1
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Voutsadakis IA. Mediator kinase module proteins, genetic alterations and expression of super-enhancer regulated genes in colorectal cancer. Pharmacol Rep 2024; 76:535-556. [PMID: 38602606 DOI: 10.1007/s43440-024-00589-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 04/12/2024]
Abstract
BACKGROUND Genetic alterations are well characterized as contributors to the pathogenesis of cancers. Epigenetic abnormalities can lead to perturbations of the expression of genes in cancer cells without structural defects. Deregulation of proteins of the transcription machinery may result in perturbations of target genes. Mediator, a multiprotein component of the transcription machinery facilitates the function of RNA polymerase II, which transcribes most human genes. A part of the mediator with kinase activity, called the Mediator kinase module shows genetic alterations in a sub-set of colorectal cancers. METHODS Data from publicly available genomic series of colorectal cancer patients were examined to determine alterations of Mediator kinase module component genes, including MED12, MED12L, MED13, MED13L, CDK8, CDK19, and CCNC. The prevalence of alterations in genomically defined colorectal cancer sub-sets was also interrogated. The effect of Mediator kinase module member gene expression on colorectal cancer relapse-free survival was investigated. RESULTS Mutations in genes of the Mediator kinase module were present in a small percentage of colorectal cancers, ranging between 2 to 10% for MED12 and MED13 and alternative units MED12L and MED13L and below 2% for kinases CDK8 and CDK19 and cyclin C. Amplifications of the CDK8 gene were observed in 3% to 5% of colorectal cancers. The highest prevalence of mutations was observed in MSI cancers and the equivalent CMS1 group, with other genomic groups showing much lower frequency. An association of higher expression of MED12 with inferior relapse-free survival was observed. In contrast, higher expression of cyclin C was associated with improved survival. Colorectal cancer cell lines with CDK8 amplifications displayed sensitivity to several small molecule inhibitors of the KRAS/PI3K pathway but not to BET inhibitors. CONCLUSION The Mediator kinase module is deregulated in a sub-set of colorectal cancers with differences observed in genomically defined groups. These variations may result in differences in sensitivity to targeted therapies and may have to be taken into consideration as such therapies are developed.
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Affiliation(s)
- Ioannis A Voutsadakis
- Algoma District Cancer Program, Sault Area Hospital, Sault Ste Marie, ON, P6B 0A8, Canada.
- Division of Clinical Sciences, Section of Internal Medicine, Northern Ontario School of Medicine, 750 Great Northern Road, Sudbury, ON, Canada.
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2
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Ziada S, Diharce J, Serillon D, Bonnet P, Aci-Sèche S. Highlighting the Major Role of Cyclin C in Cyclin-Dependent Kinase 8 Activity through Molecular Dynamics Simulations. Int J Mol Sci 2024; 25:5411. [PMID: 38791449 PMCID: PMC11121562 DOI: 10.3390/ijms25105411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/07/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Dysregulation of cyclin-dependent kinase 8 (CDK8) activity has been associated with many diseases, including colorectal and breast cancer. As usual in the CDK family, the activity of CDK8 is controlled by a regulatory protein called cyclin C (CycC). But, while human CDK family members are generally activated in two steps, that is, the binding of the cyclin to CDK and the phosphorylation of a residue in the CDK activation loop, CDK8 does not require the phosphorylation step to be active. Another peculiarity of CDK8 is its ability to be associated with CycC while adopting an inactive form. These specificities raise the question of the role of CycC in the complex CDK8-CycC, which appears to be more complex than the other members of the CDK family. Through molecular dynamics (MD) simulations and binding free energy calculations, we investigated the effect of CycC on the structure and dynamics of CDK8. In a second step, we particularly focused our investigation on the structural and molecular basis of the protein-protein interaction between the two partners by finely analyzing the energetic contribution of residues and simulating the transition between the active and the inactive form. We found that CycC has a stabilizing effect on CDK8, and we identified specific interaction hotspots within its interaction surface compared to other human CDK/Cyc pairs. Targeting these specific interaction hotspots could be a promising approach in terms of specificity to effectively disrupt the interaction between CDK8. The simulation of the conformational transition from the inactive to the active form of CDK8 suggests that the residue Glu99 of CycC is involved in the orientation of three conserved arginines of CDK8. Thus, this residue may assume the role of the missing phosphorylation step in the activation mechanism of CDK8. In a more general view, these results point to the importance of keeping the CycC in computational studies when studying the human CDK8 protein in both the active and the inactive form.
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Affiliation(s)
- Sonia Ziada
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d’Orléans 7311, Université d’Orléans BP 6759, 45067 Orléans CEDEX 2, France (P.B.)
| | - Julien Diharce
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, Biologie Intégrée du Globule Rouge, UMR_S 1134, DSIMB Bioinformatics Team, 75014 Paris, France;
| | - Dylan Serillon
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d’Orléans 7311, Université d’Orléans BP 6759, 45067 Orléans CEDEX 2, France (P.B.)
| | - Pascal Bonnet
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d’Orléans 7311, Université d’Orléans BP 6759, 45067 Orléans CEDEX 2, France (P.B.)
| | - Samia Aci-Sèche
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d’Orléans 7311, Université d’Orléans BP 6759, 45067 Orléans CEDEX 2, France (P.B.)
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3
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Tolmacheva E, Bolshakova AS, Shubina J, Rogacheva MS, Ekimov AN, Podurovskaya JL, Burov AA, Rebrikov DV, Bychenko VG, Trofimov DY, Sukhikh GT. Expanding phenotype of MED13-associated syndrome presenting novel de novo missense variant in a patient with multiple congenital anomalies. BMC Med Genomics 2024; 17:130. [PMID: 38745205 PMCID: PMC11094910 DOI: 10.1186/s12920-024-01857-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 03/29/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Whole exome sequencing allows rapid identification of causative single nucleotide variants and short insertions/deletions in children with congenital anomalies and/or intellectual disability, which aids in accurate diagnosis, prognosis, appropriate therapeutic interventions, and family counselling. Recently, de novo variants in the MED13 gene were described in patients with an intellectual developmental disorder that included global developmental delay, mild congenital heart anomalies, and hearing and vision problems in some patients. RESULTS Here we describe an infant who carried a de novo p.Pro835Ser missense variant in the MED13 gene, according to whole exome trio sequencing. He presented with congenital heart anomalies, dysmorphic features, hydrocephalic changes, hypoplastic corpus callosum, bilateral optic nerve atrophy, optic chiasm atrophy, brain stem atrophy, and overall a more severe condition compared to previously described patients. CONCLUSIONS Therefore, we propose to expand the MED13-associated phenotype to include severe complications that could end up with multiple organ failure and neonatal death.
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Affiliation(s)
- Ekaterina Tolmacheva
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
| | - Anna S Bolshakova
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
| | - Jekaterina Shubina
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia.
| | - Margarita S Rogacheva
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
| | - Alexey N Ekimov
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
| | - Julia L Podurovskaya
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
| | - Artem A Burov
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
| | - Denis V Rebrikov
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
| | - Vladimir G Bychenko
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
| | - Dmitry Yu Trofimov
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
| | - Gennady T Sukhikh
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
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4
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Pantalone G, Mancardi MM, Rossi A, Romanelli R, Marasco E, Carla M. A de novo frameshift variant in MED13 gene in a patient with autism spectrum disorder and magnetic resonance imaging abnormalities mimicking tuberous sclerosis. Am J Med Genet A 2024:e63611. [PMID: 38528425 DOI: 10.1002/ajmg.a.63611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/09/2024] [Accepted: 03/13/2024] [Indexed: 03/27/2024]
Abstract
The mediator complex subunit 13 (MED13) gene is implicated in neurodevelopmental disorders including autism spectrum disorder (ASD), intellectual disability, and speech delay with varying severity and course. Additional, extra central nervous system, features include eye or vision problems, hypotonia, congenital heart abnormalities, and dysmorphisms. We describe a 7-year- and 4-month-old girl evaluated for ASD whose brain magnetic resonance imaging was suggestive of multiple cortical tubers. The exome sequencing (ES - trio analysis) uncovered a unique, de novo, frameshift variant in the MED13 gene (c.4880del, D1627Vfs*17), with a truncating effect on the protein. This case report thus expands the phenotypic spectrum of MED13-related disorders to include brain abnormalities.
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Affiliation(s)
- Gloria Pantalone
- Child Neurology and Psychiatry Unit, "G. Salesi" Children's Hospital, Azienda Ospedaliero Universitaria delle Marche, Ancona, Italy
| | - Maria Margherita Mancardi
- Unit of Child Neuropsychiatry, EpiCARE Member for Rare Diseases, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Andrea Rossi
- Neuroradiology Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
- Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
| | | | | | - Marini Carla
- Child Neurology and Psychiatry Unit, "G. Salesi" Children's Hospital, Azienda Ospedaliero Universitaria delle Marche, Ancona, Italy
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5
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Voutsadakis IA. Targeting super-enhancer activity for colorectal cancer therapy. Am J Transl Res 2024; 16:700-719. [PMID: 38586095 PMCID: PMC10994804 DOI: 10.62347/qkhb5897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/28/2024] [Indexed: 04/09/2024]
Abstract
In addition to genetic variants and copy number alterations, epigenetic deregulation of oncogenes and tumor suppressors is a major contributor in cancer development and propagation. Regulatory elements for gene transcription regulation can be found in promoters which are located in the vicinity of transcription start sites but also at a distance, in enhancer sites, brought to interact with proximal sites when occupied by enhancer protein complexes. These sites provide most of the specific regulatory sequences recognized by transcription factors. A sub-set of enhancers characterized by a longer structure and stronger activity, called super-enhancers, are critical for the expression of specific genes, usually associated with individual cell type identity and function. Super-enhancers show deregulation in cancer, which may have profound repercussions for cancer cell survival and response to therapy. Dysfunction of super-enhancers may result from multiple mechanisms that include changes in their sequence, alterations in the topological neighborhoods where they belong, and alterations in the proteins that mediate their function, such as transcription factors and epigenetic modifiers. These can become potential targets for therapeutic interventions. Genes that are targets of super-enhancers are cell and cancer type specific and could also be of interest for therapeutic targeting. In colorectal cancer, a super-enhancer regulated and over-expressed oncogene is MYC, under the influence of the WNT/β-catenin pathway. Identification and targeting of additional oncogenes regulated by super-enhancers in colorectal cancer may pave the way for combination therapies targeting the super-enhancer machinery and signal transduction pathways that regulate the specific transcription factors operative on them.
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Affiliation(s)
- Ioannis A Voutsadakis
- Algoma District Cancer Program, Sault Area HospitalSault Ste. Marie, ON, Canada
- Division of Clinical Sciences, Section of Internal Medicine, Northern Ontario School of MedicineSudbury, ON, Canada
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6
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Talukdar PD, Chatterji U. Transcriptional co-activators: emerging roles in signaling pathways and potential therapeutic targets for diseases. Signal Transduct Target Ther 2023; 8:427. [PMID: 37953273 PMCID: PMC10641101 DOI: 10.1038/s41392-023-01651-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/27/2023] [Accepted: 09/10/2023] [Indexed: 11/14/2023] Open
Abstract
Specific cell states in metazoans are established by the symphony of gene expression programs that necessitate intricate synergic interactions between transcription factors and the co-activators. Deregulation of these regulatory molecules is associated with cell state transitions, which in turn is accountable for diverse maladies, including developmental disorders, metabolic disorders, and most significantly, cancer. A decade back most transcription factors, the key enablers of disease development, were historically viewed as 'undruggable'; however, in the intervening years, a wealth of literature validated that they can be targeted indirectly through transcriptional co-activators, their confederates in various physiological and molecular processes. These co-activators, along with transcription factors, have the ability to initiate and modulate transcription of diverse genes necessary for normal physiological functions, whereby, deregulation of such interactions may foster tissue-specific disease phenotype. Hence, it is essential to analyze how these co-activators modulate specific multilateral processes in coordination with other factors. The proposed review attempts to elaborate an in-depth account of the transcription co-activators, their involvement in transcription regulation, and context-specific contributions to pathophysiological conditions. This review also addresses an issue that has not been dealt with in a comprehensive manner and hopes to direct attention towards future research that will encompass patient-friendly therapeutic strategies, where drugs targeting co-activators will have enhanced benefits and reduced side effects. Additional insights into currently available therapeutic interventions and the associated constraints will eventually reveal multitudes of advanced therapeutic targets aiming for disease amelioration and good patient prognosis.
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Affiliation(s)
- Priyanka Dey Talukdar
- Cancer Research Laboratory, Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Urmi Chatterji
- Cancer Research Laboratory, Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India.
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7
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Ruoff R, Weber H, Wang Y, Huang H, Shapiro E, Fenyö D, Garabedian MJ. MED19 encodes two unique protein isoforms that confer prostate cancer growth under low androgen through distinct gene expression programs. Sci Rep 2023; 13:18227. [PMID: 37880276 PMCID: PMC10600210 DOI: 10.1038/s41598-023-45199-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/17/2023] [Indexed: 10/27/2023] Open
Abstract
MED19, a component of the mediator complex and a co-regulator of the androgen receptor (AR), is pivotal in prostate cancer cell proliferation. MED19 has two isoforms: a full-length "canonical" and a shorter "alternative" variant. Specific antibodies were developed to investigate these isoforms. Both exhibit similar expression in normal prostate development and adult prostate tissue, but the canonical isoform is elevated in prostate adenocarcinomas. Overexpression of canonical MED19 in LNCaP cells promotes growth under conditions of androgen deprivation in vitro and in vivo, mirroring earlier findings with alternative MED19-overexpressing LNCaP cells. Interestingly, alternative MED19 cells displayed strong colony formation in clonogenic assays under conditions of androgen deprivation, while canonical MED19 cells did not, suggesting distinct functional roles. These isoforms also modulated gene expression differently. Canonical MED19 triggered genes related to extracellular matrix remodeling while suppressing those involved in androgen-inactivating glucuronidation. In contrast, alternative MED19 elevated genes tied to cell movement and reduced those associated with cell adhesion and differentiation. The ratio of MED19 isoform expression in prostate cancers shifts with the disease stage. Early-stage cancers exhibit higher canonical MED19 expression than alternative MED19, consistent with canonical MED19's ability to promote cell proliferation under androgen deprivation. Conversely, alternative MED19 levels were higher in later-stage metastatic prostate cancer than in canonical MED19, reflecting alternative MED19's capability to enhance cell migration and autonomous cell growth. Our findings suggest that MED19 isoforms play unique roles in prostate cancer progression and highlights MED19 as a potential therapeutic target for both early and late-stage prostate cancer.
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Affiliation(s)
- Rachel Ruoff
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Hannah Weber
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Ying Wang
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Hongying Huang
- Department of Urology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Ellen Shapiro
- Department of Urology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - David Fenyö
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Michael J Garabedian
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA.
- Department of Urology, New York University Grossman School of Medicine, New York, NY, 10016, USA.
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8
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Buyukcelebi K, Chen X, Abdula F, Elkafas H, Duval AJ, Ozturk H, Seker-Polat F, Jin Q, Yin P, Feng Y, Bulun SE, Wei JJ, Yue F, Adli M. Engineered MED12 mutations drive leiomyoma-like transcriptional and metabolic programs by altering the 3D genome compartmentalization. Nat Commun 2023; 14:4057. [PMID: 37429859 DOI: 10.1038/s41467-023-39684-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/26/2023] [Indexed: 07/12/2023] Open
Abstract
Nearly 70% of Uterine fibroid (UF) tumors are driven by recurrent MED12 hotspot mutations. Unfortunately, no cellular models could be generated because the mutant cells have lower fitness in 2D culture conditions. To address this, we employ CRISPR to precisely engineer MED12 Gly44 mutations in UF-relevant myometrial smooth muscle cells. The engineered mutant cells recapitulate several UF-like cellular, transcriptional, and metabolic alterations, including altered Tryptophan/kynurenine metabolism. The aberrant gene expression program in the mutant cells is, in part, driven by a substantial 3D genome compartmentalization switch. At the cellular level, the mutant cells gain enhanced proliferation rates in 3D spheres and form larger lesions in vivo with elevated production of collagen and extracellular matrix deposition. These findings indicate that the engineered cellular model faithfully models key features of UF tumors and provides a platform for the broader scientific community to characterize genomics of recurrent MED12 mutations.
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Affiliation(s)
- Kadir Buyukcelebi
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Xintong Chen
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Fatih Abdula
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Hoda Elkafas
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Alexander James Duval
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Harun Ozturk
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Fidan Seker-Polat
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Qiushi Jin
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Ping Yin
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Yue Feng
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Serdar E Bulun
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Jian Jun Wei
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Mazhar Adli
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA.
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9
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Yang Y, Zhang Z, Li W, Si Y, Li L, Du W. αKG-driven RNA polymerase II transcription of cyclin D1 licenses malic enzyme 2 to promote cell-cycle progression. Cell Rep 2023; 42:112770. [PMID: 37422761 DOI: 10.1016/j.celrep.2023.112770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 04/28/2023] [Accepted: 06/22/2023] [Indexed: 07/11/2023] Open
Abstract
Increased metabolic activity usually provides energy and nutrients for biomass synthesis and is indispensable for the progression of the cell cycle. Here, we find a role for α-ketoglutarate (αKG) generation in regulating cell-cycle gene transcription. A reduction in cellular αKG levels triggered by malic enzyme 2 (ME2) or isocitrate dehydrogenase 1 (IDH1) depletion leads to a pronounced arrest in G1 phase, while αKG supplementation promotes cell-cycle progression. Mechanistically, αKG directly binds to RNA polymerase II (RNAPII) and increases the level of RNAPII binding to the cyclin D1 gene promoter via promoting pre-initiation complex (PIC) assembly, consequently enhancing cyclin D1 transcription. Notably, αKG addition is sufficient to restore cyclin D1 expression in ME2- or IDH1-depleted cells, facilitating cell-cycle progression and proliferation in these cells. Therefore, our findings indicate a function of αKG in gene transcriptional regulation and cell-cycle control.
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Affiliation(s)
- Yanting Yang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Zhenxi Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Wei Li
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Yufan Si
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Li Li
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Wenjing Du
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China.
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10
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Lu KK, Song RF, Guo JX, Zhang Y, Zuo JX, Chen HH, Liao CY, Hu XY, Ren F, Lu YT, Liu WC. CycC1;1-WRKY75 complex-mediated transcriptional regulation of SOS1 controls salt stress tolerance in Arabidopsis. THE PLANT CELL 2023; 35:2570-2591. [PMID: 37040621 PMCID: PMC10291036 DOI: 10.1093/plcell/koad105] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 03/20/2023] [Accepted: 03/20/2023] [Indexed: 06/15/2023]
Abstract
SALT OVERLY SENSITIVE1 (SOS1) is a key component of plant salt tolerance. However, how SOS1 transcription is dynamically regulated in plant response to different salinity conditions remains elusive. Here, we report that C-type Cyclin1;1 (CycC1;1) negatively regulates salt tolerance by interfering with WRKY75-mediated transcriptional activation of SOS1 in Arabidopsis (Arabidopsis thaliana). Disruption of CycC1;1 promotes SOS1 expression and salt tolerance in Arabidopsis because CycC1;1 interferes with RNA polymerase II recruitment by occupying the SOS1 promoter. Enhanced salt tolerance of the cycc1;1 mutant was completely compromised by an SOS1 mutation. Moreover, CycC1;1 physically interacts with the transcription factor WRKY75, which can bind to the SOS1 promoter and activate SOS1 expression. In contrast to the cycc1;1 mutant, the wrky75 mutant has attenuated SOS1 expression and salt tolerance, whereas overexpression of SOS1 rescues the salt sensitivity of wrky75. Intriguingly, CycC1;1 inhibits WRKY75-mediated transcriptional activation of SOS1 via their interaction. Thus, increased SOS1 expression and salt tolerance in cycc1;1 were abolished by WRKY75 mutation. Our findings demonstrate that CycC1;1 forms a complex with WRKY75 to inactivate SOS1 transcription under low salinity conditions. By contrast, under high salinity conditions, SOS1 transcription and plant salt tolerance are activated at least partially by increased WRKY75 expression but decreased CycC1;1 expression.
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Affiliation(s)
- Kai-Kai Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement,
Collaborative Innovation Center of Crop Stress Biology, College of Life Sciences,
Henan University, Kaifeng 475004, China
| | - Ru-Feng Song
- State Key Laboratory of Crop Stress Adaptation and Improvement,
Collaborative Innovation Center of Crop Stress Biology, College of Life Sciences,
Henan University, Kaifeng 475004, China
| | - Jia-Xing Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement,
Collaborative Innovation Center of Crop Stress Biology, College of Life Sciences,
Henan University, Kaifeng 475004, China
| | - Yu Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement,
Collaborative Innovation Center of Crop Stress Biology, College of Life Sciences,
Henan University, Kaifeng 475004, China
| | - Jia-Xin Zuo
- State Key Laboratory of Crop Stress Adaptation and Improvement,
Collaborative Innovation Center of Crop Stress Biology, College of Life Sciences,
Henan University, Kaifeng 475004, China
| | - Hui-Hui Chen
- State Key Laboratory of Crop Stress Adaptation and Improvement,
Collaborative Innovation Center of Crop Stress Biology, College of Life Sciences,
Henan University, Kaifeng 475004, China
| | - Cai-Yi Liao
- State Key Laboratory of Crop Stress Adaptation and Improvement,
Collaborative Innovation Center of Crop Stress Biology, College of Life Sciences,
Henan University, Kaifeng 475004, China
| | - Xiao-Yu Hu
- State Key Laboratory of Crop Stress Adaptation and Improvement,
Collaborative Innovation Center of Crop Stress Biology, College of Life Sciences,
Henan University, Kaifeng 475004, China
| | - Feng Ren
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School
of Life Sciences, Central China Normal University, Wuhan
430079, China
| | - Ying-Tang Lu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan
University, Wuhan 430072, China
| | - Wen-Cheng Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement,
Collaborative Innovation Center of Crop Stress Biology, College of Life Sciences,
Henan University, Kaifeng 475004, China
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11
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Buyukcelebi K, Chen X, Abdula F, Duval A, Ozturk H, Seker-Polat F, Jin Q, Yin P, Feng Y, Wei JJ, Bulun S, Yue F, Adli M. Engineered MED12 mutations drive uterine fibroid-like transcriptional and metabolic programs by altering the 3D genome compartmentalization. RESEARCH SQUARE 2023:rs.3.rs-2537075. [PMID: 36798375 PMCID: PMC9934745 DOI: 10.21203/rs.3.rs-2537075/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Uterine fibroid (UF) tumors originate from a mutated smooth muscle cell (SMC). Nearly 70% of these tumors are driven by hotspot recurrent somatic mutations in the MED12 gene; however, there are no tractable genetic models to study the biology of UF tumors because, under culture conditions, the non-mutant fibroblasts outgrow the mutant SMC cells, resulting in the conversion of the population to WT phenotype. The lack of faithful cellular models hampered our ability to delineate the molecular pathways downstream of MED12 mutations and identify therapeutics that may selectively target the mutant cells. To overcome this challenge, we employed CRISPR knock-in with a sensitive PCR-based screening strategy to precisely engineer cells with mutant MED12 Gly44, which constitutes 50% of MED12 exon two mutations. Critically, the engineered myometrial SMC cells recapitulate several UF-like cellular, transcriptional and metabolic alterations, including enhanced proliferation rates in 3D spheres and altered Tryptophan/kynurenine metabolism. Our transcriptomic analysis supported by DNA synthesis tracking reveals that MED12 mutant cells, like UF tumors, have heightened expression of DNA repair genes but reduced DNA synthesis rates. Consequently, these cells accumulate significantly higher rates of DNA damage and are selectively more sensitive to common DNA-damaging chemotherapy, indicating mutation-specific and therapeutically relevant vulnerabilities. Our high-resolution 3D chromatin interaction analysis demonstrates that the engineered MED12 mutations drive aberrant genomic activity due to a genome-wide chromatin compartmentalization switch. These findings indicate that the engineered cellular model faithfully models key features of UF tumors and provides a novel platform for the broader scientific community to characterize genomics of recurrent MED12 mutations and discover potential therapeutic targets.
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12
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Lambert É, Puwakdandawa K, Tao YF, Robert F. From structure to molecular condensates: emerging mechanisms for Mediator function. FEBS J 2023; 290:286-309. [PMID: 34698446 DOI: 10.1111/febs.16250] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/15/2021] [Accepted: 10/25/2021] [Indexed: 02/05/2023]
Abstract
Mediator is a large modular protein assembly whose function as a coactivator of transcription is conserved in all eukaryotes. The Mediator complex can integrate and relay signals from gene-specific activators bound at enhancers to activate the general transcription machinery located at promoters. It has thus been described as a bridge between these elements during initiation of transcription. Here, we review recent studies on Mediator relating to its structure, gene specificity and general requirement, roles in chromatin architecture as well as novel concepts involving phase separation and transcriptional bursting. We revisit the mechanism of action of Mediator and ultimately put forward models for its mode of action in gene activation.
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Affiliation(s)
- Élie Lambert
- Institut de recherches cliniques de Montréal, Canada
| | | | - Yi Fei Tao
- Institut de recherches cliniques de Montréal, Canada
| | - François Robert
- Institut de recherches cliniques de Montréal, Canada.,Département de Médecine, Faculté de Médecine, Université de Montréal, Canada
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13
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Eischer N, Arnold M, Mayer A. Emerging roles of BET proteins in transcription and co-transcriptional RNA processing. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1734. [PMID: 35491403 DOI: 10.1002/wrna.1734] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/06/2022] [Accepted: 04/09/2022] [Indexed: 01/31/2023]
Abstract
Transcription by RNA polymerase II (Pol II) gives rise to all nuclear protein-coding and a large set of non-coding RNAs, and is strictly regulated and coordinated with RNA processing. Bromodomain and extraterminal (BET) family proteins including BRD2, BRD3, and BRD4 have been implicated in the regulation of Pol II transcription in mammalian cells. However, only recent technological advances have allowed the analysis of direct functions of individual BET proteins with high precision in cells. These studies shed new light on the molecular mechanisms of transcription control by BET proteins challenging previous longstanding views. The most studied BET protein, BRD4, emerges as a master regulator of transcription elongation with roles also in coupling nascent transcription with RNA processing. In contrast, BRD2 is globally required for the formation of transcriptional boundaries to restrict enhancer activity to nearby genes. Although these recent findings suggest non-redundant functions of BRD4 and BRD2 in Pol II transcription, more research is needed for further clarification. Little is known about the roles of BRD3. Here, we illuminate experimental work that has initially linked BET proteins to Pol II transcription in mammalian cells, outline main methodological breakthroughs that have strongly advanced the understanding of BET protein functions, and discuss emerging roles of individual BET proteins in transcription and transcription-coupled RNA processing. Finally, we propose an updated model for the function of BRD4 in transcription and co-transcriptional RNA maturation. This article is categorized under: RNA Processing > 3' End Processing RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Nicole Eischer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Mirjam Arnold
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Andreas Mayer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
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14
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Warfield L, Donczew R, Mahendrawada L, Hahn S. Yeast Mediator facilitates transcription initiation at most promoters via a Tail-independent mechanism. Mol Cell 2022; 82:4033-4048.e7. [PMID: 36208626 PMCID: PMC9637718 DOI: 10.1016/j.molcel.2022.09.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 05/12/2022] [Accepted: 09/13/2022] [Indexed: 11/06/2022]
Abstract
Mediator (MED) is a conserved factor with important roles in basal and activated transcription. Here, we investigate the genome-wide roles of yeast MED by rapid depletion of its activator-binding domain (Tail) and monitoring changes in nascent transcription. Rapid Tail depletion surprisingly reduces transcription from only a small subset of genes. At most of these Tail-dependent genes, in unperturbed conditions, MED is detected at both the UASs and promoters. In contrast, at most Tail-independent genes, we find MED primarily at promoters but not at the UASs. These results suggest that MED Tail and activator-mediated MED recruitment regulates only a small subset of genes. Furthermore, we define three classes of genes that differ in PIC assembly pathways and the requirements for MED Tail, SAGA, TFIID, and BET factors Bdf1/2. Our combined results have broad implications for the roles of MED, other coactivators, and mechanisms of transcriptional regulation at different gene classes.
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Affiliation(s)
- Linda Warfield
- Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Mailstop A1-162, Seattle, WA 98109, USA
| | - Rafal Donczew
- Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Mailstop A1-162, Seattle, WA 98109, USA
| | - Lakshmi Mahendrawada
- Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Mailstop A1-162, Seattle, WA 98109, USA
| | - Steven Hahn
- Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Mailstop A1-162, Seattle, WA 98109, USA.
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15
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Newman SA. Inherency and agency in the origin and evolution of biological functions. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Although discussed by 20th century philosophers in terms drawn from the sciences of non-living systems, in recent decades biological function has been considered in relationship to organismal capability and purpose. Bringing two phenomena generally neglected in evolutionary theory (i.e. inherency and agency) to bear on questions of function leads to a rejection of the adaptationist ‘selected effects’ notion of biological function. I review work showing that organisms such as the placozoans can thrive with almost no functional embellishments beyond those of their constituent cells and physical properties of their simple tissues. I also discuss work showing that individual tissue cells and their artificial aggregates exhibit agential behaviours that are unprecedented in the histories of their respective lineages. I review findings on the unique metazoan mechanism of developmental gene expression that has recruited, during evolution, inherent ancestral cellular functionalities into specialized cell types and organs of the different animal groups. I conclude that most essential functions in animal species are inherent to the cells from which they evolved, not selected effects, and that many of the others are optional ‘add-ons’, a status inimical to fitness-based models of evolution positing that traits emerge from stringent cycles of selection to meet external challenges.
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Affiliation(s)
- Stuart A Newman
- Department of Cell Biology & Anatomy, New York Medical College , Valhalla, NY 10595 , USA
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16
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Zhou Z, Yan H, Kim MS, Shim WB. Distinct Function of Mediator Subunits in Fungal Development, Stress Response, and Secondary Metabolism in Maize Pathogen Fusarium verticillioides. PHYTOPATHOLOGY 2022; 112:1730-1738. [PMID: 35271780 DOI: 10.1094/phyto-12-21-0495-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Mediator is a nucleus-localized, multisubunit protein complex highly conserved across eukaryotes. It interacts with RNA polymerase II transcription machinery as well as various transcription factors to regulate gene expression. However, systematic characterization of the Mediator complex has not been performed in filamentous fungi. In our study, the goal was to investigate key biological functions of Mediator subunits in a mycotoxigenic plant pathogen Fusarium verticillioides. Although there is some level of divergence in the constituent subunits, the overall structure was conserved between Saccharomyces cerevisiae and F. verticillioides. We generated 11 Mediator subunit deletion mutants and characterized vegetative growth, conidia formation, environmental stress response, carbon and fatty acid use, virulence, and fumonisin B1 (FB1) biosynthesis. Each Mediator subunit deletion mutant showed deficiencies in at least three of the phenotypes tested, suggesting that each subunit has different principal functions in F. verticillioides development, metabolism, and virulence. The deletion of FvMed1 led to increased FB1 production, and we confirmed that FvMed1 is transported from the nucleus to the cytoplasm under fumonisin-producing conditions. Taken together, our study characterized various important functional roles for Mediator subunits in F. verticillioides and suggests that select subunits can perform unique cytoplasmic functions independent of the core Mediator in fungal nucleus.
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Affiliation(s)
- Zehua Zhou
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, U.S.A
- Hunan Agricultural University, College of Plant Protection & Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Plant Pests, Furong District, Changsha, Hunan 410128, China
| | - Huijuan Yan
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, U.S.A
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94143, U.S.A
| | - Man S Kim
- Clinical Research Institute, College of Medicine, Kyung Hee University Hospital at Gangdong, Seoul, South Korea
| | - Won Bo Shim
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, U.S.A
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17
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Sertori R, Lin JX, Martinez E, Rana S, Sharo A, Kazemian M, Sunderam U, Andrake M, Shinton S, Truong B, Dunbrack RM, Liu C, Srinivasan R, Brenner SE, Seroogy CM, Puck JM, Leonard WJ, Wiest DL. Investigation of the causal etiology in a patient with T-B+NK+ immunodeficiency. Front Immunol 2022; 13:928252. [PMID: 35967429 PMCID: PMC9372720 DOI: 10.3389/fimmu.2022.928252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/27/2022] [Indexed: 11/24/2022] Open
Abstract
Newborn screening for severe combined immunodeficiency (SCID) has not only accelerated diagnosis and improved treatment for affected infants, but also led to identification of novel genes required for human T cell development. A male proband had SCID newborn screening showing very low T cell receptor excision circles (TRECs), a biomarker for thymic output of nascent T cells. He had persistent profound T lymphopenia, but normal numbers of B and natural killer (NK) cells. Despite an allogeneic hematopoietic stem cell transplant from his brother, he failed to develop normal T cells. Targeted resequencing excluded known SCID genes; however, whole exome sequencing (WES) of the proband and parents revealed a maternally inherited X-linked missense mutation in MED14 (MED14V763A), a component of the mediator complex. Morpholino (MO)-mediated loss of MED14 function attenuated T cell development in zebrafish. Moreover, this arrest was rescued by ectopic expression of cDNA encoding the wild type human MED14 ortholog, but not by MED14V763A , suggesting that the variant impaired MED14 function. Modeling of the equivalent mutation in mouse (Med14V769A) did not disrupt T cell development at baseline. However, repopulation of peripheral T cells upon competitive bone marrow transplantation was compromised, consistent with the incomplete T cell reconstitution experienced by the proband upon transplantation with bone marrow from his healthy male sibling, who was found to have the same MED14V763A variant. Suspecting that the variable phenotypic expression between the siblings was influenced by further mutation(s), we sought to identify genetic variants present only in the affected proband. Indeed, WES revealed a mutation in the L1 cell adhesion molecule (L1CAMQ498H); however, introducing that mutation in vivo in mice did not disrupt T cell development. Consequently, immunodeficiency in the proband may depend upon additional, unidentified gene variants.
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Affiliation(s)
- Robert Sertori
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Jian-Xin Lin
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Esteban Martinez
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Sadhna Rana
- Innovation Labs, Tata Consultancy Services, Hyderabad, India
| | - Andrew Sharo
- Center for Computational Biology, University of California, Berkeley, CA, United States
| | - Majid Kazemian
- Departments of Biochemistry and Computer Science, Purdue University, West Lafayette, IN, United States
| | - Uma Sunderam
- Innovation Labs, Tata Consultancy Services, Hyderabad, India
| | - Mark Andrake
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Susan Shinton
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Billy Truong
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Roland M. Dunbrack
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Chengyu Liu
- Transgenic Core, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | | | - Steven E. Brenner
- Center for Computational Biology, University of California, Berkeley, CA, United States
| | - Christine M. Seroogy
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Jennifer M. Puck
- Department of Pediatrics, University of California San Francisco and UCSF Benioff Children’s Hospital, San Francisco, CA, United States
| | - Warren J. Leonard
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | - David L. Wiest
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, United States
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18
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Molecular Mechanisms Contributing to the Etiology of Congenital Diaphragmatic Hernia: A Review and Novel Cases. J Pediatr 2022; 246:251-265.e2. [PMID: 35314152 DOI: 10.1016/j.jpeds.2022.03.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 03/01/2022] [Accepted: 03/15/2022] [Indexed: 12/25/2022]
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19
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Multiple Mechanisms of NOTCH1 Activation in Chronic Lymphocytic Leukemia: NOTCH1 Mutations and Beyond. Cancers (Basel) 2022; 14:cancers14122997. [PMID: 35740661 PMCID: PMC9221163 DOI: 10.3390/cancers14122997] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 11/20/2022] Open
Abstract
Simple Summary Mutations of the NOTCH1 gene are a validated prognostic marker in chronic lymphocytic leukemia and a potential predictive marker for anti-CD20-based therapies. At present, the most frequent pathological alteration of the NOTCH1 gene is due to somatic genetic mutations, which have a multifaceted functional impact. However, beside NOTCH1 mutations, other factors may lead to activation of the NOTCH1 pathway, and these include mutations of FBXW7, MED12, SPEN, SF3B1 as well as other B-cell pathways. Understanding the preferential strategies though which CLL cells hijack NOTCH1 signaling may present important clues for designing targeted treatment strategies for the management of CLL. Abstract The Notch signaling pathway plays a fundamental role for the terminal differentiation of multiple cell types, including B and T lymphocytes. The Notch receptors are transmembrane proteins that, upon ligand engagement, undergo multiple processing steps that ultimately release their intracytoplasmic portion. The activated protein ultimately operates as a nuclear transcriptional co-factor, whose stability is finely regulated. The Notch pathway has gained growing attention in chronic lymphocytic leukemia (CLL) because of the high rate of somatic mutations of the NOTCH1 gene. In CLL, NOTCH1 mutations represent a validated prognostic marker and a potential predictive marker for anti-CD20-based therapies, as pathological alterations of the Notch pathway can provide significant growth and survival advantage to neoplastic clone. However, beside NOTCH1 mutation, other events have been demonstrated to perturb the Notch pathway, namely somatic mutations of upstream, or even apparently unrelated, proteins such as FBXW7, MED12, SPEN, SF3B1, as well as physiological signals from other pathways such as the B-cell receptor. Here we review these mechanisms of activation of the NOTCH1 pathway in the context of CLL; the resulting picture highlights how multiple different mechanisms, that might occur under specific genomic, phenotypic and microenvironmental contexts, ultimately result in the same search for proliferative and survival advantages (through activation of MYC), as well as immune escape and therapy evasion (from anti-CD20 biological therapies). Understanding the preferential strategies through which CLL cells hijack NOTCH1 signaling may present important clues for designing targeted treatment strategies for the management of CLL.
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20
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Substrates of the MAPK Slt2: Shaping Yeast Cell Integrity. J Fungi (Basel) 2022; 8:jof8040368. [PMID: 35448599 PMCID: PMC9031059 DOI: 10.3390/jof8040368] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 02/04/2023] Open
Abstract
The cell wall integrity (CWI) MAPK pathway of budding yeast Saccharomyces cerevisiae is specialized in responding to cell wall damage, but ongoing research shows that it participates in many other stressful conditions, suggesting that it has functional diversity. The output of this pathway is mainly driven by the activity of the MAPK Slt2, which regulates important processes for yeast physiology such as fine-tuning of signaling through the CWI and other pathways, transcriptional activation in response to cell wall damage, cell cycle, or determination of the fate of some organelles. To this end, Slt2 precisely phosphorylates protein substrates, modulating their activity, stability, protein interaction, and subcellular localization. Here, after recapitulating the methods that have been employed in the discovery of proteins phosphorylated by Slt2, we review the bona fide substrates of this MAPK and the growing set of candidates still to be confirmed. In the context of the complexity of MAPK signaling regulation, we discuss how Slt2 determines yeast cell integrity through phosphorylation of these substrates. Increasing data from large-scale analyses and the available methodological approaches pave the road to early identification of new Slt2 substrates and functions.
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21
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Wu S, Li Q, Cao Y, Luo S, Wang Z, Zhang T. Mediator complex subunit 8 is a prognostic biomarker in hepatocellular carcinoma. Am J Transl Res 2022; 14:1765-1777. [PMID: 35422940 PMCID: PMC8991165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Mediator complex subunit 8 (MED8) is known for its role in encoding a subunit of the mediator complex (MED), that is critical for transcription. MED8 is significantly expressed in various tumors and has been correlated with an unfavorable prognosis. Nevertheless, no relationships have been found between MED8 and the clinical characteristics of hepatocellular carcinoma (HCC). METHODS To conduct an evaluation of correlations between clinicopathologic characteristics and MED8 expression, the logistic regression, Wilcoxon signed-rank test, and Kruskal-Wallis test were used. To perform analysis of factors contributing to prognosis, the Kaplan-Meier approach and the Cox regression analyses were used. A nomogram on the basis of a Cox multivariate analysis was employed to anticipate the influence of MED8 on patient prognosis. The receiver operating characteristic (ROC) curves were plotted and the areas under the curve (AUC) were calculated to assess the prognostic value of MED8. Both immune infiltration analysis and Gene Set Enrichment Analysis (GSEA) were applied to reveal significant enrichment differences among TCGA data. Quantitative RT-PCR (qRT-PCR) and western blotting were used to verify the difference in the expression of MED8 in normal and hepatocellular carcinoma cells. The immunohistochemical method was used to validate the MED8 expression in tumor and adjoining tissues of HCC patients. RESULTS A univariate analysis showed that high MED8 expression predicts poor disease-specific survival (DSS) (HR: 2.57; 95% confidence interval (CI) 1.62, 4.07; P<0.001). Multivariate regression analysis showed that high MED8 (adjusted HR: 3.032 (1.817, 5.060); P<0.001) expression and M stage (adjusted HR=4.075 (1.179-14.091) for M1 vs. M0, P=0.026) served as prognostic indicators of unfavorable overall survival in an independent manner in patients with HCC. The C-index for the nomogram was 0.732 (95% CI: 0.698, 0.766) and the AUC of MED8 was 0.817 (95% CI: 0.778, 0.857). Functional analysis showed that the cell cycle checkpoints, p53 dependent G1-DNA damage response, mitotic G1-G1-S phases, and mitotic G2-G2-M phases, were significantly enriched in DEGs associated with MED8 expression. Th2 cells were positively correlated with MED8 expression. CONCLUSIONS MED8 predicts poor prognosis in HCC, possibly through modulating the cell cycle and Th2 cells.
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Affiliation(s)
- Shuang Wu
- Clinical Laboratory, The Affiliated Children Hospital of Xi’an Jiaotong UniversityXi’an, Shaanxi, China
| | - Qiao Li
- Clinical Laboratory, The Affiliated Children Hospital of Xi’an Jiaotong UniversityXi’an, Shaanxi, China
| | - Yuan Cao
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Xi’an Jiaotong University (Xibei Hospital)Xi’an, Shaanxi, China
| | - Senyuan Luo
- Department of Pathology, Taihe Hospital, Hubei Medical UniversityShiyan, Hubei, China
| | - Zengguo Wang
- Clinical Laboratory, The Affiliated Children Hospital of Xi’an Jiaotong UniversityXi’an, Shaanxi, China
| | - Taoyuan Zhang
- Department of Anesthesiology, Rizhao International Heart HospitalRizhao, Shandong, China
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22
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Degree of Freedom of Gene Expression in Saccharomyces cerevisiae. Microbiol Spectr 2022; 10:e0083821. [PMID: 35230153 PMCID: PMC9045123 DOI: 10.1128/spectrum.00838-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The complexity of genome-wide gene expression has not yet been adequately addressed due to a lack of comprehensive statistical analyses. In the present study, we introduce degree of freedom (DOF) as a summary statistic for evaluating gene expression complexity. Because DOF can be interpreted by a state-space representation, application of the DOF is highly useful for understanding gene activities. We used over 11,000 gene expression data sets to reveal that the DOF of gene expression in Saccharomyces cerevisiae is not greater than 450. We further demonstrated that various degrees of freedom of gene expression can be interpreted by different sequence motifs within promoter regions and Gene Ontology (GO) terms. The well-known TATA box is the most significant one among the identified motifs, while the GO term "ribosome genesis" is an associated biological process. On the basis of transcriptional freedom, our findings suggest that the regulation of gene expression can be modeled using only a few state variables. IMPORTANCE Yeast works like a well-organized factory. Each of its components works in its own way, while affecting the activities of others. The order of all activities is largely governed by the regulation of gene expression. In recent decades, biologists have recognized many regulations for yeast genes. However, it is not known how closely the regulation links each gene together to make all components of the cell work as a whole. In other words, biologists are very interested in how many independent control factors are needed to operate an artificial "cell" that works the same as a real one. In this work, we suggested that only 450 control factors were sufficient to represent the regulation of all 5800 yeast genes.
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23
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Faergeman SL, Becher N, Andreasen L, Christiansen M, Frost L, Vogel I. A novel nonsense variant in MED12 associated with malformations in a female fetus. Clin Case Rep 2021; 9:e05124. [PMID: 34987808 PMCID: PMC8693823 DOI: 10.1002/ccr3.5124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 10/12/2021] [Accepted: 11/03/2021] [Indexed: 11/19/2022] Open
Abstract
Pathogenic variants in the MED12 gene located on the X-chromosome have primarily been reported in males with Lujan-Fryns syndrome, Ohdo syndrome and the Opits-Kaveggia syndrome. However, earlier reports of female patients and female mice suggest that MED12 deficiency causes severe malformations. We report a novel example of a MED12 de novo nonsense variant in a female fetus with severe malformations identified by trio-exome sequencing. This finding further expands the clinical spectrum of MED12-related disorders, which is vital for prenatal diagnosis and genetic counselling of couples.
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Affiliation(s)
| | - Naja Becher
- Department of Clinical GeneticsAarhus University HospitalAarhusDenmark
- Center for Fetal DiagnosticsAarhus University HospitalAarhusDenmark
| | - Lotte Andreasen
- Department of Clinical GeneticsAarhus University HospitalAarhusDenmark
| | - Marianne Christiansen
- Fetal Medicine UnitDepartment of Obstetrics and GynecologyAarhus University HospitalAarhusDenmark
| | - Lise Frost
- Department of Forensic MedicineAarhus UniversityAarhusDenmark
| | - Ida Vogel
- Department of Clinical GeneticsAarhus University HospitalAarhusDenmark
- Center for Fetal DiagnosticsAarhus University HospitalAarhusDenmark
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Shi Y, Chen J, Zeng WJ, Li M, Zhao W, Zhang XD, Yao J. Formation of nuclear condensates by the Mediator complex subunit Med15 in mammalian cells. BMC Biol 2021; 19:245. [PMID: 34789250 PMCID: PMC8597291 DOI: 10.1186/s12915-021-01178-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 10/28/2021] [Indexed: 11/13/2022] Open
Abstract
Background The Mediator complex is an evolutionarily conserved multi-subunit protein complex that plays major roles in transcriptional activation and is essential for cell growth, proliferation, and differentiation. Recent studies revealed that some Mediator subunits formed nuclear condensates that may facilitate enhancer-promoter interactions and gene activation. The assembly, regulation, and functions of these nuclear condensates remain to be further understood. Results We found that Med15, a subunit in the tail module of the Mediator complex, formed nuclear condensates through a novel mechanism. Nuclear foci of Med15 were detected by both immunostaining of endogenous proteins and live cell imaging. Like Med1 foci and many other biomolecular condensates, Med15 foci were sensitive to 1, 6-Hexanediol and showed rapid recovery during fluorescence recovery after photobleaching. Interestingly, overexpressing DYRK3, a dual-specificity kinase that controls the phase transition of membraneless organelles, appeared to disrupt Med1 foci and Med15 foci. We identified two regions that are required to form Med15 nuclear condensates: the glutamine-rich intrinsically disordered region (IDR) and a short downstream hydrophobic motif. The optodroplet assay revealed that both the IDR and the C-terminal region of Med15 contributed to intracellular phase separation. Conclusions We identified that the Mediator complex subunit Med15 formed nuclear condensates and characterized their features in living cells. Our work suggests that Med15 plays a role in the assembly of transcription coactivator condensates in the nucleus and identifies Med15 regions that contribute to phase separation. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01178-y.
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Affiliation(s)
- Yuanyuan Shi
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Jian Chen
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Wei-Jie Zeng
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Miao Li
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Wenxue Zhao
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Xing-Ding Zhang
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
| | - Jie Yao
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China. .,Present Address: Allen Institute for Cell Science, Seattle, WA, 98109, USA.
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Choi EB, Vodnala M, Zerbato M, Wang J, Ho JJ, Inouye C, Ding L, Fong YW. ATP-binding cassette protein ABCF1 couples transcription and genome surveillance in embryonic stem cells through low-complexity domain. SCIENCE ADVANCES 2021; 7:eabk2775. [PMID: 34714667 PMCID: PMC8555894 DOI: 10.1126/sciadv.abk2775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
OCT4 and SOX2 confer pluripotency by recruiting coactivators to activate stem cell–specific transcription. However, the composition of coactivator complexes and their roles in maintaining stem cell fidelity remain unclear. Here, we report the ATP-binding cassette subfamily F member 1 (ABCF1) as a coactivator for OCT4/SOX2 critical for stem cell self-renewal. The intrinsically disordered low-complexity domain (LCD) of ABCF1 contributes to phase separation in vitro and transcriptional activation of pluripotency genes by mediating multivalent interactions with SOX2 and co-dependent coactivators XPC and DKC1. These LCD-driven transcription factor–coactivator interactions critical for pluripotency gene expression are disrupted by DNA damage, likely due to LCD-dependent binding of ABCF1 to damage-generated intracellular DNA fragments instead of SOX2. This study identifies a transcriptional coactivator that uses its LCD to form selective multivalent interactions to regulate stem cell self-renewal and exit from pluripotency when genome integrity is compromised.
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Affiliation(s)
- Eun-Bee Choi
- Brigham Regenerative Medicine Center, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Cardiovascular Medicine Division, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Munender Vodnala
- Brigham Regenerative Medicine Center, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Cardiovascular Medicine Division, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Madeleine Zerbato
- Brigham Regenerative Medicine Center, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Cardiovascular Medicine Division, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Jianing Wang
- Brigham Regenerative Medicine Center, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Cardiovascular Medicine Division, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Jaclyn J. Ho
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California at Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, Berkeley, CA, USA
| | - Carla Inouye
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California at Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, Berkeley, CA, USA
| | - Lai Ding
- Department of Neurology, Program for Interdisciplinary Neuroscience, Brigham and Women’s Hospital, Boston, MA, USA
| | - Yick W. Fong
- Brigham Regenerative Medicine Center, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Cardiovascular Medicine Division, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
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Cdk8 Kinase Module: A Mediator of Life and Death Decisions in Times of Stress. Microorganisms 2021; 9:microorganisms9102152. [PMID: 34683473 PMCID: PMC8540245 DOI: 10.3390/microorganisms9102152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 01/18/2023] Open
Abstract
The Cdk8 kinase module (CKM) of the multi-subunit mediator complex plays an essential role in cell fate decisions in response to different environmental cues. In the budding yeast S. cerevisiae, the CKM consists of four conserved subunits (cyclin C and its cognate cyclin-dependent kinase Cdk8, Med13, and Med12) and predominantly negatively regulates a subset of stress responsive genes (SRG’s). Derepression of these SRG’s is accomplished by disassociating the CKM from the mediator, thus allowing RNA polymerase II-directed transcription. In response to cell death stimuli, cyclin C translocates to the mitochondria where it induces mitochondrial hyper-fission and promotes regulated cell death (RCD). The nuclear release of cyclin C requires Med13 destruction by the ubiquitin-proteasome system (UPS). In contrast, to protect the cell from RCD following SRG induction induced by nutrient deprivation, cyclin C is rapidly destroyed by the UPS before it reaches the cytoplasm. This enables a survival response by two mechanisms: increased ATP production by retaining reticular mitochondrial morphology and relieving CKM-mediated repression on autophagy genes. Intriguingly, nitrogen starvation also stimulates Med13 destruction but through a different mechanism. Rather than destruction via the UPS, Med13 proteolysis occurs in the vacuole (yeast lysosome) via a newly identified Snx4-assisted autophagy pathway. Taken together, these findings reveal that the CKM regulates cell fate decisions by both transcriptional and non-transcriptional mechanisms, placing it at a convergence point between cell death and cell survival pathways.
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Bhardwaj R, Thakur JK, Kumar S. MedProDB: A database of Mediator proteins. Comput Struct Biotechnol J 2021; 19:4165-4176. [PMID: 34527190 PMCID: PMC8342855 DOI: 10.1016/j.csbj.2021.07.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/08/2021] [Accepted: 07/24/2021] [Indexed: 12/03/2022] Open
Abstract
Mediator complex is a key component of transcriptional regulation in eukaryotes. Identification of Mediator subunits was done by using computational approaches. Different physicochemical properties, and functions of Mediators were discussed. We have developed first database of Mediator proteins e.g. MedProDB. MedProDB contains different types of search and browse options, and various tools.
In the last three decades, the multi-subunit Mediator complex has emerged as the key component of transcriptional regulation of eukaryotic gene expression. Although there were initial hiccups, recent advancements in bioinformatics tools contributed significantly to in-silico prediction and characterization of Mediator subunits from several organisms belonging to different eukaryotic kingdoms. In this study, we have developed the first database of Mediator proteins named MedProDB with 33,971 Mediator protein entries. Out of those, 12531, 11545, and 9895 sequences belong to metazoans, plants, and fungi, respectively. Apart from the core information consisting of sequence, length, position, organism, molecular weight, and taxonomic lineage, additional information of each Mediator sequence like aromaticity, hydropathy, instability index, isoelectric point, functions, interactions, repeat regions, diseases, sequence alignment to Mediator subunit family, Intrinsically Disordered Regions (IDRs), Post-translation modifications (PTMs), and Molecular Recognition Features (MoRFs) may be of high utility to the users. Furthermore, different types of search and browse options with four different tools namely BLAST, Smith-Waterman Align, IUPred, and MoRF-Chibi_Light are provided at MedProDB to perform different types of analysis. Being a critical component of the transcriptional machinery and regulating almost all the aspects of transcription, it generated lots of interest in structural and functional studies of Mediator functioning. So, we think that the MedProDB database will be very useful for researchers studying the process of transcription. This database is freely available at www.nipgr.ac.in/MedProDB.
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Affiliation(s)
- Rohan Bhardwaj
- Bioinformatics Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.,Plant Mediator Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Jitendra Kumar Thakur
- Plant Mediator Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.,Plant Transcription Regulation, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shailesh Kumar
- Bioinformatics Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
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Steroid receptor-coregulator transcriptional complexes: new insights from CryoEM. Essays Biochem 2021; 65:857-866. [PMID: 34061186 DOI: 10.1042/ebc20210019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 01/14/2023]
Abstract
Steroid receptors activate gene transcription through recruitment of a number of coregulators to facilitate histone modification, chromatin remodeling, and general transcription machinery stabilization. Understanding the structures of full-length steroid receptor and coregulatory complexes has been difficult due to their large molecular sizes and dynamic structural conformations. Recent developments in cryo-electron microscopy (cryoEM) technology and proteomics have advanced the structural studies of steroid receptor complexes. Here, we will review the insights we learned from cryoEM studies of the estrogen and androgen receptor transcriptional complexes. Despite similar domain organizations, the two receptors have different coregulator interaction modes. The cryoEM structures now have revealed the fundamental differences between the two receptors and their functional mechanisms.
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Rogers AP, Friend K, Rawlings L, Barnett CP. A de novo missense variant in MED13 in a patient with global developmental delay, marked facial dysmorphism, macroglossia, short stature, and macrocephaly. Am J Med Genet A 2021; 185:2586-2592. [PMID: 33931951 DOI: 10.1002/ajmg.a.62238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 12/16/2022]
Affiliation(s)
- Alice P Rogers
- Women's and Children's Hospital, Paediatric and Reproductive Genetics Unit, North Adelaide, South Australia, Australia
| | - Kathryn Friend
- Genetics and Molecular Pathology, Women's and Children's Hospital, North Adelaide, South Australia, Australia
| | - Lesley Rawlings
- Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Christopher P Barnett
- Women's and Children's Hospital, Paediatric and Reproductive Genetics Unit, North Adelaide, South Australia, Australia
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Guo P, Chong L, Wu F, Hsu CC, Li C, Zhu JK, Zhu Y. Mediator tail module subunits MED16 and MED25 differentially regulate abscisic acid signaling in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:802-815. [PMID: 33369119 DOI: 10.1111/jipb.13062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/19/2020] [Indexed: 05/06/2023]
Abstract
MED25 has been implicated as a negative regulator of the abscisic acid (ABA) signaling pathway. However, it is unclear whether other Mediator subunits could associate with MED25 to participate in the ABA response. Here, we used affinity purification followed by mass spectrometry to uncover Mediator subunits that associate with MED25 in transgenic plants. We found that at least 26 Mediator subunits, belonging to the head, middle, tail, and CDK8 kinase modules, were co-purified with MED25 in vivo. Interestingly, the tail module subunit MED16 was identified to associate with MED25 under both mock and ABA treatments. We further showed that the disruption of MED16 led to reduced ABA sensitivity compared to the wild type. Transcriptomic analysis revealed that the expression of several ABA-responsive genes was significantly lower in med16 than those in wild type. Furthermore, we discovered that MED16 may possibly compete with MED25 to interact with the key transcription factor ABA INSENSITIVE 5 (ABI5) to positively regulate ABA signaling. Consistently, med16 and med25 mutants displayed opposite phenotypes in ABA response, cuticle permeability, and differential ABI5-mediated EM1 and EM6 expression. Together, our data indicate that MED16 and MED25 differentially regulate ABA signaling by antagonistically affecting ABI5-mediated transcription in Arabidopsis.
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Affiliation(s)
- Pengcheng Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Leelyn Chong
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Fangming Wu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Chuan-Chih Hsu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529
| | - Chuanyou Li
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, Shanghai, 200032, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Yingfang Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475001, China
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Łukasik P, Załuski M, Gutowska I. Cyclin-Dependent Kinases (CDK) and Their Role in Diseases Development-Review. Int J Mol Sci 2021; 22:ijms22062935. [PMID: 33805800 PMCID: PMC7998717 DOI: 10.3390/ijms22062935] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/07/2021] [Accepted: 03/09/2021] [Indexed: 12/13/2022] Open
Abstract
Cyclin-dependent kinases (CDKs) are involved in many crucial processes, such as cell cycle and transcription, as well as communication, metabolism, and apoptosis. The kinases are organized in a pathway to ensure that, during cell division, each cell accurately replicates its DNA, and ensure its segregation equally between the two daughter cells. Deregulation of any of the stages of the cell cycle or transcription leads to apoptosis but, if uncorrected, can result in a series of diseases, such as cancer, neurodegenerative diseases (Alzheimer’s or Parkinson’s disease), and stroke. This review presents the current state of knowledge about the characteristics of cyclin-dependent kinases as potential pharmacological targets.
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Affiliation(s)
- Paweł Łukasik
- Department of Medical Chemistry, Pomeranian Medical University in Szczecin, Powstancow Wlkp. 72 Av., 70-111 Szczecin, Poland;
| | - Michał Załuski
- Department of Pharmaceutical Chemistry, Pomeranian Medical University in Szczecin, Powstancow Wlkp. 72 Av., 70-111 Szczecin, Poland;
| | - Izabela Gutowska
- Department of Medical Chemistry, Pomeranian Medical University in Szczecin, Powstancow Wlkp. 72 Av., 70-111 Szczecin, Poland;
- Correspondence:
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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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De novo loss-of-function variants in X-linked MED12 are associated with Hardikar syndrome in females. Genet Med 2020; 23:637-644. [PMID: 33244166 DOI: 10.1038/s41436-020-01031-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/15/2020] [Indexed: 12/21/2022] Open
Abstract
PURPOSE Hardikar syndrome (MIM 612726) is a rare multiple congenital anomaly syndrome characterized by facial clefting, pigmentary retinopathy, biliary anomalies, and intestinal malrotation, but with preserved cognition. Only four patients have been reported previously, and none had a molecular diagnosis. Our objective was to identify the genetic basis of Hardikar syndrome (HS) and expand the phenotypic spectrum of this disorder. METHODS We performed exome sequencing on two previously reported and five unpublished female patients with a clinical diagnosis of HS. X-chromosome inactivation (XCI) studies were also performed. RESULTS We report clinical features of HS with previously undescribed phenotypes, including a fatal unprovoked intracranial hemorrhage at age 21. We additionally report the discovery of de novo pathogenic nonsense and frameshift variants in MED12 in these seven individuals and evidence of extremely skewed XCI in all patients with informative testing. CONCLUSION Pathogenic missense variants in the X-chromosome gene MED12 have previously been associated with Opitz-Kaveggia syndrome, Lujan syndrome, Ohdo syndrome, and nonsyndromic intellectual disability, primarily in males. We propose a fifth, female-specific phenotype for MED12, and suggest that nonsense and frameshift loss-of-function MED12 variants in females cause HS. This expands the MED12-associated phenotype in females beyond intellectual disability.
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Binding and folding in transcriptional complexes. Curr Opin Struct Biol 2020; 66:156-162. [PMID: 33248428 DOI: 10.1016/j.sbi.2020.10.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 10/16/2020] [Accepted: 10/27/2020] [Indexed: 01/13/2023]
Abstract
Transcription factors are among the classes of proteins with the highest levels of disorder. Investigation of these regulatory proteins is uncovering not just the mechanisms that underlie gene regulation, but relationships that apply to all intrinsically disordered proteins. Recent studies confirm that binding does not necessarily induce folding but that when it does, it tends to follow induced fit mechanisms. Other work emphasises the importance of electrostatics to interactions involving intrinsically disordered proteins, and roles of intrinsic disorder in phase transitions. All these features help direct transcription factors to target sites in the genome to upregulate or downregulate transcription.
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Al-Husini N, Medler S, Ansari A. Crosstalk of promoter and terminator during RNA polymerase II transcription cycle. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194657. [PMID: 33246184 DOI: 10.1016/j.bbagrm.2020.194657] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/16/2022]
Abstract
The transcription cycle of RNAPII is comprised of three consecutive steps; initiation, elongation and termination. It has been assumed that the initiation and termination steps occur in spatial isolation, essentially as independent events. A growing body of evidence, however, has challenged this dogma. First, factors involved in initiation and termination exhibit both a genetic and a physical interaction during transcription. Second, the initiation and termination factors have been found to occupy both ends of a transcribing gene. Third, physical interaction of initiation and termination factors occupying distal ends of a gene sometime results in the entire terminator region of a genes looping back and contact its cognate promoter, thereby forming a looped gene architecture during transcription. A logical interpretation of these findings is that the initiation and termination steps of transcription do not occur in isolation. There is extensive communication of factors occupying promoter and terminator ends of a gene during transcription cycle. This review entails a discussion of the promoter-terminator crosstalk and its implication in the context of transcription.
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Affiliation(s)
- Nadra Al-Husini
- Department of Biological Science, Wayne State University, Detroit, MI, United States of America
| | - Scott Medler
- Department of Biological Science, Wayne State University, Detroit, MI, United States of America
| | - Athar Ansari
- Department of Biological Science, Wayne State University, Detroit, MI, United States of America.
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Wu D, Zhang Z, Chen X, Yan Y, Liu X. Angel or Devil ? - CDK8 as the new drug target. Eur J Med Chem 2020; 213:113043. [PMID: 33257171 DOI: 10.1016/j.ejmech.2020.113043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/19/2022]
Abstract
Cyclin-dependent kinase 8 (CDK8) plays an momentous role in transcription regulation by forming kinase module or transcription factor phosphorylation. A large number of evidences have identified CDK8 as an important factor in cancer occurrence and development. In addition, CDK8 also participates in the regulation of cancer cell stress response to radiotherapy and chemotherapy, assists tumor cell invasion, metastasis, and drug resistance. Therefore, CDK8 is regarded as a promising target for cancer therapy. Most studies in recent years supported the role of CDK8 as a carcinogen, however, under certain conditions, CDK8 exists as a tumor suppressor. The functional diversity of CDK8 and its exceptional role in different types of cancer have aroused great interest from scientists but even more controversy during the discovery of CDK8 inhibitors. In addition, CDK8 appears to be an effective target for inflammation diseases and immune system disorders. Therefore, we summarized the research results of CDK8, involving physiological/pathogenic mechanisms and the development status of compounds targeting CDK8, provide a reference for the feasibility evaluation of CDK8 as a therapeutic target, and guidance for researchers who are involved in this field for the first time.
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Affiliation(s)
- Dan Wu
- School of Biological Engineering, Hefei Technology College, Hefei, 238000, PR China
| | - Zhaoyan Zhang
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, Anhui Medical University, Hefei, 230032, PR China
| | - Xing Chen
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, Anhui Medical University, Hefei, 230032, PR China
| | - Yaoyao Yan
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, Anhui Medical University, Hefei, 230032, PR China
| | - Xinhua Liu
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, Anhui Medical University, Hefei, 230032, PR China.
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Chong L, Guo P, Zhu Y. Mediator Complex: A Pivotal Regulator of ABA Signaling Pathway and Abiotic Stress Response in Plants. Int J Mol Sci 2020; 21:ijms21207755. [PMID: 33092161 PMCID: PMC7588972 DOI: 10.3390/ijms21207755] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/16/2020] [Accepted: 10/19/2020] [Indexed: 01/09/2023] Open
Abstract
As an evolutionarily conserved multi-protein complex, the Mediator complex modulates the association between transcription factors and RNA polymerase II to precisely regulate gene transcription. Although numerous studies have shown the diverse functions of Mediator complex in plant development, flowering, hormone signaling, and biotic stress response, its roles in the Abscisic acid (ABA) signaling pathway and abiotic stress response remain largely unclear. It has been recognized that the phytohormone, ABA, plays a predominant role in regulating plant adaption to various abiotic stresses as ABA can trigger extensive changes in the transcriptome to help the plants respond to environmental stimuli. Over the past decade, the Mediator complex has been revealed to play key roles in not only regulating the ABA signaling transduction but also in the abiotic stress responses. In this review, we will summarize current knowledge of the Mediator complex in regulating the plants’ response to ABA as well as to the abiotic stresses of cold, drought and high salinity. We will particularly emphasize the involvement of multi-functional subunits of MED25, MED18, MED16, and CDK8 in response to ABA and environmental perturbation. Additionally, we will discuss potential research directions available for further deciphering the role of Mediator complex in regulating ABA and other abiotic stress responses.
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A review on kinases phosphorylating the carboxyl-terminal domain of RNA polymerase II-Biological functions and inhibitors. Bioorg Chem 2020; 104:104318. [PMID: 33142427 DOI: 10.1016/j.bioorg.2020.104318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/18/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022]
Abstract
RNA polymerase II (RNA Pol II) plays a major role in gene transcription for eukaryote. One of the major modes of regulation in eukaryotes is the phosphorylation of the carboxyl-terminal domain (CTD) of RNA Pol II. The current study found that the phosphorylation of Ser2, Ser5, Ser7, Thr4 and Tyr1 among the heptapeptide repeats of CTD plays a key role in the transcription process. We therefore review the biological functions and inhibitors of kinases that phosphorylate these amino acid residues including transcriptional cyclin-dependent protein kinases (CDKs), bromodomain-containing protein 4 (BRD4), Polo-like kinases 3 (Plk3) and Abelson murine leukemia viral oncogene 1 and 2 (c-Abl1/2).
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Trichoderma reesei XYR1 activates cellulase gene expression via interaction with the Mediator subunit TrGAL11 to recruit RNA polymerase II. PLoS Genet 2020; 16:e1008979. [PMID: 32877410 PMCID: PMC7467262 DOI: 10.1371/journal.pgen.1008979] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 07/06/2020] [Indexed: 12/22/2022] Open
Abstract
The ascomycete Trichoderma reesei is a highly prolific cellulase producer. While XYR1 (Xylanase regulator 1) has been firmly established to be the master activator of cellulase gene expression in T. reesei, its precise transcriptional activation mechanism remains poorly understood. In the present study, TrGAL11, a component of the Mediator tail module, was identified as a putative interacting partner of XYR1. Deletion of Trgal11 markedly impaired the induced expression of most (hemi)cellulase genes, but not that of the major β-glucosidase encoding genes. This differential involvement of TrGAL11 in the full induction of cellulase genes was reflected by the RNA polymerase II (Pol II) recruitment on their core promoters, indicating that TrGAL11 was required for the efficient transcriptional initiation of the majority of cellulase genes. In addition, we found that TrGAL11 recruitment to cellulase gene promoters largely occurred in an XYR1-dependent manner. Although xyr1 expression was significantly tuned down without TrGAL11, the binding of XYR1 to cellulase gene promoters did not entail TrGAL11. These results indicate that TrGAL11 represents a direct in vivo target of XYR1 and may play a critical role in contributing to Mediator and the following RNA Pol II recruitment to ensure the induced cellulase gene expression. As a model cellulolytic fungus, T. reesei is capable of rapidly producing a large quantity of (hemi)cellulases when appropriate substrates are present. This outstanding characteristic has made T. reesei a prominent producer of cellulase in industry and also a model organism for studying eukaryotic gene expression. The expression of these hydrolytic enzymes encoding genes in T. reesei is precisely regulated at a transcriptional level and controlled by a suite of transcription factors. Among others, the transcription activator XYR1 has been firmly established to be absolutely necessary for activating the expression of almost all cellulase genes. However, the precise mechanism it acts remains largely unknown. In eukaryotes, the multisubunit Mediator complex has been shown to be critical for expression of most, if not all, protein-coding genes by conveying regulatory information to the basal transcription machinery. Here, we find that XYR1 interacts with the Mediator tail module subunit, TrGAL11, which contributes to cellobiohydrolase (cbh) and endoglucanase (eg) genes but not β-glucosidase (bgl) genes expression. Thus, the induced XYR1 binding to cellulase gene promoters led to TrGAL11 and RNA Pol II recruitment to these promoters. These results show that TrGAL11 represents a direct in vivo target of XYR1 and provide evidence for not only the evolutionarily conserved function of Mediator, but also for the existence of some subtle difference in its action to mediate gene expression in different eukaryotes.
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40
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Castañeda AF, Didychuk AL, Louder RK, McCollum CO, Davis ZH, Nogales E, Glaunsinger BA. The gammaherpesviral TATA-box-binding protein directly interacts with the CTD of host RNA Pol II to direct late gene transcription. PLoS Pathog 2020; 16:e1008843. [PMID: 32886723 PMCID: PMC7498053 DOI: 10.1371/journal.ppat.1008843] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 09/17/2020] [Accepted: 07/28/2020] [Indexed: 12/11/2022] Open
Abstract
β- and γ-herpesviruses include the oncogenic human viruses Kaposi's sarcoma-associated virus (KSHV) and Epstein-Barr virus (EBV), and human cytomegalovirus (HCMV), which is a significant cause of congenital disease. Near the end of their replication cycle, these viruses transcribe their late genes in a manner distinct from host transcription. Late gene transcription requires six virally encoded proteins, one of which is a functional mimic of host TATA-box-binding protein (TBP) that is also involved in recruitment of RNA polymerase II (Pol II) via unknown mechanisms. Here, we applied biochemical protein interaction studies together with electron microscopy-based imaging of a reconstituted human preinitiation complex to define the mechanism underlying Pol II recruitment. These data revealed that the herpesviral TBP, encoded by ORF24 in KSHV, makes a direct protein-protein contact with the C-terminal domain of host RNA polymerase II (Pol II), which is a unique feature that functionally distinguishes viral from cellular TBP. The interaction is mediated by the N-terminal domain (NTD) of ORF24 through a conserved motif that is shared in its β- and γ-herpesvirus homologs. Thus, these herpesviruses employ an unprecedented strategy in eukaryotic transcription, wherein promoter recognition and polymerase recruitment are facilitated by a single transcriptional activator with functionally distinct domains.
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Affiliation(s)
- Angelica F. Castañeda
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States of America
| | - Allison L. Didychuk
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States of America
| | - Robert K. Louder
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
- Biophysics Graduate Group, University of California, Berkeley, CA, United States of America
| | - Chloe O. McCollum
- Department of Molecular and Cell Biology, University of California Berkeley, CA, United States of America
| | - Zoe H. Davis
- Division of Infectious Diseases and Immunity, School of Public Health, University of California, Berkeley, CA, United States of America
| | - Eva Nogales
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
- Department of Molecular and Cell Biology, University of California Berkeley, CA, United States of America
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, United States of America
- Howard Hughes Medical Institute, Berkeley, CA, United States of America
| | - Britt A. Glaunsinger
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States of America
- Department of Molecular and Cell Biology, University of California Berkeley, CA, United States of America
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, United States of America
- Howard Hughes Medical Institute, Berkeley, CA, United States of America
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Fan D, Wang M, Cheng A, Jia R, Yang Q, Wu Y, Zhu D, Zhao X, Chen S, Liu M, Zhang S, Ou X, Mao S, Gao Q, Sun D, Wen X, Liu Y, Yu Y, Zhang L, Tian B, Pan L, Chen X. The Role of VP16 in the Life Cycle of Alphaherpesviruses. Front Microbiol 2020; 11:1910. [PMID: 33013729 PMCID: PMC7461839 DOI: 10.3389/fmicb.2020.01910] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 07/21/2020] [Indexed: 12/12/2022] Open
Abstract
The protein encoded by the UL48 gene of alphaherpesviruses is named VP16 or alpha-gene-transactivating factor (α-TIF). In the early stage of viral replication, VP16 is an important transactivator that can activate the transcription of viral immediate-early genes, and in the late stage of viral replication, VP16, as a tegument, is involved in viral assembly. This review will explain the mechanism of VP16 acting as α-TIF to activate the transcription of viral immediate-early genes, its role in the transition from viral latency to reactivation, and its effects on viral assembly and maturation. In addition, this review also provides new insights for further research on the life cycle of alphaherpesviruses and the role of VP16 in the viral life cycle.
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Affiliation(s)
- Dengjian Fan
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dekang Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xingjian Wen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yunya Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yanling Yu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Leichang Pan
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xiaoyue Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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42
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Zhang N, Song Y, Xu Y, Liu J, Shen Y, Zhou L, Yu J, Yang M. MED13L integrates Mediator-regulated epigenetic control into lung cancer radiosensitivity. Am J Cancer Res 2020; 10:9378-9394. [PMID: 32802198 PMCID: PMC7415817 DOI: 10.7150/thno.48247] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 07/03/2020] [Indexed: 12/13/2022] Open
Abstract
To date, efforts to improve non-small-cell lung cancer (NSCLC) outcomes with increased radiation dose have not been successful. Identification of novel druggable targets that are capable to modulate NSCLC radiosensitivity may provide a way forward. Mediator complex is implicated in gene expression control, but it remains unclear how Mediator dysfunction is involved in cancer radiotherapy. Methods: The biologic functions of miR-4497, MED13L and PRKCA in NSCLC radiosensitivity were examined through biochemical assays including gene expression profilling, cell proliferation assay, colony formation assay, wound healing assay, transwell assay, dual luciferase reporter assay, xenograft models, immunoprecipitation, and chromatin immunoprecipitation sequencing. Clinical implications of miR-4497, MED13L and PRKCA in radiosensitivity were evaluated in NSCLC patients treated with concurrent chemoradiotherapy or radiotherapy alone. Results: We found that radiation can trigger disassemble of Mediator complex via silencing of MED13L by miR-4497 in NSCLC. Although not interrupting structure integrity of the core Mediator or the CDK8 kinase module, suppression of MED13L attenuated their physical interactions and reduced recruitment of acetyltransferase P300 to chromatin via Mediator. Silencing of MED13L therefore diminishes global H3K27ac signals written by P300, activities of enhancer and/or promoters and expression of multiple oncogenes, especially PRKCA. Inhibition of PRKCA expression potentiates the killing effect of radiotherapy in vitro and in vivo. Remarkably, high PRKCA expression in NSCLC tissues is correlated with poor prognosis of patients received radiotherapy. Conclusions: Our study linking PRKCA to radiosensitivity through a novel mechanism may enable the rational targeting of PRKCA to unlock therapeutic potentials of NSCLC.
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Stortz M, Pecci A, Presman DM, Levi V. Unraveling the molecular interactions involved in phase separation of glucocorticoid receptor. BMC Biol 2020; 18:59. [PMID: 32487073 PMCID: PMC7268505 DOI: 10.1186/s12915-020-00788-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 05/05/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Functional compartmentalization has emerged as an important factor modulating the kinetics and specificity of biochemical reactions in the nucleus, including those involved in transcriptional regulation. The glucocorticoid receptor (GR) is a ligand-activated transcription factor that translocates to the nucleus upon hormone stimulation and distributes between the nucleoplasm and membraneless compartments named nuclear foci. While a liquid-liquid phase separation process has been recently proposed to drive the formation of many nuclear compartments, the mechanisms governing the heterogeneous organization of GR in the nucleus and the functional relevance of foci formation remain elusive. RESULTS We dissected some of the molecular interactions involved in the formation of GR condensates and analyzed the GR structural determinants relevant to this process. We show that GR foci present properties consistent with those expected for biomolecular condensates formed by a liquid-liquid phase separation process in living human cells. Their formation requires an initial interaction of GR with certain chromatin regions at specific locations within the nucleus. Surprisingly, the intrinsically disordered region of GR is not essential for condensate formation, in contrast to many nuclear proteins that require disordered regions to phase separate, while the ligand-binding domain seems essential for that process. We finally show that GR condensates include Mediator, a protein complex involved in transcription regulation. CONCLUSIONS We show that GR foci have properties of liquid condensates and propose that active GR molecules interact with chromatin and recruit multivalent cofactors whose interactions with additional molecules lead to the formation of a focus. The biological relevance of the interactions occurring in GR condensates supports their involvement in transcription regulation.
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Affiliation(s)
- Martin Stortz
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, C1428EGA, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular, Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
| | - Adali Pecci
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, C1428EGA, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
| | - Diego M Presman
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, C1428EGA, Buenos Aires, Argentina.
| | - Valeria Levi
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, C1428EGA, Buenos Aires, Argentina.
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina.
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The Important Function of Mediator Complex in Controlling the Developmental Transitions in Plants. Int J Mol Sci 2020; 21:ijms21082733. [PMID: 32326439 PMCID: PMC7215822 DOI: 10.3390/ijms21082733] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/09/2020] [Accepted: 04/11/2020] [Indexed: 12/24/2022] Open
Abstract
Developmental transitions in plants are tightly associated with changes in the transcriptional regulation of gene expression. One of the most important regulations is conferred by cofactors of RNA polymerase II including the mediator complex, a large complex with a modular organization. The mediator complex recruits transcription factors to bind to the specific sites of genes including protein-coding genes and non-coding RNA genes to promote or repress the transcription initiation and elongation using a protein-protein interaction module. Mediator complex subunits have been isolated and identified in plants and the function of most mediator subunits in whole life cycle plants have been revealed. Studies have shown that the Mediator complex is indispensable for the regulation of plant developmental transitions by recruiting age-, flowering-, or hormone-related transcription factors. Here, we first overviewed the Mediator subunits in plants, and then we summarized the specific Mediator subunits involved in developmental transitions, including vegetative phase change and floral transition. Finally, we proposed the future directions to further explore their roles in plants. The link between Mediator subunits and developmental transitions implies the necessity to explore targets of this complex as a potential application in developing high quality crop varieties.
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45
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Abstract
RNA polymerase II (Pol II) transcribes all protein-coding genes and many noncoding RNAs in eukaryotic genomes. Although Pol II is a complex, 12-subunit enzyme, it lacks the ability to initiate transcription and cannot consistently transcribe through long DNA sequences. To execute these essential functions, an array of proteins and protein complexes interact with Pol II to regulate its activity. In this review, we detail the structure and mechanism of over a dozen factors that govern Pol II initiation (e.g., TFIID, TFIIH, and Mediator), pausing, and elongation (e.g., DSIF, NELF, PAF, and P-TEFb). The structural basis for Pol II transcription regulation has advanced rapidly in the past decade, largely due to technological innovations in cryoelectron microscopy. Here, we summarize a wealth of structural and functional data that have enabled a deeper understanding of Pol II transcription mechanisms; we also highlight mechanistic questions that remain unanswered or controversial.
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Affiliation(s)
- Allison C Schier
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80303, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80303, USA
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Cyclin-dependent kinase inhibition: an opportunity to target protein-protein interactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 121:115-141. [PMID: 32312419 DOI: 10.1016/bs.apcsb.2019.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Cyclin-dependent kinases (CDKs) play an integral part in cellular activities. To date, most of the activities have been evaluated in the cell cycle and transcription. Several diseases are affected by abnormalities in CDKs, related-pathways, or proteins that regulate CDK activity. CDKs are primarily dependent on activation by binding other proteins, namely Cyclins. In addition, phosphorylation of key CDK residues also plays a major part in CDK activity. To date, the most successful drugs have been developed against CDK4 and CDK6 and are FDA approved for use in advanced breast cancer. However, this is likely only a small fraction of the potential for targeting CDKs as a strategy against cancer and other diseases. Based on the extensive protein-protein interactions made by CDKs with other proteins (Cyclins and others), there are numerous possibilities for targeting strategies against protein-protein interactions. Here we describe the predominant roles of CDKs in the cell, key interacting proteins, significant 3-dimensional structural characteristics, and summarize the work-to-date in inhibition of CDKs.
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47
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Maji S, Dahiya P, Waseem M, Dwivedi N, Bhat DS, Dar TH, Thakur JK. Interaction map of Arabidopsis Mediator complex expounding its topology. Nucleic Acids Res 2019; 47:3904-3920. [PMID: 30793213 PMCID: PMC6486561 DOI: 10.1093/nar/gkz122] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 01/04/2019] [Accepted: 02/20/2019] [Indexed: 01/28/2023] Open
Abstract
Understanding of mechanistic details of Mediator functioning in plants is impeded as the knowledge of subunit organization and structure is lacking. In this study, an interaction map of Arabidopsis Mediator complex was analyzed to understand the arrangement of the subunits in the core part of the complex. Combining this interaction map with homology-based modeling, probable structural topology of core part of the Arabidopsis Mediator complex was deduced. Though the overall topology of the complex was similar to that of yeast, several differences were observed. Many interactions discovered in this study are not yet reported in other systems. AtMed14 and AtMed17 emerged as the key component providing important scaffold for the whole complex. AtMed6 and AtMed10 were found to be important for linking head with middle and middle with tail, respectively. Some Mediator subunits were found to form homodimers and some were found to possess transactivation property. Subcellular localization suggested that many of the Mediator subunits might have functions beyond the process of transcription. Overall, this study reveals role of individual subunits in the organization of the core complex, which can be an important resource for understanding the molecular mechanism of functioning of Mediator complex and its subunits in plants.
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Affiliation(s)
- Sourobh Maji
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Pradeep Dahiya
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Mohd Waseem
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Nidhi Dwivedi
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Divya S Bhat
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Tanvir H Dar
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Jitendra K Thakur
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
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48
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Poot M. Mutations in Mediator Complex Genes CDK8, MED12, MED13, and MEDL13 Mediate Overlapping Developmental Syndromes. Mol Syndromol 2019; 10:239-242. [PMID: 32021594 DOI: 10.1159/000502346] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/22/2019] [Indexed: 12/18/2022] Open
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49
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Lorton BM, Shechter D. Cellular consequences of arginine methylation. Cell Mol Life Sci 2019; 76:2933-2956. [PMID: 31101937 PMCID: PMC6642692 DOI: 10.1007/s00018-019-03140-2] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/22/2019] [Accepted: 05/10/2019] [Indexed: 02/07/2023]
Abstract
Arginine methylation is a ubiquitous post-translational modification. Three predominant types of arginine-guanidino methylation occur in Eukarya: mono (Rme1/MMA), symmetric (Rme2s/SDMA), and asymmetric (Rme2a/ADMA). Arginine methylation frequently occurs at sites of protein-protein and protein-nucleic acid interactions, providing specificity for binding partners and stabilization of important biological interactions in diverse cellular processes. Each methylarginine isoform-catalyzed by members of the protein arginine methyltransferase family, Type I (PRMT1-4,6,8) and Type II (PRMT5,9)-has unique downstream consequences. Methylarginines are found in ordered domains, domains of low complexity, and in intrinsically disordered regions of proteins-the latter two of which are intimately connected with biological liquid-liquid phase separation. This review highlights discoveries illuminating how arginine methylation affects genome integrity, gene transcription, mRNA splicing and mRNP biology, protein translation and stability, and phase separation. As more proteins and processes are found to be regulated by arginine methylation, its importance for understanding cellular physiology will continue to grow.
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Affiliation(s)
- Benjamin M Lorton
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - David Shechter
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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50
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Abstract
Mediator is a large, multi-module complex that plays a key role in transcription regulation in eukaryotes. A divergent Mediator from a unicellular eukaryote has been identified and characterized, revealing novel adaptations to mRNA and ncRNA transcription.
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Affiliation(s)
- Xiaolu Zhao
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yifan Liu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
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