microscopy (EM) projection map of Mediator leading to the canonical view of its division in three topological modules named Head, Middle and Tail, was published in 1999. Within the last few years, optimization of Mediator purification combined with technical and methodological advances in cryo-electron microscopy (cryo-EM) have revealed unprecedented details of Mediator subunit organization, interactions with RNA polymerase II and parts of its core structure at high resolution. To celebrate the twentieth anniversary of the first Mediator EM reconstruction, we look back on the structural studies of Mediator complex from a historical perspective and discuss them in the light of our current understanding of its role in transcriptional regulation.
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Wang X, Mittal P, Castro CA, Rajkovic G, Rajkovic A. Med12 regulates ovarian steroidogenesis, uterine development and maternal effects in the mammalian egg. Biol Reprod 2019; 97:822-834. [PMID: 29126187 DOI: 10.1093/biolre/iox143] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 11/07/2017] [Indexed: 12/21/2022] Open
Abstract
The transcriptional factor MED12 is part of the essential mediator transcriptional complex that acts as a transcriptional coactivator in all eukaryotes. Missense gain-of-function mutations in human MED12 are associated with uterine leiomyomas, yet the role of MED12 deficiency in tumorigenesis and reproductive biology has not been fully explored. We generated a Med12 reproductive conditional knockout mouse model to evaluate its role in uterine mesenchyme, granulosa cells, and oocytes. Mice heterozygous for Med12 deficiency in granulosa cells and uterus (Med12fl/+ Amhr2-Cre) were subfertile, while mice homozygous for Med12 deficiency in granulosa cells and uterus (Med12fl/fl Amhr2-Cre) were infertile. Morphological and histological analysis of the Med12fl/fl Amhr2-Cre reproductive tract revealed atrophic uteri and hyperchromatic granulosa cells with disrupted expression of Lhcgr, Esr1, and Esr2. Med12fl/fl Amhr2-Cre mice estrous cycle was disrupted, and serum analysis showed blunted rise in estradiol in response to pregnant mare serum gonadotropin. Uterine atrophy was partially rescued by exogenous steroid supplementation with dysregulation of Notch1 and Smo expression in steroid supplemented Med12fl/fl Amhr2-Cre uteri, indicating intrinsic uterine defects. Oocyte-specific ablation of Med12 caused infertility without disrupting normal folliculogenesis and ovulation, consistent with maternal effects of Med12 in early embryo development. These results show the critical importance of Med12 in reproductive tract development and that Med12 loss of function does not cause tumorigenesis in reproductive tissues.
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Affiliation(s)
- Xinye Wang
- Tsinghua MD Program, Tsinghua University School of Medicine, Beijing, China.,Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Womens Research Institute, Pittsburgh, Pennsylvania, USA
| | - Priya Mittal
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Carlos A Castro
- Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Womens Research Institute, Pittsburgh, Pennsylvania, USA
| | - Gabriel Rajkovic
- Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Womens Research Institute, Pittsburgh, Pennsylvania, USA
| | - Aleksandar Rajkovic
- Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Womens Research Institute, Pittsburgh, Pennsylvania, USA.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Greber BJ, Nogales E. The Structures of Eukaryotic Transcription Pre-initiation Complexes and Their Functional Implications. Subcell Biochem 2019; 93:143-192. [PMID: 31939151 DOI: 10.1007/978-3-030-28151-9_5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transcription is a highly regulated process that supplies living cells with coding and non-coding RNA molecules. Failure to properly regulate transcription is associated with human pathologies, including cancers. RNA polymerase II is the enzyme complex that synthesizes messenger RNAs that are then translated into proteins. In spite of its complexity, RNA polymerase requires a plethora of general transcription factors to be recruited to the transcription start site as part of a large transcription pre-initiation complex, and to help it gain access to the transcribed strand of the DNA. This chapter reviews the structure and function of these eukaryotic transcription pre-initiation complexes, with a particular emphasis on two of its constituents, the multisubunit complexes TFIID and TFIIH. We also compare the overall architecture of the RNA polymerase II pre-initiation complex with those of RNA polymerases I and III, involved in transcription of ribosomal RNA and non-coding RNAs such as tRNAs and snRNAs, and discuss the general, conserved features that are applicable to all eukaryotic RNA polymerase systems.
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Affiliation(s)
- Basil J Greber
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA.
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Eva Nogales
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
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Mediator, known as a coactivator, can act in transcription initiation in an activator-independent manner in vivo. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:687-696. [DOI: 10.1016/j.bbagrm.2018.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/28/2018] [Accepted: 07/04/2018] [Indexed: 01/20/2023]
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16
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CDK8 regulates the angiogenesis of pancreatic cancer cells in part via the CDK8-β-catenin-KLF2 signal axis. Exp Cell Res 2018; 369:304-315. [PMID: 29856990 DOI: 10.1016/j.yexcr.2018.05.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 05/18/2018] [Accepted: 05/28/2018] [Indexed: 11/20/2022]
Abstract
BACKGROUND CDK8 is associated with the transcriptional Mediator complex and has been shown to regulate several transcription factors implicated in cancer. As a pancreatic cancer oncogene, the role of CDK8 in cancer angiogenesis remains unclear. Here, we investigated the contribution of CDK8 in pancreatic cancer angiogenesis and examined the underlying molecular mechanisms. METHODS CDK8 expression was evaluated via immunohistochemistry, western blotting, and qRT-PCR in relation to the clinicopathological characteristics of pancreatic cancer patients. The effects of silencing or overexpressing CDK8 on cancer angiogenesis were assessed in vitro by western blotting assays in pancreatic cancer cell lines and in vivo with nude mice xenograft models. RESULTS Compared with adjacent normal tissues, pancreatic cancer tissues showed upregulation of CDK8 expression, which was inversely correlated with T grade, liver metastasis, size, lymph node metastasis and poor survival. CDK8 overexpression promoted angiogenesis in pancreatic cancer via activation of the CDK8-β-catenin-KLF2 signaling axis, as demonstrated by the upregulation and downregulation of signals representing the rate-limiting steps in angiogenesis. Silencing CDK8 inhibited angiogenesis in pancreatic cancer in vitro. Additionally, these results were confirmed in nude mice xenograft models in vivo. CONCLUSIONS CDK8 promotes angiogenesis in pancreatic cancer via activation of the CDK8-β-catenin-KLF2 signaling axis, thus providing valid targets for the treatment of pancreatic cancer.
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Li X, Pei Y, Sun Y, Liu N, Wang P, Liu D, Ge X, Li F, Hou Y. A Cotton Cyclin-Dependent Kinase E Confers Resistance to Verticillium dahliae Mediated by Jasmonate-Responsive Pathway. FRONTIERS IN PLANT SCIENCE 2018; 9:642. [PMID: 29881391 PMCID: PMC5976743 DOI: 10.3389/fpls.2018.00642] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 04/26/2018] [Indexed: 05/20/2023]
Abstract
Many subunits of the Mediator transcriptional co-activator complex are multifunctional proteins that regulate plant immunity in Arabidopsis. Cotton cyclin-dependent kinase E (GhCDKE), which is a subunit of the cotton (Gossypium hirsutum) Mediator complex, has been annotated, but the biological functions of this gene associated with regulating disease resistance have not been characterized. Here, we cloned GhCDKE from cotton and confirmed that GhCDKE belonged to the E-type CDK family in the phylogenetic tree, and, as in other eukaryotes, we found that GhCDKE interacted with C-type cyclin (GhCycC) by yeast two-hybrid and luciferase complementation imaging assays. Expression of GhCDKE in cotton was induced by Verticillium dahliae infection and MeJA treatment, and silencing of GhCDKE expression in cotton led to enhanced susceptibility to V. dahliae, while overexpression of GhCDKE in Arabidopsis thaliana enhanced resistance to this pathogen. Transgenic expression assay demonstrated that the transcriptional activity of GhPDF1.2pro:LUC in GhCDKE-silenced cotton was dramatically inhibited. In addition, the expression of jasmonic acid (JA)-regulated pathogen-responsive genes was dramatically upregulated in GhCDKE-overexpressed plants after inoculation with V. dahliae, and the roots of GhCDKE-overexpressed A. thaliana were more susceptible to JA treatment. These results indicated that GhCDKE regulates resistance against V. dahliae and that this resistance is mediated by JA response pathway.
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Affiliation(s)
- Xiancai Li
- College of Science, China Agricultural University, Beijing, China
| | - Yakun Pei
- College of Science, China Agricultural University, Beijing, China
| | - Yun Sun
- College of Science, China Agricultural University, Beijing, China
| | - Nana Liu
- College of Science, China Agricultural University, Beijing, China
| | - Ping Wang
- College of Science, China Agricultural University, Beijing, China
| | - Di Liu
- College of Science, China Agricultural University, Beijing, China
| | - Xiaoyang Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- *Correspondence: Fuguang Li, Yuxia Hou,
| | - Yuxia Hou
- College of Science, China Agricultural University, Beijing, China
- *Correspondence: Fuguang Li, Yuxia Hou,
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Malik N, Agarwal P, Tyagi A. Emerging functions of multi-protein complex Mediator with special emphasis on plants. Crit Rev Biochem Mol Biol 2017; 52:475-502. [DOI: 10.1080/10409238.2017.1325830] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Naveen Malik
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Pinky Agarwal
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Akhilesh Tyagi
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
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Banyai G, Szilagyi Z, Baraznenok V, Khorosjutina O, Gustafsson CM. Cyclin C influences the timing of mitosis in fission yeast. Mol Biol Cell 2017; 28:1738-1744. [PMID: 28515143 PMCID: PMC5491182 DOI: 10.1091/mbc.e16-11-0787] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 05/04/2017] [Accepted: 05/09/2017] [Indexed: 12/25/2022] Open
Abstract
A number of genes are periodically transcribed during cell cycle progression. How the periodic transcription patterns of these genes are achieved is not completely understood. Cyclin C, a component of Mediator, plays an essential role in periodic transcription and the timing of cell cycle progression. The multiprotein Mediator complex is required for the regulated transcription of nearly all RNA polymerase II–dependent genes. Mediator contains the Cdk8 regulatory subcomplex, which directs periodic transcription and influences cell cycle progression in fission yeast. Here we investigate the role of CycC, the cognate cyclin partner of Cdk8, in cell cycle control. Previous reports suggested that CycC interacts with other cellular Cdks, but a fusion of CycC to Cdk8 reported here did not cause any obvious cell cycle phenotypes. We find that Cdk8 and CycC interactions are stabilized within the Mediator complex and the activity of Cdk8-CycC is regulated by other Mediator components. Analysis of a mutant yeast strain reveals that CycC, together with Cdk8, primarily affects M-phase progression but mutations that release Cdk8 from CycC control also affect timing of entry into S phase.
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Affiliation(s)
- Gabor Banyai
- Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Zsolt Szilagyi
- Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | | | - Olga Khorosjutina
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Claes M Gustafsson
- Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
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Mittal P, Wang X, Rajkovic A. The Role of Mediator Complex Subunit 12 in Leiomyoma Biology. CURRENT GENETIC MEDICINE REPORTS 2016. [DOI: 10.1007/s40142-016-0106-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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De novo mutations in genes of mediator complex causing syndromic intellectual disability: mediatorpathy or transcriptomopathy? Pediatr Res 2016; 80:809-815. [PMID: 27500536 DOI: 10.1038/pr.2016.162] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 06/13/2016] [Indexed: 12/24/2022]
Abstract
BACKGROUND Mutations in the X-linked gene MED12 cause at least three different, but closely related, entities of syndromic intellectual disability. Recently, a new syndrome caused by MED13L deleterious variants has been described, which shows similar clinical manifestations including intellectual disability, hypotonia, and other congenital anomalies. METHODS Genotyping of 1,256 genes related with neurodevelopment was performed by next-generation sequencing in three unrelated patients and their healthy parents. Clinically relevant findings were confirmed by conventional sequencing. RESULTS Each patient showed one de novo variant not previously reported in the literature or databases. Two different missense variants were found in the MED12 or MED13L genes and one nonsense mutation was found in the MED13L gene. CONCLUSION The phenotypic consequences of these mutations are closely related and/or have been previously reported in one or other gene. Additionally, MED12 and MED13L code for two closely related partners of the mediator kinase module. Consequently, we propose the concept of a common MED12/MED13L clinical spectrum, encompassing Opitz-Kaveggia syndrome, Lujan-Fryns syndrome, Ohdo syndrome, MED13L haploinsufficiency syndrome, and others.
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22
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Cao S, Zhang S, Hao C, Liu H, Xu JR, Jin Q. FgSsn3 kinase, a component of the mediator complex, is important for sexual reproduction and pathogenesis in Fusarium graminearum. Sci Rep 2016; 6:22333. [PMID: 26931632 PMCID: PMC4773989 DOI: 10.1038/srep22333] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 02/08/2016] [Indexed: 01/05/2023] Open
Abstract
Fusarium graminearum is an important pathogen of wheat and barley. In addition to severe yield losses, infested grains are often contaminated with harmful mycotoxins. In this study, we characterized the functions of FgSSN3 kinase gene in different developmental and infection processes and gene regulation in F. graminearum. The FgSSN3 deletion mutant had a nutrient-dependent growth defects and abnormal conidium morphology. It was significantly reduced in DON production, TRI gene expression, and virulence. Deletion of FgSSN3 also resulted in up-regulation of HTF1 and PCS1 expression in juvenile cultures, and repression of TRI genes in DON-producing cultures. In addition, Fgssn3 was female sterile and defective in hypopodium formation and infectious growth. RNA-seq analysis showed that FgSsn3 is involved in the transcriptional regulation of a wide variety genes acting as either a repressor or activator. FgSsn3 physically interacted with C-type cyclin Cid1 and the cid1 mutant had similar phenotypes with Fgssn3, indicating that FgSsn3 and Cid1 form the CDK-cyclin pair as a component of the mediator complex in F. graminearum. Taken together, our results indicate that FgSSN3 is important for secondary metabolism, sexual reproduction, and plant infection, as a subunit of mediator complex contributing to transcriptional regulation of diverse genes.
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Affiliation(s)
- Shulin Cao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Shijie Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Chaofeng Hao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Jin-Rong Xu
- Dept. of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA
| | - Qiaojun Jin
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
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Schneider M, Hellerschmied D, Schubert T, Amlacher S, Vinayachandran V, Reja R, Pugh BF, Clausen T, Köhler A. The Nuclear Pore-Associated TREX-2 Complex Employs Mediator to Regulate Gene Expression. Cell 2015; 162:1016-28. [PMID: 26317468 PMCID: PMC4644235 DOI: 10.1016/j.cell.2015.07.059] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 05/05/2015] [Accepted: 07/06/2015] [Indexed: 11/27/2022]
Abstract
Nuclear pore complexes (NPCs) influence gene expression besides their established function in nuclear transport. The TREX-2 complex localizes to the NPC basket and affects gene-NPC interactions, transcription, and mRNA export. How TREX-2 regulates the gene expression machinery is unknown. Here, we show that TREX-2 interacts with the Mediator complex, an essential regulator of RNA Polymerase (Pol) II. Structural and biochemical studies identify a conserved region on TREX-2, which directly binds the Mediator Med31/Med7N submodule. TREX-2 regulates assembly of Mediator with the Cdk8 kinase and is required for recruitment and site-specific phosphorylation of Pol II. Transcriptome and phenotypic profiling confirm that TREX-2 and Med31 are functionally interdependent at specific genes. TREX-2 additionally uses its Mediator-interacting surface to regulate mRNA export suggesting a mechanism for coupling transcription initiation and early steps of mRNA processing. Our data provide mechanistic insight into how an NPC-associated adaptor complex accesses the core transcription machinery. The nuclear pore-associated TREX-2 complex directly interacts with Mediator TREX-2 regulates Mediator association with Cdk8 and RNA Pol II Ser5 phosphorylation TREX-2 and the Med31 submodule co-regulate specific inducible and constitutive genes A similar TREX-2 surface promotes both transcription and mRNA export
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Affiliation(s)
- Maren Schneider
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9/3, 1030 Vienna, Austria
| | - Doris Hellerschmied
- Research Institute of Molecular Pathology, Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Tobias Schubert
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9/3, 1030 Vienna, Austria
| | - Stefan Amlacher
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9/3, 1030 Vienna, Austria
| | - Vinesh Vinayachandran
- Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA 16802, USA
| | - Rohit Reja
- Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA 16802, USA
| | - B Franklin Pugh
- Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA 16802, USA
| | - Tim Clausen
- Research Institute of Molecular Pathology, Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Alwin Köhler
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9/3, 1030 Vienna, Austria.
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Gutin J, Sadeh A, Rahat A, Aharoni A, Friedman N. Condition-specific genetic interaction maps reveal crosstalk between the cAMP/PKA and the HOG MAPK pathways in the activation of the general stress response. Mol Syst Biol 2015; 11:829. [PMID: 26446933 PMCID: PMC4631200 DOI: 10.15252/msb.20156451] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Cells must quickly respond and efficiently adapt to environmental changes. The yeast Saccharomyces cerevisiae has multiple pathways that respond to specific environmental insults, as well as a generic stress response program. The later is regulated by two transcription factors, Msn2 and Msn4, that integrate information from upstream pathways to produce fast, tunable, and robust response to different environmental changes. To understand this integration, we employed a systematic approach to genetically dissect the contribution of various cellular pathways to Msn2/4 regulation under a range of stress and growth conditions. We established a high-throughput liquid handling and automated flow cytometry system and measured GFP levels in 68 single-knockout and 1,566 double-knockout strains that carry an HSP12-GFP allele as a reporter for Msn2/4 activity. Based on the expression of this Msn2/4 reporter in five different conditions, we identified numerous genetic and epistatic interactions between different components in the network upstream to Msn2/4. Our analysis gains new insights into the functional specialization of the RAS paralogs in the repression of stress response and identifies a three-way crosstalk between the Mediator complex, the HOG MAPK pathway, and the cAMP/PKA pathway.
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Affiliation(s)
- Jenia Gutin
- School of Computer Science & Engineering Institute of Life Sciences Hebrew University, Jerusalem, Israel
| | - Amit Sadeh
- School of Computer Science & Engineering Institute of Life Sciences Hebrew University, Jerusalem, Israel
| | - Ayelet Rahat
- School of Computer Science & Engineering Institute of Life Sciences Hebrew University, Jerusalem, Israel
| | - Amir Aharoni
- Department of Life Science, National Institute for Biotechnology in the Negev Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Nir Friedman
- School of Computer Science & Engineering Institute of Life Sciences Hebrew University, Jerusalem, Israel
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Mühlbacher W, Mayer A, Sun M, Remmert M, Cheung ACM, Niesser J, Soeding J, Cramer P. Structure of Ctk3, a subunit of the RNA polymerase II CTD kinase complex, reveals a noncanonical CTD-interacting domain fold. Proteins 2015. [PMID: 26219431 DOI: 10.1002/prot.24869] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
CTDK-I is a yeast kinase complex that phosphorylates the C-terminal repeat domain (CTD) of RNA polymerase II (Pol II) to promote transcription elongation. CTDK-I contains the cyclin-dependent kinase Ctk1 (homologous to human CDK9/CDK12), the cyclin Ctk2 (human cyclin K), and the yeast-specific subunit Ctk3, which is required for CTDK-I stability and activity. Here we predict that Ctk3 consists of a N-terminal CTD-interacting domain (CID) and a C-terminal three-helix bundle domain. We determine the X-ray crystal structure of the N-terminal domain of the Ctk3 homologue Lsg1 from the fission yeast Schizosaccharomyces pombe at 2.0 Å resolution. The structure reveals eight helices arranged into a right-handed superhelical fold that resembles the CID domain present in transcription termination factors Pcf11, Nrd1, and Rtt103. Ctk3 however shows different surface properties and no binding to CTD peptides. Together with the known structure of Ctk1 and Ctk2 homologues, our results lead to a molecular framework for analyzing the structure and function of the CTDK-I complex.
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Affiliation(s)
- Wolfgang Mühlbacher
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, Göttingen, 37077, Germany
| | - Andreas Mayer
- Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, Munich, 81377, Germany
| | - Mai Sun
- Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, Munich, 81377, Germany
| | - Michael Remmert
- Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, Munich, 81377, Germany
| | - Alan C M Cheung
- Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, Munich, 81377, Germany
| | - Jürgen Niesser
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, Göttingen, 37077, Germany
| | - Johannes Soeding
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, Göttingen, 37077, Germany
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, Göttingen, 37077, Germany
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Clark AD, Oldenbroek M, Boyer TG. Mediator kinase module and human tumorigenesis. Crit Rev Biochem Mol Biol 2015; 50:393-426. [PMID: 26182352 DOI: 10.3109/10409238.2015.1064854] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mediator is a conserved multi-subunit signal processor through which regulatory informatiosn conveyed by gene-specific transcription factors is transduced to RNA Polymerase II (Pol II). In humans, MED13, MED12, CDK8 and Cyclin C (CycC) comprise a four-subunit "kinase" module that exists in variable association with a 26-subunit Mediator core. Genetic and biochemical studies have established the Mediator kinase module as a major ingress of developmental and oncogenic signaling through Mediator, and much of its function in signal-dependent gene regulation derives from its resident CDK8 kinase activity. For example, CDK8-targeted substrate phosphorylation impacts transcription factor half-life, Pol II activity and chromatin chemistry and functional status. Recent structural and biochemical studies have revealed a precise network of physical and functional subunit interactions required for proper kinase module activity. Accordingly, pathologic change in this activity through altered expression or mutation of constituent kinase module subunits can have profound consequences for altered signaling and tumor formation. Herein, we review the structural organization, biological function and oncogenic potential of the Mediator kinase module. We focus principally on tumor-associated alterations in kinase module subunits for which mechanistic relationships as opposed to strictly correlative associations are established. These considerations point to an emerging picture of the Mediator kinase module as an oncogenic unit, one in which pathogenic activation/deactivation through component change drives tumor formation through perturbation of signal-dependent gene regulation. It follows that therapeutic strategies to combat CDK8-driven tumors will involve targeted modulation of CDK8 activity or pharmacologic manipulation of dysregulated CDK8-dependent signaling pathways.
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Affiliation(s)
- Alison D Clark
- a Department of Molecular Medicine , Institute of Biotechnology, University of Texas Health Science Center at San Antonio , San Antonio , TX , USA
| | - Marieke Oldenbroek
- a Department of Molecular Medicine , Institute of Biotechnology, University of Texas Health Science Center at San Antonio , San Antonio , TX , USA
| | - Thomas G Boyer
- a Department of Molecular Medicine , Institute of Biotechnology, University of Texas Health Science Center at San Antonio , San Antonio , TX , USA
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Retroviral cyclin controls cyclin-dependent kinase 8-mediated transcription elongation and reinitiation. J Virol 2015; 89:5450-61. [PMID: 25741012 DOI: 10.1128/jvi.00464-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 02/24/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Walleye dermal sarcoma virus (WDSV) infection is associated with the seasonal development and regression of walleye dermal sarcoma. Previous work showed that the retroviral cyclin (RV-cyclin), encoded by WDSV, has separable cyclin box and transcription activation domains. It binds to cyclin-dependent kinase 8 (CDK8) and enhances its kinase activity. CDK8 is evolutionarily conserved and is frequently overexpressed in human cancers. It is normally activated by cyclin C and is required for transcription elongation of the serum response genes (immediate early genes [IEGs]) FOS, EGR1, and cJUN. The IEGs drive cell proliferation, and their expression is brief and highly regulated. Here we show that constitutive expression of RV-cyclin in the HCT116 colon cancer cell line significantly increases the level of IEG expression in response to serum stimulation. Quantitative reverse transcription-PCR (RT-PCR) and nuclear run-on assays provide evidence that RV-cyclin does not alter the initiation of IEG transcription but does enhance the overall rate of transcription elongation and maintains transcription reinitiation. RV-cyclin does not increase activating phosphorylation events in the mitogen-activated protein kinase pathway and does not inhibit decay of IEG mRNAs. At the EGR1 gene locus, RV-cyclin increases and maintains RNA polymerase II (Pol II) occupancy after serum stimulation, in conjunction with increased and extended EGR1 gene expression. The RV-cyclin increases CDK8 occupancy at the EGR1 gene locus before and after serum stimulation. Both of RV-cyclin's functional domains, i.e., the cyclin box and the activation domain, are necessary for the overall enhancement of IEG expression. RV-cyclin presents a novel and ancient mechanism of retrovirus-induced oncogenesis. IMPORTANCE The data reported here are important to both virology and cancer biology. The novel mechanism pinpoints CDK8 in the development of walleye dermal sarcoma and sheds light on CDK8's role in many human cancers. CDK8 controls expression from highly regulated genes, including the interferon-stimulated genes. Its function is likely the target of many viral interferon-resistance mechanisms. CDK8 also controls cellular responses to metabolic stimuli, stress, and hypoxia, in addition to the serum response. The retroviral cyclin (RV-cyclin) represents a highly selected probe of CDK8 function. RV-cyclin does not control CDK8 specificity but instead enhances CDK8's effects on regulated genes, an important distinction for its use to delineate natural CDK8 targets. The outcomes of this research are applicable to investigations of normal and abnormal CDK8 functions. The mechanisms defined here will contribute directly to the dermal sarcoma model in fish and clarify an important path for oncogenesis and innate resistance to viruses.
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Fine-tuning of histone H3 Lys4 methylation during pseudohyphal differentiation by the CDK submodule of RNA polymerase II. Genetics 2014; 199:435-53. [PMID: 25467068 DOI: 10.1534/genetics.114.172841] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Transcriptional regulation is dependent upon the interactions between the RNA pol II holoenzyme complex and chromatin. RNA pol II is part of a highly conserved multiprotein complex that includes the core mediator and CDK8 subcomplex. In Saccharomyces cerevisiae, the CDK8 subcomplex, composed of Ssn2p, Ssn3p, Ssn8p, and Srb8p, is thought to play important roles in mediating transcriptional control of stress-responsive genes. Also central to transcriptional control are histone post-translational modifications. Lysine methylation, dynamically balanced by lysine methyltransferases and demethylases, has been intensively studied, uncovering significant functions in transcriptional control. A key question remains in understanding how these enzymes are targeted during stress response. To determine the relationship between lysine methylation, the CDK8 complex, and transcriptional control, we performed phenotype analyses of yeast lacking known lysine methyltransferases or demethylases in isolation or in tandem with SSN8 deletions. We show that the RNA pol II CDK8 submodule components SSN8/SSN3 and the histone demethylase JHD2 are required to inhibit pseudohyphal growth-a differentiation pathway induced during nutrient limitation-under rich conditions. Yeast lacking both SSN8 and JHD2 constitutively express FLO11, a major regulator of pseudohyphal growth. Interestingly, deleting known FLO11 activators including FLO8, MSS11, MFG1, TEC1, SNF1, KSS1, and GCN4 results in a range of phenotypic suppression. Using chromatin immunoprecipitation, we found that SSN8 inhibits H3 Lys4 trimethylation independently of JHD2 at the FLO11 locus, suggesting that H3 Lys4 hypermethylation is locking FLO11 into a transcriptionally active state. These studies implicate the CDK8 subcomplex in fine-tuning H3 Lys4 methylation levels during pseudohyphal differentiation.
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Lindsay AK, Morales DK, Liu Z, Grahl N, Zhang A, Willger SD, Myers LC, Hogan DA. Analysis of Candida albicans mutants defective in the Cdk8 module of mediator reveal links between metabolism and biofilm formation. PLoS Genet 2014; 10:e1004567. [PMID: 25275466 PMCID: PMC4183431 DOI: 10.1371/journal.pgen.1004567] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 06/30/2014] [Indexed: 12/29/2022] Open
Abstract
Candida albicans biofilm formation is a key virulence trait that involves hyphal growth and adhesin expression. Pyocyanin (PYO), a phenazine secreted by Pseudomonas aeruginosa, inhibits both C. albicans biofilm formation and development of wrinkled colonies. Using a genetic screen, we identified two mutants, ssn3Δ/Δ and ssn8Δ/Δ, which continued to wrinkle in the presence of PYO. Ssn8 is a cyclin-like protein and Ssn3 is similar to cyclin-dependent kinases; both proteins are part of the heterotetrameric Cdk8 module that forms a complex with the transcriptional co-regulator, Mediator. Ssn3 kinase activity was also required for PYO sensitivity as a kinase dead mutant maintained a wrinkled colony morphology in the presence of PYO. Furthermore, similar phenotypes were observed in mutants lacking the other two components of the Cdk8 module-Srb8 and Srb9. Through metabolomics analyses and biochemical assays, we showed that a compromised Cdk8 module led to increases in glucose consumption, glycolysis-related transcripts, oxidative metabolism and ATP levels even in the presence of PYO. In the mutant, inhibition of respiration to levels comparable to the PYO-treated wild type inhibited wrinkled colony development. Several lines of evidence suggest that PYO does not act through Cdk8. Lastly, the ssn3 mutant was a hyperbiofilm former, and maintained higher biofilm formation in the presence of PYO than the wild type. Together these data provide novel insights into the role of the Cdk8 module of Mediator in regulation of C. albicans physiology and the links between respiratory activity and both wrinkled colony and biofilm development.
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Affiliation(s)
- Allia K. Lindsay
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Diana K. Morales
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Zhongle Liu
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Nora Grahl
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Anda Zhang
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Sven D. Willger
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Lawrence C. Myers
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Deborah A. Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- * E-mail:
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Zhu Y, Schluttenhoffer CM, Wang P, Fu F, Thimmapuram J, Zhu JK, Lee SY, Yun DJ, Mengiste T. CYCLIN-DEPENDENT KINASE8 differentially regulates plant immunity to fungal pathogens through kinase-dependent and -independent functions in Arabidopsis. THE PLANT CELL 2014; 26:4149-70. [PMID: 25281690 PMCID: PMC4247566 DOI: 10.1105/tpc.114.128611] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 08/28/2014] [Accepted: 09/17/2014] [Indexed: 05/18/2023]
Abstract
CYCLIN-DEPENDENT KINASE8 (CDK8) is a widely studied component of eukaryotic Mediator complexes. However, the biological and molecular functions of plant CDK8 are not well understood. Here, we provide evidence for regulatory functions of Arabidopsis thaliana CDK8 in defense and demonstrate its functional and molecular interactions with other Mediator and non-Mediator subunits. The cdk8 mutant exhibits enhanced resistance to Botrytis cinerea but susceptibility to Alternaria brassicicola. The contributions of CDK8 to the transcriptional activation of defensin gene PDF1.2 and its interaction with MEDIATOR COMPLEX SUBUNIT25 (MED25) implicate CDK8 in jasmonate-mediated defense. Moreover, CDK8 associates with the promoter of AGMATINE COUMAROYLTRANSFERASE to promote its transcription and regulate the biosynthesis of the defense-active secondary metabolites hydroxycinnamic acid amides. CDK8 also interacts with the transcription factor WAX INDUCER1, implying its additional role in cuticle development. In addition, overlapping functions of CDK8 with MED12 and MED13 and interactions between CDK8 and C-type cyclins suggest the conserved configuration of the plant Mediator kinase module. In summary, while CDK8's positive transcriptional regulation of target genes and its phosphorylation activities underpin its defense functions, the impaired defense responses in the mutant are masked by its altered cuticle, resulting in specific resistance to B. cinerea.
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Affiliation(s)
- Yingfang Zhu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | | | - Pengcheng Wang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
| | - Fuyou Fu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | | | - Jian-Kang Zhu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
| | - Sang Yeol Lee
- Division of Applied Life Sciences (BK21 Plus Program), Gyeongsang National University, Jinju City 660-701, Korea
| | - Dae-Jin Yun
- Division of Applied Life Sciences (BK21 Plus Program), Gyeongsang National University, Jinju City 660-701, Korea
| | - Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
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Strich R, Cooper KF. The dual role of cyclin C connects stress regulated gene expression to mitochondrial dynamics. MICROBIAL CELL 2014; 1:318-324. [PMID: 28357211 PMCID: PMC5349174 DOI: 10.15698/mic2014.10.169] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Following exposure to cytotoxic agents, cellular damage is first recognized by a
variety of sensor mechanisms. Thenceforth, the damage signal is transduced to
the nucleus to install the correct gene expression program including the
induction of genes whose products either detoxify destructive compounds or
repair the damage they cause. Next, the stress signal is disseminated throughout
the cell to effect the appropriate changes at organelles including the
mitochondria. The mitochondria represent an important signaling platform for the
stress response. An initial stress response of the mitochondria is extensive
fragmentation. If the damage is prodigious, the mitochondria fragment (fission)
and lose their outer membrane integrity leading to the release of pro-apoptotic
factors necessary for programmed cell death (PCD) execution. As this complex
biological process contains many moving parts, it must be exquisitely
coordinated as the ultimate decision is life or death. The conserved C-type
cyclin plays an important role in executing this molecular Rubicon by coupling
changes in gene expression to mitochondrial fission and PCD. Cyclin C, along
with its cyclin dependent kinase partner Cdk8, associates with the RNA
polymerase holoenzyme to regulate transcription. In particular, cyclin C-Cdk8
repress many stress responsive genes. To relieve this repression, cyclin C is
destroyed in cells exposed to pro-oxidants and other stressors. However, prior
to its destruction, cyclin C, but not Cdk8, is released from its nuclear anchor
(Med13), translocates from the nucleus to the cytoplasm where it interacts with
the fission machinery and is both necessary and sufficient to induce extensive
mitochondria fragmentation. Furthermore, cytoplasmic cyclin C promotes PCD
indicating that it mediates both mitochondrial fission and cell death pathways.
This review will summarize the role cyclin C plays in regulating
stress-responsive transcription. In addition, we will detail this new function
mediating mitochondrial fission and PCD. Although both these roles of cyclin C
are conserved, this review will concentrate on cyclin C's dual role in the
budding yeast Saccharomyces cerevisiae.
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Affiliation(s)
- Randy Strich
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford NJ, USA
| | - Katrina F Cooper
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford NJ, USA
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Genomics of uterine leiomyomas: insights from high-throughput sequencing. Fertil Steril 2014; 102:621-9. [PMID: 25106763 DOI: 10.1016/j.fertnstert.2014.06.050] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 06/27/2014] [Accepted: 06/27/2014] [Indexed: 02/07/2023]
Abstract
Uterine leiomyomas are benign smooth-muscle tumors of extremely low malignant potential. Early work utilizing classical cytogenetics revealed that a subset of uterine leiomyomas harbor recurrent chromosomal rearrangements, such as translocations affecting the HMGA2 gene. Our understanding of the genetics of many tumor types has deepened remarkably with the emergence of next-generation sequencing technologies. Exome sequencing identified that the majority of leiomyomas display highly specific MED12 mutations. Further studies suggest that these MED12 hotspot mutations are also frequent in breast fibroadenomas, but not in other human tumors. Whole-genome sequencing showed that a subset of leiomyomas display complex chromosomal rearrangements resembling chromothripsis. These were formed in a single event of chromosomal breakage and random reassembly involving one or a limited number of chromosomes. Although most leiomyomas have been shown to arise independently, these studies also revealed that distinct nodules within a uterus may display identical genetic changes indicating a common clonal origin. A minority of leiomyomas were also found to display deletions within the COL4A5-COL4A6 genes, leading to upregulation of the adjacent gene IRS4. The findings derived from high-throughput sequencing combined with previous knowledge have led to an emerging molecular classification of leiomyomas, suggesting that there are several distinct pathogenic pathways involved in leiomyoma formation. The evidence points to at least 4 molecular subclasses: leiomyomas with MED12 mutation, FH inactivation, HMGA2 overexpression, and COL4A6-COL4A5 deletion. Elucidating the molecular pathogenesis of leiomyomas should be relevant for developing treatments for this very common disease.
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Khakhina S, Cooper KF, Strich R. Med13p prevents mitochondrial fission and programmed cell death in yeast through nuclear retention of cyclin C. Mol Biol Cell 2014; 25:2807-16. [PMID: 25057017 PMCID: PMC4161515 DOI: 10.1091/mbc.e14-05-0953] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In response to oxidative stress, cyclin C translocates from the nucleus to the cytoplasm, where it interacts with the mitochondrial fission machinery and induces extensive fragmentation of this organelle. Med13p is identified as the anchor protein that retains cyclin C in the nucleus. The yeast cyclin C-Cdk8 kinase forms a complex with Med13p to repress the transcription of genes involved in the stress response and meiosis. In response to oxidative stress, cyclin C displays nuclear to cytoplasmic relocalization that triggers mitochondrial fission and promotes programmed cell death. In this report, we demonstrate that Med13p mediates cyclin C nuclear retention in unstressed cells. Deleting MED13 allows aberrant cytoplasmic cyclin C localization and extensive mitochondrial fragmentation. Loss of Med13p function resulted in mitochondrial dysfunction and hypersensitivity to oxidative stress–induced programmed cell death that were dependent on cyclin C. The regulatory system controlling cyclin C-Med13p interaction is complex. First, a previous study found that cyclin C phosphorylation by the stress-activated MAP kinase Slt2p is required for nuclear to cytoplasmic translocation. This study found that cyclin C-Med13p association is impaired when the Slt2p target residue is substituted with a phosphomimetic amino acid. The second step involves Med13p destruction mediated by the 26S proteasome and cyclin C-Cdk8p kinase activity. In conclusion, Med13p maintains mitochondrial structure, function, and normal oxidative stress sensitivity through cyclin C nuclear retention. Releasing cyclin C from the nucleus involves both its phosphorylation by Slt2p coupled with Med13p destruction.
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Affiliation(s)
- Svetlana Khakhina
- Department of Molecular Biology, Rowan University-School of Osteopathic Medicine, Stratford, NJ 08084
| | - Katrina F Cooper
- Department of Molecular Biology, Rowan University-School of Osteopathic Medicine, Stratford, NJ 08084
| | - Randy Strich
- Department of Molecular Biology, Rowan University-School of Osteopathic Medicine, Stratford, NJ 08084
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Kämpjärvi K, Park MJ, Mehine M, Kim NH, Clark AD, Bützow R, Böhling T, Böhm J, Mecklin JP, Järvinen H, Tomlinson IPM, van der Spuy ZM, Sjöberg J, Boyer TG, Vahteristo P. Mutations in Exon 1 highlight the role of MED12 in uterine leiomyomas. Hum Mutat 2014; 35:1136-41. [PMID: 24980722 DOI: 10.1002/humu.22612] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 06/17/2014] [Indexed: 01/05/2023]
Abstract
Mediator regulates transcription by connecting gene-specific transcription factors to the RNA polymerase II initiation complex. We recently discovered by exome sequencing that specific exon 2 mutations in mediator complex subunit 12 (MED12) are extremely common in uterine leiomyomas. Subsequent screening studies have focused on this mutational hot spot, and mutations have been detected in uterine leiomyosarcomas, extrauterine leiomyomas and leiomyosarcomas, endometrial polyps, and colorectal cancers. All mutations have been missense changes or in-frame insertions/deletions. Here, we have analyzed 611 samples representing all above-mentioned tumor types for possible exon 1 mutations. Five mutations were observed, all of which were in-frame insertion/deletions in uterine leiomyomas. Transcriptome-wide expression data revealed that MED12 exon 1 and exon 2 mutations lead to the same unique global gene expression pattern with RAD51B being the most upregulated gene. Immunoprecipitation and kinase activity assays showed that both exon 1 and exon 2 mutations disrupt the interaction between MED12 and Cyclin C and CDK8/19 and abolish the mediator-associated CDK kinase activity. These results further emphasize the role of MED12 in uterine leiomyomas, show that exon 1 and exon 2 exert their tumorigenic effect in similar manner, and stress that exon 1 should be included in subsequent MED12 screenings.
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Affiliation(s)
- Kati Kämpjärvi
- Department of Medical Genetics, Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
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Mao F, Yang X, Fu L, Lv X, Zhang Z, Wu W, Yang S, Zhou Z, Zhang L, Zhao Y. The Kto-Skd complex can regulate ptc expression by interacting with Cubitus interruptus (Ci) in the Hedgehog signaling pathway. J Biol Chem 2014; 289:22333-41. [PMID: 24962581 DOI: 10.1074/jbc.m114.560995] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hedgehog (Hh) signaling pathway plays a very important role in metazoan development by controlling pattern formation. Drosophila imaginal discs are subdivided into anterior and posterior compartments that derive from adjacent cell populations. The anterior/posterior (A/P) boundaries, which are critical to maintaining the position of organizers, are established by a complex mechanism involving Hh signaling. Here, we uncover the regulation of ptc in the Hh signaling pathway by two subunits of mediator complex, Kto and Skd, which can also regulate boundary location. Collectively, we provide further evidence that Kto-Skd affects the A/P-axial development of the whole wing disc. Kto can interact with Cubitus interruptus (Ci), bind to the Ci-binding region on ptc promoter, which are both regulated by Hh signals to down-regulate ptc expression.
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Affiliation(s)
- Feifei Mao
- From the State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Xiaofeng Yang
- From the State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Lin Fu
- From the State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Xiangdong Lv
- From the State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Zhao Zhang
- From the State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Wenqing Wu
- From the State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Siqi Yang
- From the State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Zhaocai Zhou
- From the State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Lei Zhang
- From the State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Yun Zhao
- From the State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
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Mäkinen N, Heinonen HR, Sjöberg J, Taipale J, Vahteristo P, Aaltonen LA. Mutation analysis of components of the Mediator kinase module in MED12 mutation-negative uterine leiomyomas. Br J Cancer 2014; 110:2246-9. [PMID: 24642626 PMCID: PMC4007231 DOI: 10.1038/bjc.2014.138] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 02/14/2014] [Accepted: 02/21/2014] [Indexed: 02/06/2023] Open
Abstract
Background: Kinase module of Mediator complex (‘CDK8 submodule') consists of four subunits: CDK8, Cyclin C, MED12, and MED13. Recently, we reported recurrent MED12 mutations in 70% of uterine leiomyomas. The aim of this study was to analyse whether mutations in other components of the module contribute to the development of these lesions. Methods: Mutation screening of altogether 70 MED12 mutation-negative uterine leiomyomas was carried out by direct sequencing. Results: None of the tumours displayed somatic mutations in the coding regions of CDK8/CDK19, CCNC, or MED13. Conclusions: Mutations in CDK8/CDK19, CCNC, and MED13 do not frequently contribute to genesis of uterine leiomyomas.
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Affiliation(s)
- N Mäkinen
- Department of Medical Genetics, Genome-Scale Biology Research Program, University of Helsinki, PO Box 63, 00014 Helsinki, Finland
| | - H-R Heinonen
- Department of Medical Genetics, Genome-Scale Biology Research Program, University of Helsinki, PO Box 63, 00014 Helsinki, Finland
| | - J Sjöberg
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, PO Box 140, 00029 Helsinki, Finland
| | - J Taipale
- 1] Genome-Scale Biology Research Program and Department of Pathology, Haartman Institute, University of Helsinki, PO Box 63, 00014 Helsinki, Finland [2] Science for Life Laboratory, Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | - P Vahteristo
- Department of Medical Genetics, Genome-Scale Biology Research Program, University of Helsinki, PO Box 63, 00014 Helsinki, Finland
| | - L A Aaltonen
- Department of Medical Genetics, Genome-Scale Biology Research Program, University of Helsinki, PO Box 63, 00014 Helsinki, Finland
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37
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Cross-talk of phosphorylation and prolyl isomerization of the C-terminal domain of RNA Polymerase II. Molecules 2014; 19:1481-511. [PMID: 24473209 PMCID: PMC4350670 DOI: 10.3390/molecules19021481] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 01/06/2014] [Accepted: 01/21/2014] [Indexed: 12/04/2022] Open
Abstract
Post-translational modifications of the heptad repeat sequences in the C-terminal domain (CTD) of RNA polymerase II (Pol II) are well recognized for their roles in coordinating transcription with other nuclear processes that impinge upon transcription by the Pol II machinery; and this is primarily achieved through CTD interactions with the various nuclear factors. The identification of novel modifications on new regulatory sites of the CTD suggests that, instead of an independent action for all modifications on CTD, a combinatorial effect is in operation. In this review we focus on two well-characterized modifications of the CTD, namely serine phosphorylation and prolyl isomerization, and discuss the complex interplay between the enzymes modifying their respective regulatory sites. We summarize the current understanding of how the prolyl isomerization state of the CTD dictates the specificity of writers (CTD kinases), erasers (CTD phosphatases) and readers (CTD binding proteins) and how that correlates to transcription status. Subtle changes in prolyl isomerization states cannot be detected at the primary sequence level, we describe the methods that have been utilized to investigate this mode of regulation. Finally, a general model of how prolyl isomerization regulates the phosphorylation state of CTD, and therefore transcription-coupled processes, is proposed.
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38
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Corden JL. RNA polymerase II C-terminal domain: Tethering transcription to transcript and template. Chem Rev 2013; 113:8423-55. [PMID: 24040939 PMCID: PMC3988834 DOI: 10.1021/cr400158h] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jeffry L Corden
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore Maryland 21205, United States
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39
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Nemet J, Jelicic B, Rubelj I, Sopta M. The two faces of Cdk8, a positive/negative regulator of transcription. Biochimie 2013; 97:22-7. [PMID: 24139904 DOI: 10.1016/j.biochi.2013.10.004] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 10/07/2013] [Indexed: 12/16/2022]
Abstract
Three cyclin dependent kinases, Cdk7, Cdk8 and Cdk9 are intimately connected with the processes of RNA polymerase II dependent transcription initiation and elongation in eukaryotic cells. Each of these kinases is part of a larger multisubunit complex, TFIIH, Mediator and p-TEFb respectively. Of the three kinases, Cdk8 is the most complex given that it has been associated with both positive and negative effects on transcription via mechanisms that include regulation of transcription factor turnover, regulation of CTD phosphorylation and regulation of activator or repressor function. Furthermore, Cdk8 has emerged as a key regulator of multiple transcriptional programs linked to nutrient/growth factor sensing and differentiation control. As such Cdk8 represents a potentially interesting therapeutic drug target. In this review we summarize the current state of knowledge on Cdk8 function both in yeast and higher eukaryotes as well as discussing the effects of Cdk8 null mutations at the organismal level.
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Affiliation(s)
- Josipa Nemet
- Department of Molecular Biology, Ruđer Bošković Institute, Bijenicka 54, 10000 Zagreb, Croatia
| | - Branka Jelicic
- Department of Molecular Biology, Ruđer Bošković Institute, Bijenicka 54, 10000 Zagreb, Croatia
| | - Ivica Rubelj
- Department of Molecular Biology, Ruđer Bošković Institute, Bijenicka 54, 10000 Zagreb, Croatia
| | - Mary Sopta
- Department of Molecular Biology, Ruđer Bošković Institute, Bijenicka 54, 10000 Zagreb, Croatia.
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40
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Abstract
The Mediator complex is a multi-subunit assembly that appears to be required for regulating expression of most RNA polymerase II (pol II) transcripts, which include protein-coding and most non-coding RNA genes. Mediator and pol II function within the pre-initiation complex (PIC), which consists of Mediator, pol II, TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH and is approximately 4.0 MDa in size. Mediator serves as a central scaffold within the PIC and helps regulate pol II activity in ways that remain poorly understood. Mediator is also generally targeted by sequence-specific, DNA-binding transcription factors (TFs) that work to control gene expression programs in response to developmental or environmental cues. At a basic level, Mediator functions by relaying signals from TFs directly to the pol II enzyme, thereby facilitating TF-dependent regulation of gene expression. Thus, Mediator is essential for converting biological inputs (communicated by TFs) to physiological responses (via changes in gene expression). In this review, we summarize an expansive body of research on the Mediator complex, with an emphasis on yeast and mammalian complexes. We focus on the basics that underlie Mediator function, such as its structure and subunit composition, and describe its broad regulatory influence on gene expression, ranging from chromatin architecture to transcription initiation and elongation, to mRNA processing. We also describe factors that influence Mediator structure and activity, including TFs, non-coding RNAs and the CDK8 module.
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Affiliation(s)
- Zachary C Poss
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, CO , USA
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Wang X, Wang J, Ding Z, Ji J, Sun Q, Cai G. Structural flexibility and functional interaction of Mediator Cdk8 module. Protein Cell 2013; 4:911-20. [PMID: 24043446 DOI: 10.1007/s13238-013-3069-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 08/26/2013] [Indexed: 11/25/2022] Open
Abstract
Mediator is a highly conserved large protein complex (25 proteins, >1000 kDa) and preeminently responsible for eukaryotic transcription, which contains a dissociable 'Cdk8 module'. Although increasing evidence demonstrates that Cdk8 module plays both positive and negative roles in transcription regulation, the detailed structure, and subunit organization, molecular mechanism how it regulates transcription remain elusive. Here we used single-particle electron microscopy to characterize the structure and subunit organization of the Cdk8 module and illuminated the substantial mobility of the Med13 subunit results in the structural flexibility. The Cdk8 module interaction with core Mediator is concurrent with active transcription in vivo. An interaction with the Cdk8 module induces core Mediator into very extended conformation in vitro, which is presumed to be an active functional state of Mediator. Taken together, our results illuminated the detailed architecture of Cdk8 module, and suggested the Cdk8 module could positively regulate transcription by modulating Mediator conformation.
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Affiliation(s)
- Xuejuan Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
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Lacombe T, Poh SL, Barbey R, Kuras L. Mediator is an intrinsic component of the basal RNA polymerase II machinery in vivo. Nucleic Acids Res 2013; 41:9651-62. [PMID: 23963697 PMCID: PMC3834807 DOI: 10.1093/nar/gkt701] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Mediator is a prominent multisubunit coactivator that functions as a bridge between gene-specific activators and the basal RNA polymerase (Pol) II initiation machinery. Here, we study the poorly documented role of Mediator in basal, or activator-independent, transcription in vivo. We show that Mediator is still present at the promoter when the Pol II machinery is recruited in the absence of an activator, in this case through a direct fusion between a basal transcription factor and a heterologous DNA binding protein bound to the promoter. Moreover, transcription resulting from activator-independent recruitment of the Pol II machinery is impaired by inactivation of the essential Mediator subunit Med17 due to the loss of Pol II from the promoter. Our results strongly support that Mediator is an integral component of the minimal machinery essential in vivo for stable Pol II association with the promoter.
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Affiliation(s)
- Thierry Lacombe
- Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique, affiliated with Université Paris-Sud, Gif-sur-Yvette 91198, France
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Differential regulation of white-opaque switching by individual subunits of Candida albicans mediator. EUKARYOTIC CELL 2013; 12:1293-304. [PMID: 23873866 DOI: 10.1128/ec.00137-13] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The multisubunit eukaryotic Mediator complex integrates diverse positive and negative gene regulatory signals and transmits them to the core transcription machinery. Mutations in individual subunits within the complex can lead to decreased or increased transcription of certain subsets of genes, which are highly specific to the mutated subunit. Recent studies suggest a role for Mediator in epigenetic silencing. Using white-opaque morphological switching in Candida albicans as a model, we have shown that Mediator is required for the stability of both the epigenetic silenced (white) and active (opaque) states of the bistable transcription circuit driven by the master regulator Wor1. Individual deletions of eight C. albicans Mediator subunits have shown that different Mediator subunits have dramatically diverse effects on the directionality, frequency, and environmental induction of epigenetic switching. Among the Mediator deletion mutants analyzed, only Med12 has a steady-state transcriptional effect on the components of the Wor1 circuit that clearly corresponds to its effect on switching. The MED16 and MED9 genes have been found to be among a small subset of genes that are required for the stability of both the white and opaque states. Deletion of the Med3 subunit completely destabilizes the opaque state, even though the Wor1 transcription circuit is intact and can be driven by ectopic expression of Wor1. The highly impaired ability of the med3 deletion mutant to mate, even when Wor1 expression is ectopically induced, reveals that the activation of the Wor1 circuit can be decoupled from the opaque state and one of its primary biological consequences.
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Wang W, Yao X, Huang Y, Hu X, Liu R, Hou D, Chen R, Wang G. Mediator MED23 regulates basal transcription in vivo via an interaction with P-TEFb. Transcription 2013; 4:39-51. [PMID: 23340209 DOI: 10.4161/trns.22874] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The Mediator is a multi-subunit complex that transduces regulatory information from transcription regulators to the RNA polymerase II apparatus. Growing evidence suggests that Mediator plays roles in multiple stages of eukaryotic transcription, including elongation. However, the detailed mechanism by which Mediator regulates elongation remains elusive. In this study, we demonstrate that Mediator MED23 subunit controls a basal level of transcription by recruiting elongation factor P-TEFb, via an interaction with its CDK9 subunit. The mRNA level of Egr1, a MED23-controlled model gene, is reduced 4-5 fold in Med23 (-/-) ES cells under an unstimulated condition, but Med23-deficiency does not alter the occupancies of RNAP II, GTFs, Mediator complex, or activator ELK1 at the Egr1 promoter. Instead, Med23 depletion results in a significant decrease in P-TEFb and RNAP II (Ser2P) binding at the coding region, but no changes for several other elongation regulators, such as DSIF and NELF. ChIP-seq revealed that Med23-deficiency partially reduced the P-TEFb occupancy at a set of MED23-regulated gene promoters. Further, we demonstrate that MED23 interacts with CDK9 in vivo and in vitro. Collectively, these results provide the mechanistic insight into how Mediator promotes RNAP II into transcription elongation.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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Sox10 cooperates with the mediator subunit 12 during terminal differentiation of myelinating glia. J Neurosci 2013; 33:6679-90. [PMID: 23575864 DOI: 10.1523/jneurosci.5178-12.2013] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Several transcription factors are essential for terminal differentiation of myelinating glia, among them the high-mobility-group-domain-containing protein Sox10. To better understand how these factors exert their effects and shape glial expression programs, we identified and characterized a physical and functional link between Sox10 and the Med12 subunit of the Mediator complex that serves as a conserved multiprotein interphase between transcription factors and the general transcription machinery. We found that Sox10 bound with two of its conserved domains to the C-terminal region of Med12 and its close relative, Med12-like. In contrast to Med12-like, substantial amounts of Med12 were detected in both Schwann cells and oligodendrocytes. Its conditional glia-specific deletion in mice led to terminal differentiation defects that were highly reminiscent of those obtained after Sox10 deletion. In support of a functional cooperation, both proteins were jointly required for Krox20 induction and were physically associated with the critical regulatory region of the Krox20 gene in myelinating Schwann cells. We conclude that Sox10 functions during terminal differentiation of myelinating glia, at least in part by Med12-dependent recruitment of the Mediator complex.
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Steimel A, Suh J, Hussainkhel A, Deheshi S, Grants JM, Zapf R, Moerman DG, Taubert S, Hutter H. The C. elegans CDK8 Mediator module regulates axon guidance decisions in the ventral nerve cord and during dorsal axon navigation. Dev Biol 2013; 377:385-98. [PMID: 23458898 DOI: 10.1016/j.ydbio.2013.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 01/21/2013] [Accepted: 02/14/2013] [Indexed: 11/30/2022]
Abstract
Receptors expressed on the growth cone of outgrowing axons detect cues required for proper navigation. The pathway choices available to an axon are in part defined by the set of guidance receptors present on the growth cone. Regulated expression of receptors and genes controlling the localization and activity of receptors ensures that axons respond only to guidance cues relevant for reaching their targets. In genetic screens for axon guidance mutants, we isolated an allele of let-19/mdt-13, a component of the Mediator, a large ~30 subunit protein complex essential for gene transcription by RNA polymerase II. LET-19/MDT-13 is part of the CDK8 module of the Mediator. By testing other Mediator components, we found that all subunits of the CDK8 module as well as some other Mediator components are required for specific axon navigation decisions in a subset of neurons. Expression profiling demonstrated that let-19/mdt-13 regulates the expression of a large number of genes in interneurons. A mutation in the sax-3 gene, encoding a receptor for the repulsive guidance cue SLT-1, suppresses the commissure navigation defects found in cdk-8 mutants. This suggests that the CDK8 module specifically represses the SAX-3/ROBO pathway to ensure proper commissure navigation.
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Affiliation(s)
- Andreas Steimel
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
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Tsai KL, Sato S, Tomomori-Sato C, Conaway RC, Conaway JW, Asturias FJ. A conserved Mediator-CDK8 kinase module association regulates Mediator-RNA polymerase II interaction. Nat Struct Mol Biol 2013; 20:611-9. [PMID: 23563140 PMCID: PMC3648612 DOI: 10.1038/nsmb.2549] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 02/26/2013] [Indexed: 01/24/2023]
Abstract
The CDK8 kinase module (CKM) is a conserved, dissociable Mediator subcomplex whose component subunits were genetically linked to the RNA polymerase II (RNAPII) carboxy-terminal domain (CTD) and individually recognized as transcriptional repressors before Mediator was identified as a preeminent complex in eukaryotic transcription regulation. We used macromolecular electron microscopy and biochemistry to investigate the subunit organization, structure, and Mediator interaction of the Saccharomyces cerevisiae CKM. We found that interaction of the CKM with Mediator’s Middle module interferes with CTD-dependent RNAPII binding to a previously unknown Middle module CTD-binding site targeted early on in a multi-step holoenzyme formation process. Taken together, our results reveal the basis for CKM repression, clarify the origin of the connection between CKM subunits and the CTD, and suggest that a combination of competitive interactions and conformational changes that facilitate holoenzyme formation underlie the Mediator mechanism.
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Affiliation(s)
- Kuang-Lei Tsai
- Department of Cell Biology, Scripps Research Institute, La Jolla, California, USA
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Vulto-van Silfhout A, de Vries B, van Bon B, Hoischen A, Ruiterkamp-Versteeg M, Gilissen C, Gao F, van Zwam M, Harteveld C, van Essen A, Hamel B, Kleefstra T, Willemsen M, Yntema H, van Bokhoven H, Brunner H, Boyer T, de Brouwer A. Mutations in MED12 cause X-linked Ohdo syndrome. Am J Hum Genet 2013; 92:401-6. [PMID: 23395478 DOI: 10.1016/j.ajhg.2013.01.007] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 11/27/2012] [Accepted: 01/18/2013] [Indexed: 01/22/2023] Open
Abstract
Ohdo syndrome comprises a heterogeneous group of disorders characterized by intellectual disability (ID) and typical facial features, including blepharophimosis. Clinically, these blepharophimosis-ID syndromes have been classified in five distinct subgroups, including the Maat-Kievit-Brunner (MKB) type, which, in contrast to the others, is characterized by X-linked inheritance and facial coarsening at older age. We performed exome sequencing in two families, each with two affected males with Ohdo syndrome MKB type. In the two families, MED12 missense mutations (c.3443G>A [p.Arg1148His] or c.3493T>C [p.Ser1165Pro]) segregating with the phenotype were identified. Upon subsequent analysis of an additional cohort of nine simplex male individuals with Ohdo syndrome, one additional de novo missense change (c.5185C>A [p.His1729Asn]) in MED12 was detected. The occurrence of three different hemizygous missense mutations in three unrelated families affected by Ohdo syndrome MKB type shows that mutations in MED12 are the underlying cause of this X-linked form of Ohdo syndrome. Together with the recently described KAT6B mutations resulting in Ohdo syndrome Say/Barber/Biesecker/Young/Simpson type, our findings point to aberrant chromatin modification as being central to the pathogenesis of Ohdo syndrome.
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Woloshuk CP, Shim WB. Aflatoxins, fumonisins, and trichothecenes: a convergence of knowledge. FEMS Microbiol Rev 2012; 37:94-109. [PMID: 23078349 DOI: 10.1111/1574-6976.12009] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 09/27/2012] [Accepted: 10/15/2012] [Indexed: 01/03/2023] Open
Abstract
Plant pathogenic fungi Aspergillus flavus, Fusarium verticillioides, and Fusarium graminearum infect seeds of the most important food and feed crops, including maize, wheat, and barley. More importantly, these fungi produce aflatoxins, fumonisins, and trichothecenes, respectively, which threaten health and food security worldwide. In this review, we examine the molecular mechanisms and environmental factors that regulate mycotoxin biosynthesis in each fungus, and discuss the similarities and differences in the collective body of knowledge. Whole-genome sequences are available for these fungi, providing reference databases for genomic, transcriptomic, and proteomic analyses. It is well recognized that genes responsible for mycotoxin biosynthesis are organized in clusters. However, recent research has documented the intricate transcriptional and epigenetic regulation that affects these gene clusters. Significantly, molecular networks that respond to environmental factors, namely nitrogen, carbon, and pH, are connected to components regulating mycotoxin production. Furthermore, the developmental status of seeds and specific tissue types exert conditional influences during fungal colonization. A comparison of the three distinct mycotoxin groups provides insight into new areas for research collaborations that will lead to innovative strategies to control mycotoxin contamination of grain.
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Affiliation(s)
- Charles P Woloshuk
- Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA.
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Liu Z, Myers LC. Med5(Nut1) and Med17(Srb4) are direct targets of mediator histone H4 tail interactions. PLoS One 2012; 7:e38416. [PMID: 22693636 PMCID: PMC3367926 DOI: 10.1371/journal.pone.0038416] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 05/09/2012] [Indexed: 11/18/2022] Open
Abstract
The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. In addition to its canonical role in transcriptional activation, recent studies have demonstrated that S. cerevisiae Mediator can interact directly with nucleosomes, and their histone tails. Mutations in Mediator subunits have shown that Mediator and certain chromatin structures mutually impact each other structurally and functionally in vivo. We have taken a UV photo cross-linking approach to further delineate the molecular basis of Mediator chromatin interactions and help determine whether the impact of certain Mediator mutants on chromatin is direct. Specifically, by using histone tail peptides substituted with an amino acid analog that is a UV activatible crosslinker, we have identified specific subunits within Mediator that participate in histone tail interactions. Using Mediator purified from mutant yeast strains we have evaluated the impact of these subunits on histone tail binding. This analysis has identified the Med5 subunit of Mediator as a target for histone tail interactions and suggests that the previously observed effect of med5 mutations on telomeric heterochromatin and silencing is direct.
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Affiliation(s)
- Zhongle Liu
- Department of Biochemistry, Dartmouth Medical School, Hanover, New Hampshire, United States of America
| | - Lawrence C. Myers
- Department of Biochemistry, Dartmouth Medical School, Hanover, New Hampshire, United States of America
- * E-mail:
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