1
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Liu K, Li W, Xiao Y, Lei M, Zhang M, Min J. Molecular mechanism of specific DNA sequence recognition by NRF1. Nucleic Acids Res 2024; 52:953-966. [PMID: 38055835 PMCID: PMC10810270 DOI: 10.1093/nar/gkad1162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 11/09/2023] [Accepted: 11/17/2023] [Indexed: 12/08/2023] Open
Abstract
Nuclear respiratory factor 1 (NRF1) regulates the expression of genes that are vital for mitochondrial biogenesis, respiration, and various other cellular processes. While NRF1 has been reported to bind specifically to GC-rich promoters as a homodimer, the precise molecular mechanism governing its recognition of target gene promoters has remained elusive. To unravel the recognition mechanism, we have determined the crystal structure of the NRF1 homodimer bound to an ATGCGCATGCGCAT dsDNA. In this complex, NRF1 utilizes a flexible linker to connect its dimerization domain (DD) and DNA binding domain (DBD). This configuration allows one NRF1 monomer to adopt a U-turn conformation, facilitating the homodimer to specifically bind to the two TGCGC motifs in the GCGCATGCGC consensus sequence from opposite directions. Strikingly, while the NRF1 DBD alone could also bind to the half-site (TGCGC) DNA of the consensus sequence, the cooperativity between DD and DBD is essential for the binding of the intact GCGCATGCGC sequence and the transcriptional activity of NRF1. Taken together, our results elucidate the molecular mechanism by which NRF1 recognizes specific DNA sequences in the promoters to regulate gene expression.
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Affiliation(s)
- Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Weifang Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Yuqing Xiao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Ming Lei
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Ming Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
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2
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Elliott K, Singh VK, Boström M, Larsson E. Base-resolution UV footprinting by sequencing reveals distinctive damage signatures for DNA-binding proteins. Nat Commun 2023; 14:2701. [PMID: 37169761 PMCID: PMC10175305 DOI: 10.1038/s41467-023-38266-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 03/30/2023] [Indexed: 05/13/2023] Open
Abstract
Decades ago, it was shown that proteins binding to DNA can quantitatively alter the formation of DNA damage by UV light. This established the principle of UV footprinting for non-intrusive study of protein-DNA contacts in living cells, albeit at limited scale and precision. Here, we perform deep base-resolution quantification of the principal UV damage lesion, the cyclobutane pyrimidine dimer (CPD), at select human promoter regions using targeted CPD sequencing. Several transcription factors exhibited distinctive and repeatable damage signatures indicative of site occupancy, involving strong (up to 17-fold) position-specific elevations and reductions in CPD formation frequency relative to naked DNA. Positive damage modulation at some ETS transcription factor binding sites coincided at base level with melanoma somatic mutation hotspots. Our work provides proof of concept for the study of protein-DNA interactions at individual loci using light and sequencing, and reveals widespread and potent modulation of UV damage in regulatory regions.
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Affiliation(s)
- Kerryn Elliott
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Vinod Kumar Singh
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Martin Boström
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Erik Larsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, SE-405 30, Gothenburg, Sweden.
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3
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Ducker C, Ratnam M, Shaw PE, Layfield R. Comparative analysis of protein expression systems and PTM landscape in the study of transcription factor ELK-1. Protein Expr Purif 2023; 203:106216. [PMID: 36528218 DOI: 10.1016/j.pep.2022.106216] [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: 10/11/2022] [Revised: 12/06/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Post-translational modifications (PTMs) are important for protein folding and activity, and the ability to recreate physiologically relevant PTM profiles on recombinantly-expressed proteins is vital for meaningful functional analysis. The ETS transcription factor ELK-1 serves as a paradigm for cellular responses to mitogens and can synergise with androgen receptor to promote prostate cancer progression, although in vitro protein function analyses to date have largely overlooked its complex PTM landscapes. We expressed and purified human ELK-1 using mammalian (HEK293T), insect (Sf9) and bacterial (E. coli) systems in parallel and compared PTMs imparted upon purified proteins, along with their performance in DNA and protein interaction assays. Phosphorylation of ELK-1 within its transactivation domain, known to promote DNA binding, was most apparent in protein isolated from human cells and accordingly conferred the strongest DNA binding in vitro, while protein expressed in insect cells bound most efficiently to the androgen receptor. We observed lysine acetylation, a hitherto unreported PTM of ELK-1, which appeared highest in insect cell-derived ELK-1 but was also present in HEK293T-derived ELK-1. Acetylation of ELK-1 was enhanced in HEK293T cells following starvation and mitogen stimulation, and modified lysines showed overlap with previously identified regulatory SUMOylation and ubiquitination sites. Our data demonstrate that the choice of recombinant expression system can be tailored to suit biochemical application rather than to maximise soluble protein production and suggest the potential for crosstalk and antagonism between different PTMs of ELK-1.
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Affiliation(s)
- Charles Ducker
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom.
| | - Manohar Ratnam
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Cancer Institute, Detroit, MI, USA
| | - Peter E Shaw
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - Robert Layfield
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
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4
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Zhu T, Wang X, Zheng Z, Quan J, Liu Y, Wang Y, Liu T, Liu X, Wang M, Zhang Z. ZIP12 Contributes to Hypoxic Pulmonary Hypertension by Driving Phenotypic Switching of Pulmonary Artery Smooth Muscle Cells. J Cardiovasc Pharmacol 2022; 79:235-243. [PMID: 34694243 DOI: 10.1097/fjc.0000000000001156] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/27/2021] [Indexed: 11/26/2022]
Abstract
ABSTRACT ZIP12, a plasmalemmal zinc transporter, reportedly promotes pulmonary vascular remodeling (PVR) by enhancing proliferation of pulmonary artery smooth muscle cells (PASMCs). However, the mechanisms of ZIP12 facilitating PASMCs proliferation remain incompletely appreciated. It has been acknowledged that proliferation-predisposing phenotypic switching of PASMCs can lead to PVR. Given that hypoxia triggers phenotypic switching of PASMCs and ZIP12 mediates PVR, this study aims to explore whether ZIP12-mediated phenotypic switching of PASMCs contributes to hypoxia-induced PVR. Rats were exposed to hypoxia (10% O2) for 3 weeks to induce PVR, and primary rat PASMCs were cultured under hypoxic condition (3% O2) for 48 hours to induce proliferation. Immunofluorescence, quantitative reverse transcription-polymerase chain reaction, and Western blot analysis were performed to detect the expression of target mRNAs and proteins. EdU incorporation and 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium assay were conducted to measure the proliferation of PASMCs. Hypoxia upregulated ZIP12 expression (both mRNA and protein) in pulmonary arteries and PASMCs. Knockdown of ZIP12 inhibited phenotypic switching of PASMCs induced by hypoxia. We propose that HIF-1α/ZIP12/pERK pathway could represent a novel mechanism underlying hypoxia-induced phenotypic switching of PASMCs. Therapeutic targeting of ZIP12 could be exploited to treat PVR.
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Affiliation(s)
- Tiantian Zhu
- Department of Clinical Pharmacy, College of Pharmacy, Xinxiang Medical University, Xinxiang, Henan, China
| | - Xuan Wang
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410078, China ; and
| | - Zijie Zheng
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410078, China ; and
| | - Jinping Quan
- Department of Clinical Pharmacy, College of Pharmacy, Xinxiang Medical University, Xinxiang, Henan, China
| | - Yuhao Liu
- Department of Clinical Pharmacy, College of Pharmacy, Xinxiang Medical University, Xinxiang, Henan, China
| | - Yuting Wang
- Department of Clinical Pharmacy, College of Pharmacy, Xinxiang Medical University, Xinxiang, Henan, China
| | - Tianheng Liu
- Department of Clinical Pharmacy, College of Pharmacy, Xinxiang Medical University, Xinxiang, Henan, China
| | - Xu Liu
- Department of Clinical Pharmacy, College of Pharmacy, Xinxiang Medical University, Xinxiang, Henan, China
| | - Mi Wang
- The Department of Cardiology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zheng Zhang
- Department of Clinical Pharmacy, College of Pharmacy, Xinxiang Medical University, Xinxiang, Henan, China
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410078, China ; and
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5
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Liu H, Jia Y, Chai Y, Wang S, Chen H, Zhou X, Huang C, Guo S, Chen D. Whole-transcriptome analysis of differentially expressed genes between ray and disc florets and identification of flowering regulatory genes in Chrysanthemum morifolium. FRONTIERS IN PLANT SCIENCE 2022; 13:947331. [PMID: 35991433 PMCID: PMC9388166 DOI: 10.3389/fpls.2022.947331] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/29/2022] [Indexed: 05/13/2023]
Abstract
Chrysanthemum morifolium has ornamental and economic values. However, there has been minimal research on the morphology of the chrysanthemum florets and related genes. In this study, we used the leaves as a control to screen for differentially expressed genes between ray and disc florets in chrysanthemum flowers. A total of 8,359 genes were differentially expressed between the ray and disc florets, of which 3,005 were upregulated and 5,354 were downregulated in the disc florets. Important regulatory genes that control flower development and flowering determination were identified. Among them, we identified a TM6 gene (CmTM6-mu) that belongs to the Class B floral homeotic MADS-box transcription factor family, which was specifically expressed in disc florets. We isolated this gene and found it was highly similar to other typical TM6 lineage genes, but a single-base deletion at the 3' end of the open reading frame caused a frame shift that generated a protein in which the TM6-specific paleoAP3 motif was missing at the C terminus. The CmTM6-mu gene was ectopically expressed in Arabidopsis thaliana. Petal and stamen developmental processes were unaffected in transgenic A. thaliana lines; however, the flowering time was earlier than in the wild-type control. Thus, the C-terminal of paleoAP3 appears to be necessary for the functional performance in regulating the development of petals or stamens and CmTM6-mu may be involved in the regulation of flowering time in chrysanthemum. The results of this study will be useful for future research on flowering molecular mechanisms and for the breeding of novel flower types.
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Affiliation(s)
- Hua Liu
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yin Jia
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Yuhong Chai
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, China
| | - Sen Wang
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Haixia Chen
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xiumei Zhou
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, China
| | - Conglin Huang
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- *Correspondence: Conglin Huang,
| | - Shuang Guo
- Chengdu Park City Construction Development Research Institute, Chengdu, China
- *Correspondence: Conglin Huang,
| | - Dongliang Chen
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- *Correspondence: Conglin Huang,
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6
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Thiel G, Backes TM, Guethlein LA, Rössler OG. Critical Protein-Protein Interactions Determine the Biological Activity of Elk-1, a Master Regulator of Stimulus-Induced Gene Transcription. Molecules 2021; 26:molecules26206125. [PMID: 34684708 PMCID: PMC8541449 DOI: 10.3390/molecules26206125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/03/2021] [Accepted: 10/05/2021] [Indexed: 12/22/2022] Open
Abstract
Elk-1 is a transcription factor that binds together with a dimer of the serum response factor (SRF) to the serum-response element (SRE), a genetic element that connects cellular stimulation with gene transcription. Elk-1 plays an important role in the regulation of cellular proliferation and apoptosis, thymocyte development, glucose homeostasis and brain function. The biological function of Elk-1 relies essentially on the interaction with other proteins. Elk-1 binds to SRF and generates a functional ternary complex that is required to activate SRE-mediated gene transcription. Elk-1 is kept in an inactive state under basal conditions via binding of a SUMO-histone deacetylase complex. Phosphorylation by extracellular signal-regulated protein kinase, c-Jun N-terminal protein kinase or p38 upregulates the transcriptional activity of Elk-1, mediated by binding to the mediator of RNA polymerase II transcription (Mediator) and the transcriptional coactivator p300. Strong and extended phosphorylation of Elk-1 attenuates Mediator and p300 recruitment and allows the binding of the mSin3A-histone deacetylase corepressor complex. The subsequent dephosphorylation of Elk-1, catalyzed by the protein phosphatase calcineurin, facilitates the re-SUMOylation of Elk-1, transforming Elk-1 back to a transcriptionally inactive state. Thus, numerous protein–protein interactions control the activation cycle of Elk-1 and are essential for its biological function.
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Affiliation(s)
- Gerald Thiel
- Department of Medical Biochemistry and Molecular Biology, Saarland University Medical Faculty, D-66421 Homburg, Germany; (T.M.B.); (O.G.R.)
- Correspondence: ; Tel.: +49-6841-1626506; Fax: +49-6841-1626500
| | - Tobias M. Backes
- Department of Medical Biochemistry and Molecular Biology, Saarland University Medical Faculty, D-66421 Homburg, Germany; (T.M.B.); (O.G.R.)
| | - Lisbeth A. Guethlein
- Department of Structural Biology and Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA;
| | - Oliver G. Rössler
- Department of Medical Biochemistry and Molecular Biology, Saarland University Medical Faculty, D-66421 Homburg, Germany; (T.M.B.); (O.G.R.)
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7
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Crystal Structures of Ternary Complexes of MEF2 and NKX2-5 Bound to DNA Reveal a Disease Related Protein-Protein Interaction Interface. J Mol Biol 2020; 432:5499-5508. [PMID: 32681840 DOI: 10.1016/j.jmb.2020.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 11/22/2022]
Abstract
MEF2 and NKX2-5 transcription factors interact with each other in cardiogenesis and are necessary for normal heart formation. Despite evidence suggesting that these two transcription factors function synergistically and possibly through direct physical interactions, molecular mechanisms by which they interact are not clear. Here we determined the crystal structures of ternary complexes of MEF2 and NKX2-5 bound to myocardin enhancer DNA in two crystal forms. These crystal structures are the first example of human MADS-box/homeobox ternary complex structures involved in cardiogenesis. Our structures reveal two possible modes of interactions between MEF2 and NKX2-5: MEF2 and NKX bind to adjacent DNA sites to recognize DNA in cis; and MEF2 and NKX bind to different DNA strands to interact with each other in trans via a conserved protein-protein interface observed in both crystal forms. Disease-related mutations are mapped to the observed protein-protein interface. Our structural studies provide a starting point to understand and further study the molecular mechanisms of the interactions between MEF2 and NKX2.5 and their roles in cardiogenesis.
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8
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Nicholas TR, Strittmatter BG, Hollenhorst PC. Oncogenic ETS Factors in Prostate Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1210:409-436. [PMID: 31900919 DOI: 10.1007/978-3-030-32656-2_18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Prostate cancer is unique among carcinomas in that a fusion gene created by a chromosomal rearrangement is a common driver of the disease. The TMPRSS2/ERG rearrangement drives aberrant expression of the ETS family transcription factor ERG in 50% of prostate tumors. Similar rearrangements promote aberrant expression of the ETS family transcription factors ETV1 and ETV4 in another 10% of cases. Together, these three ETS factors are thought to promote tumorigenesis in the majority of prostate cancers. A goal of precision medicine is to be able to apply targeted therapeutics that are specific to disease subtypes. ETS gene rearrangement positive tumors represent the largest molecular subtype of prostate cancer, but to date there is no treatment specific to this marker. In this chapter we will review the latest findings regarding the molecular mechanisms of ETS factor function in the prostate. These molecular details may provide a path towards new therapeutic targets for this subtype of prostate cancer. Further, we will describe efforts to target the oncogenic functions of ETS family transcription factors directly as well as indirectly.
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Affiliation(s)
| | - Brady G Strittmatter
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA
| | - Peter C Hollenhorst
- Medical Sciences, Indiana University School of Medicine, Bloomington, IN, USA.
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9
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Lei X, Kou Y, Fu Y, Rajashekar N, Shi H, Wu F, Xu J, Luo Y, Chen L. The Cancer Mutation D83V Induces an α-Helix to β-Strand Conformation Switch in MEF2B. J Mol Biol 2018; 430:1157-1172. [PMID: 29477338 DOI: 10.1016/j.jmb.2018.02.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 02/13/2018] [Accepted: 02/17/2018] [Indexed: 12/29/2022]
Abstract
MEF2B is a major target of somatic mutations in non-Hodgkin lymphoma. Most of these mutations are non-synonymous substitutions of surface residues in the MADS-box/MEF2 domain. Among them, D83V is the most frequent mutation found in tumor cells. The link between this hotspot mutation and cancer is not well understood. Here we show that the D83V mutation induces a dramatic α-helix to β-strand switch in the MEF2 domain. Located in an α-helix region rich in β-branched residues, the D83V mutation not only removes the extensive helix stabilization interactions but also introduces an additional β-branched residue that further shifts the conformation equilibrium from α-helix to β-strand. Cross-database analyses of cancer mutations and chameleon sequences revealed a number of well-known cancer targets harboring β-strand favoring mutations in chameleon α-helices, suggesting a commonality of such conformational switch in certain cancers and a new factor to consider when stratifying the rapidly expanding cancer mutation data.
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Affiliation(s)
- Xiao Lei
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Yi Kou
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA; Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA; USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Yang Fu
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Niroop Rajashekar
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Haoran Shi
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Fang Wu
- Department of Statistics and Applied Probability, University of California, Santa Barbara, CA 93106, USA
| | - Jiang Xu
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA; Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA; USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Yibing Luo
- Department of Statistics, University of California, Davis, CA 95616, USA
| | - Lin Chen
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA; Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA; USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
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10
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Lovell MA, Lynn BC, Fister S, Bradley-Whitman M, Murphy MP, Beckett TL, Norris CM. A Novel Small Molecule Modulator of Amyloid Pathology. J Alzheimers Dis 2018; 53:273-87. [PMID: 27163808 DOI: 10.3233/jad-151160] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Because traditional approaches to drug development for Alzheimer's disease are becoming increasingly expensive and in many cases disappointingly unsuccessful, alternative approaches are required to shift the paradigm. Following leads from investigations of dihydropyridine calcium channel blockers, we observed unique properties from a class of functionalized naphthyridines and sought to develop these as novel therapeutics that minimize amyloid pathology without the adverse effects associated with current therapeutics. Our data show methyl 2,4-dimethyl-5-oxo-5,6-dihydrobenzo[c][2,7]naphthyridine-1-carboxylate (BNC-1) significantly decreases amyloid burden in a well-established mouse model of amyloid pathology through a unique mechanism mediated by Elk-1, a transcriptional repressor of presenilin-1. Additionally, BNC-1 treatment leads to increased levels of synaptophysin and synapsin, markers of synaptic integrity, but does not adversely impact presenilin-2 or processing of Notch-1, thus avoiding negative off target effects associated with pan-gamma secretase inhibition. Overall, our data show BNC-1 significantly decreases amyloid burden and improves markers of synaptic integrity in a well-established mouse model of amyloid deposition by promoting phosphorylation and activation of Elk-1, a transcriptional repressor of presenilin-1 but not presenilin-2. These data suggest BNC-1 might be a novel, disease-modifying therapeutic that will alter the pathogenesis of Alzheimer's disease.
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Affiliation(s)
- Mark A Lovell
- Department of Chemistry, University of Kentucky, Lexington, KY, USA.,Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Bert C Lynn
- Department of Chemistry, University of Kentucky, Lexington, KY, USA.,Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA.,Universisty of Kentucky Mass Spectrometry Center, Lexington, KY, USA
| | - Shuling Fister
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | | | - M Paul Murphy
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA.,Department of Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Tina L Beckett
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Christopher M Norris
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA.,Department of Pharmacology, University of Kentucky, Lexington, KY, USA
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11
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Mylona A, Carr S, Aller P, Moraes I, Treisman R, Evans G, Foadi J. A Novel Approach to Data Collection for Difficult Structures: Data Management for Large Numbers of Crystals with the BLEND Software. CRYSTALS 2017; 7:242. [PMID: 29456874 PMCID: PMC5813789 DOI: 10.3390/cryst7080242] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The present article describes how to use the computer program BLEND to help assemble complete datasets for the solution of macromolecular structures, starting from partial or complete datasets, derived from data collection from multiple crystals. The program is demonstrated on more than two hundred X-ray diffraction datasets obtained from 50 crystals of a complex formed between the SRF transcription factor, its cognate DNA, and a peptide from the SRF cofactor MRTF-A. This structure is currently in the process of being fully solved. While full details of the structure are not yet available, the repeated application of BLEND on data from this structure, as they have become available, has made it possible to produce electron density maps clear enough to visualise the potential location of MRTF sequences.
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Affiliation(s)
- Anastasia Mylona
- Signalling and Transcription Laboratory, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stephen Carr
- Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford OX11 0FA, UK
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Pierre Aller
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Isabel Moraes
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Richard Treisman
- Signalling and Transcription Laboratory, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Gwyndaf Evans
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - James Foadi
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
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12
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Zeng C, Mulas F, Sui Y, Guan T, Miller N, Tan Y, Liu F, Jin W, Carrano AC, Huising MO, Shirihai OS, Yeo GW, Sander M. Pseudotemporal Ordering of Single Cells Reveals Metabolic Control of Postnatal β Cell Proliferation. Cell Metab 2017; 25:1160-1175.e11. [PMID: 28467932 PMCID: PMC5501713 DOI: 10.1016/j.cmet.2017.04.014] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 02/28/2017] [Accepted: 04/13/2017] [Indexed: 01/28/2023]
Abstract
Pancreatic β cell mass for appropriate blood glucose control is established during early postnatal life. β cell proliferative capacity declines postnatally, but the extrinsic cues and intracellular signals that cause this decline remain unknown. To obtain a high-resolution map of β cell transcriptome dynamics after birth, we generated single-cell RNA-seq data of β cells from multiple postnatal time points and ordered cells based on transcriptional similarity using a new analytical tool. This analysis captured signatures of immature, proliferative β cells and established high expression of amino acid metabolic, mitochondrial, and Srf/Jun/Fos transcription factor genes as their hallmark feature. Experimental validation revealed high metabolic activity in immature β cells and a role for reactive oxygen species and Srf/Jun/Fos transcription factors in driving postnatal β cell proliferation and mass expansion. Our work provides the first high-resolution molecular characterization of state changes in postnatal β cells and paves the way for the identification of novel therapeutic targets to stimulate β cell regeneration.
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Affiliation(s)
- Chun Zeng
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Francesca Mulas
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yinghui Sui
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Tiffany Guan
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nathanael Miller
- Departments of Medicine and Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA; Department of Medicine, Boston University, School of Medicine, Boston, MA 02118, USA
| | - Yuliang Tan
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Fenfen Liu
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wen Jin
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Andrea C Carrano
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mark O Huising
- Department of Neurobiology, Physiology & Behavior, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Orian S Shirihai
- Departments of Medicine and Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA; Department of Medicine, Boston University, School of Medicine, Boston, MA 02118, USA
| | - Gene W Yeo
- Department of Cellular & Molecular Medicine and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Maike Sander
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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13
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Rizzo F, Coffman JA, Arnone MI. An Elk transcription factor is required for Runx-dependent survival signaling in the sea urchin embryo. Dev Biol 2016; 416:173-186. [PMID: 27235147 DOI: 10.1016/j.ydbio.2016.05.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/23/2016] [Accepted: 05/23/2016] [Indexed: 12/20/2022]
Abstract
Elk proteins are Ets family transcription factors that regulate cell proliferation, survival, and differentiation in response to ERK (extracellular-signal regulated kinase)-mediated phosphorylation. Here we report the embryonic expression and function of Sp-Elk, the single Elk gene of the sea urchin Strongylocentrotus purpuratus. Sp-Elk is zygotically expressed throughout the embryo beginning at late cleavage stage, with peak expression occurring at blastula stage. Morpholino antisense-mediated knockdown of Sp-Elk causes blastula-stage developmental arrest and embryo disintegration due to apoptosis, a phenotype that is rescued by wild-type Elk mRNA. Development is also rescued by Elk mRNA encoding a serine to aspartic acid substitution (S402D) that mimics ERK-mediated phosphorylation of a conserved site that enhances DNA binding, but not by Elk mRNA encoding an alanine substitution at the same site (S402A). This demonstrates both that the apoptotic phenotype of the morphants is specifically caused by Elk depletion, and that phosphorylation of serine 402 of Sp-Elk is critical for its anti-apoptotic function. Knockdown of Sp-Elk results in under-expression of several regulatory genes involved in cell fate specification, cell cycle control, and survival signaling, including the transcriptional regulator Sp-Runt-1 and its target Sp-PKC1, both of which were shown previously to be required for cell survival during embryogenesis. Both Sp-Runt-1 and Sp-PKC1 have sequences upstream of their transcription start sites that specifically bind Sp-Elk. These results indicate that Sp-Elk is the signal-dependent activator of a feed-forward gene regulatory circuit, consisting also of Sp-Runt-1 and Sp-PKC1, which actively suppresses apoptosis in the early embryo.
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Affiliation(s)
- Francesca Rizzo
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli 80121, Italy
| | | | - Maria Ina Arnone
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli 80121, Italy.
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14
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Saxton J, Ferjentsik Z, Ducker C, Johnson AD, Shaw PE. Stepwise evolution of Elk-1 in early deuterostomes. FEBS J 2016; 283:1025-38. [PMID: 26613204 DOI: 10.1111/febs.13607] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 11/16/2015] [Accepted: 11/23/2015] [Indexed: 11/29/2022]
Abstract
Metazoans have multiple ETS paralogues with overlapping or indiscriminate biological functions. Elk-1, one of three mammalian ternary complex factors (TCFs), is a well-conserved, ETS domain-containing transcriptional regulator of mitogen-responsive genes that operates in concert with serum response factor (SRF). Nonetheless, its genetic role remains unresolved because the elk-1 gene could be deleted from the mouse genome seemingly without adverse effect. Here we have explored the evolution of Elk-1 to gain insight into its conserved biological role. We identified antecedent Elk-1 proteins in extant early metazoans and used amino acid sequence alignments to chart the appearance of domains characteristic of human Elk-1. We then performed biochemical studies to determine whether putative domains apparent in the Elk-1 protein of a primitive hemichordate were functionally orthologous to those of human Elk-1. Our findings imply the existence of primordial Elk-1 proteins in primitive deuterostomes that could operate as mitogen-responsive ETS transcription factors but not as TCFs. The role of TCF was acquired later, but presumably prior to the whole genome duplications in the basal vertebrate lineage. Thus its evolutionary origins link Elk-1 to the appearance of mesoderm.
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Affiliation(s)
- Janice Saxton
- School of Life Sciences, University of Nottingham, UK
| | | | | | | | - Peter E Shaw
- School of Life Sciences, University of Nottingham, UK
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15
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Buffet C, Catelli MG, Hecale-Perlemoine K, Bricaire L, Garcia C, Gallet-Dierick A, Rodriguez S, Cormier F, Groussin L. Dual Specificity Phosphatase 5, a Specific Negative Regulator of ERK Signaling, Is Induced by Serum Response Factor and Elk-1 Transcription Factor. PLoS One 2015; 10:e0145484. [PMID: 26691724 PMCID: PMC4687125 DOI: 10.1371/journal.pone.0145484] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 10/29/2015] [Indexed: 12/11/2022] Open
Abstract
Serum stimulation of mammalian cells induces, via the MAPK pathway, the nuclear protein DUSP5 (dual-specificity phosphatase 5), which specifically interacts with and inactivates the ERK1/2 MAP kinases. However, molecular mechanisms underlying DUSP5 induction are not well known. Here, we found that the DUSP5 mRNA induction depends on a transcriptional regulation by the MAPK pathway, without any modification of the mRNA stability. Two contiguous CArG boxes that bind serum response factor (SRF) were found in a 1 Kb promoter region, as well as several E twenty-six transcription factor family binding sites (EBS). These sites potentially bind Elk-1, a transcription factor activated by ERK1/2. Using wild type or mutated DUSP5 promoter reporters, we demonstrated that SRF plays a crucial role in serum induction of DUSP5 promoter activity, the proximal CArG box being important for SRF binding in vitro and in living cells. Moreover, in vitro and in vivo binding data of Elk-1 to the same promoter region further demonstrate a role for Elk-1 in the transcriptional regulation of DUSP5. SRF and Elk-1 form a ternary complex (Elk-1-SRF-DNA) on DUSP5 promoter, consequently providing a link to an important negative feedback tightly regulating phosphorylated ERK levels.
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Affiliation(s)
- Camille Buffet
- Endocrinology-Metabolism-Diabetes Department, Institut Cochin, Université Paris Descartes, CNRS (UMR8104), INSERM U1016, Paris, France
| | - Maria-Grazia Catelli
- Endocrinology-Metabolism-Diabetes Department, Institut Cochin, Université Paris Descartes, CNRS (UMR8104), INSERM U1016, Paris, France
| | - Karine Hecale-Perlemoine
- Endocrinology-Metabolism-Diabetes Department, Institut Cochin, Université Paris Descartes, CNRS (UMR8104), INSERM U1016, Paris, France
| | - Léopoldine Bricaire
- Endocrinology-Metabolism-Diabetes Department, Institut Cochin, Université Paris Descartes, CNRS (UMR8104), INSERM U1016, Paris, France
| | - Camille Garcia
- Endocrinology-Metabolism-Diabetes Department, Institut Cochin, Université Paris Descartes, CNRS (UMR8104), INSERM U1016, Paris, France
| | - Anne Gallet-Dierick
- Endocrinology-Metabolism-Diabetes Department, Institut Cochin, Université Paris Descartes, CNRS (UMR8104), INSERM U1016, Paris, France
| | - Stéphanie Rodriguez
- Endocrinology-Metabolism-Diabetes Department, Institut Cochin, Université Paris Descartes, CNRS (UMR8104), INSERM U1016, Paris, France
| | - Françoise Cormier
- Endocrinology-Metabolism-Diabetes Department, Institut Cochin, Université Paris Descartes, CNRS (UMR8104), INSERM U1016, Paris, France
| | - Lionel Groussin
- Endocrinology-Metabolism-Diabetes Department, Institut Cochin, Université Paris Descartes, CNRS (UMR8104), INSERM U1016, Paris, France
- Department of Endocrinology, Cochin Hospital, Paris, France
- * E-mail:
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16
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Xia M, Erickson A, Yi X, Moreau R. Mapping the response of human fibroblast growth factor 21 (FGF21) promoter to serum availability and lipoic acid in HepG2 hepatoma cells. Biochim Biophys Acta Gen Subj 2015; 1860:498-507. [PMID: 26691139 DOI: 10.1016/j.bbagen.2015.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/23/2015] [Accepted: 12/11/2015] [Indexed: 12/15/2022]
Abstract
The hormone-like polypeptide, fibroblast growth factor 21 (FGF21), is a major modulator of lipid and glucose metabolism and an exploratory treatment strategy for obesity related metabolic disorders. The costs of recombinant FGF21 and mode of delivery by injection are important constraints to its wide therapeutic use. The stimulation of endogenous FGF21 production through diet is being explored as an alternative approach. To that end, we examined the mechanism(s) by which serum manipulation and lipoic acid (a dietary activator of FGF21) induce FGF21 in human hepatocellular carcinoma HepG2 cells. Serum withdrawal markedly induced FGF21 mRNA levels (88 fold) and FGF21 secreted in the media (19 fold). Lipoic acid induced FGF21 mRNA 7 fold above DMSO-treated control cells and FGF21 secretion 3 fold. These effects were several-fold greater than those of PPARα agonist, Wy14643, which failed to induce FGF21 above and beyond the induction seen with serum withdrawal. The use of transcription inhibitor, actinomycin D, revealed that de novo mRNA synthesis drives FGF21 secretion in response to serum starvation. Four previously unrecognized loci in FGF21 promoter were nucleosome depleted and enriched in acetylated histone H3 revealing their role as transcriptional enhancers and putative transcription factor binding sites. FGF21 did not accumulate to a significant degree in induced HepG2 cells, which secreted FGF21 time dependently in media. We conclude that lipoic acid cell signaling connects with the transcriptional upregulation of FGF21 and it may prove to be a safe and affordable means to stimulate FGF21 production.
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Affiliation(s)
- Mengna Xia
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Anjeza Erickson
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Xiaohua Yi
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Régis Moreau
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA.
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17
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Liu M, Gao W, van Velkinburgh JC, Wu Y, Ni B, Tian Y. Role of Ets Proteins in Development, Differentiation, and Function of T-Cell Subsets. Med Res Rev 2015; 36:193-220. [PMID: 26301869 DOI: 10.1002/med.21361] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 07/12/2015] [Accepted: 07/23/2015] [Indexed: 12/18/2022]
Abstract
Through positive selection, double-positive cells in the thymus differentiate into CD4(+) or CD8(+) T single-positive cells that subsequently develop into different types of effective T cells, such as T-helper and cytotoxic T lymphocyte cells, that play distinctive roles in the immune system. Development, differentiation, and function of thymocytes and CD4(+) and CD8(+) T cells are controlled by a multitude of secreted and intracellular factors, ranging from cytokine signaling modules to transcription factors and epigenetic modifiers. Members of the E26 transformation specific (Ets) family of transcription factors, in particular, are potent regulators of these CD4(+) or CD8(+) T-cell processes. In this review, we summarize and discuss the functions and underlying mechanisms of the Ets family members that have been characterized as involved in these processes. Ongoing research of these factors is expected to identify practical applications for the Ets family members as novel therapeutic targets for inflammation-related diseases.
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Affiliation(s)
- Mian Liu
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, 400038, P.R. China.,Battalion 10 of Cadet Brigade, Third Military Medical University, Chongqing, 400038, P.R. China
| | - Weiwu Gao
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, 400038, P.R. China
| | | | - Yuzhang Wu
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, 400038, P.R. China
| | - Bing Ni
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, 400038, P.R. China
| | - Yi Tian
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, 400038, P.R. China
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18
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He Y, Chen Y, Mooney SM, Rajagopalan K, Bhargava A, Sacho E, Weninger K, Bryan PN, Kulkarni P, Orban J. Phosphorylation-induced Conformational Ensemble Switching in an Intrinsically Disordered Cancer/Testis Antigen. J Biol Chem 2015; 290:25090-102. [PMID: 26242913 DOI: 10.1074/jbc.m115.658583] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Indexed: 11/06/2022] Open
Abstract
Prostate-associated gene 4 (PAGE4) is an intrinsically disordered cancer/testis antigen that is up-regulated in the fetal and diseased human prostate. Knocking down PAGE4 expression results in cell death, whereas its overexpression leads to a growth advantage of prostate cancer cells (Zeng, Y., He, Y., Yang, F., Mooney, S. M., Getzenberg, R. H., Orban, J., and Kulkarni, P. (2011) The cancer/testis antigen prostate-associated gene 4 (PAGE4) is a highly intrinsically disordered protein. J. Biol. Chem. 286, 13985-13994). Phosphorylation of PAGE4 at Thr-51 is critical for potentiating c-Jun transactivation, an important factor in controlling cell growth, apoptosis, and stress response. Using NMR spectroscopy, we show that the PAGE4 polypeptide chain has local and long-range conformational preferences that are perturbed by site-specific phosphorylation at Thr-51. The population of transient turn-like structures increases upon phosphorylation in an ∼20-residue acidic region centered on Thr-51. This central region therefore becomes more compact and more negatively charged, with increasing intramolecular contacts to basic sequence motifs near the N and C termini. Although flexibility is decreased in the central region of phospho-PAGE4, the polypeptide chain remains highly dynamic overall. PAGE4 utilizes a transient helical structure adjacent to the central acidic region to bind c-Jun with low affinity in vitro. The binding interaction is attenuated by phosphorylation at Thr-51, most likely because of masking the effects of the more compact phosphorylated state. Therefore, phosphorylation of PAGE4 leads to conformational shifts in the dynamic ensemble, with large functional consequences. The changes in the structural ensemble induced by posttranslational modifications are similar conceptually to the conformational switching events seen in some marginally stable ("metamorphic") folded proteins in response to mutation or environmental triggers.
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Affiliation(s)
- Yanan He
- From the W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, the Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| | - Yihong Chen
- From the W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, the Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| | - Steven M Mooney
- the Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Krithika Rajagopalan
- the Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Ajay Bhargava
- Shakti BioResearch, Woodbridge, Connecticut 06525, and
| | - Elizabeth Sacho
- the Department of Physics, North Carolina State University, Raleigh, North Carolina 27695
| | - Keith Weninger
- the Department of Physics, North Carolina State University, Raleigh, North Carolina 27695
| | - Philip N Bryan
- From the W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850
| | - Prakash Kulkarni
- the Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287,
| | - John Orban
- From the W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, the Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742,
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19
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Chevigny M, Guérin-Montpetit K, Vargas A, Lefebvre-Lavoie J, Lavoie JP. Contribution of SRF, Elk-1, and myocardin to airway smooth muscle remodeling in heaves, an asthma-like disease of horses. Am J Physiol Lung Cell Mol Physiol 2015; 309:L37-45. [PMID: 25979077 DOI: 10.1152/ajplung.00050.2015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 05/11/2015] [Indexed: 12/28/2022] Open
Abstract
Myocyte hyperplasia and hypertrophy contribute to the increased mass of airway smooth muscle (ASM) in asthma. Serum-response factor (SRF) is a transcription factor that regulates myocyte differentiation in vitro in vascular and intestinal smooth muscles. When SRF is associated with phosphorylated (p)Elk-1, it promotes ASM proliferation while binding to myocardin (MYOCD) leading to the expression of contractile elements in these tissues. The objective of this study was therefore to characterize the expression of SRF, pElk-1, and MYOCD in ASM cells from central and peripheral airways in heaves, a spontaneously occurring asthma-like disease of horses, and in controls. Six horses with heaves and five aged-matched controls kept in the same environment were studied. Nuclear protein expression of SRF, pElk-1, and MYOCD was evaluated in peripheral airways and endobronchial biopsies obtained during disease remission and after 1 and 30 days of naturally occurring antigenic exposure using immunohistochemistry and immunofluorescence techniques. Nuclear expression of SRF (P = 0.03, remission vs. 30 days) and MYOCD (P = 0.05, controls vs. heaves at 30 days) increased in the peripheral airways of horses with heaves during disease exacerbation, while MYOCD (P = 0.04, remission vs. 30 days) decreased in the central airways of control horses. No changes were observed in the expression of pElk-1 protein in either tissue. In conclusion, SRF and its cofactor MYOCD likely contribute to the hypertrophy of peripheral ASM observed in equine asthmatic airways, while the remodeling of the central airways is more static or involves different transcription factors.
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Affiliation(s)
- Mylène Chevigny
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
| | - Karine Guérin-Montpetit
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
| | - Amandine Vargas
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
| | - Josiane Lefebvre-Lavoie
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
| | - Jean-Pierre Lavoie
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
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20
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Profantová B, Coïc YM, Profant V, Štěpánek J, Kopecký V, Turpin PY, Alpert B, Zentz C. Organization of the MADS box from human SRF revealed by tyrosine perturbation. J Phys Chem B 2015; 119:1793-801. [PMID: 25558766 DOI: 10.1021/jp508897p] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
MADS box family transcription factors are involved in signal transduction and development control through DNA specific sequence recognition. The DNA binding domain of these proteins contains a conservative 55-60 amino acid sequence which defines the membership of this large family. Here we present a thorough study of the MADS segment of serum response factor (MADS(SRF)). Fluorescence, UV-absorption, and Raman spectroscopy studies were performed in order to disclose its behavior and basic functional properties in an aqueous environment. The secondary structure of MADS(SRF) estimated by analysis of Raman spectra and supported by CD has revealed only the C-terminal part as homologous with those of free core-SRF, while the N-terminal part has lost the stable α-helical structure found in both the free core-SRF and its specific complex with DNA. The three tyrosine residues of the MADS(SRF) were used as spectroscopic inner probes. The effect of environmental conditions, especially pH variations and addition of variously charged quenchers, on their spectra was examined. Two-component fluorescence quenching was revealed using factor analysis and corresponding Stern-Volmer constants determined. Factor analysis of absorbance and fluorescence pH titration led to determination of three dissociation constants pKa1 = 6.4 ± 0.2, pKa2 = 7.3 ± 0.2, and pKa3 = 9.6 ± 0.6. Critical comparison of all experiments identified the deprotonation of His193 hydrogen bonded to Tyr195 as a candidate for pKa1 (and that of Tyr158 as a candidate for pKa2). Within MADS(SRF), His193 is a key intermediary between the N-terminal primary DNA binding element and the hydrophobic C-terminal protein dimerization element.
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Affiliation(s)
- Barbora Profantová
- Lab. Jean Perrin, CNRS UMR 8237, UPMC Université Paris 6 , 4 place Jussieu, 75252 Paris Cedex 05, France
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21
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Puranik S, Acajjaoui S, Conn S, Costa L, Conn V, Vial A, Marcellin R, Melzer R, Brown E, Hart D, Theißen G, Silva CS, Parcy F, Dumas R, Nanao M, Zubieta C. Structural basis for the oligomerization of the MADS domain transcription factor SEPALLATA3 in Arabidopsis. THE PLANT CELL 2014; 26:3603-15. [PMID: 25228343 PMCID: PMC4213154 DOI: 10.1105/tpc.114.127910] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 08/20/2014] [Accepted: 08/29/2014] [Indexed: 05/19/2023]
Abstract
In plants, MADS domain transcription factors act as central regulators of diverse developmental pathways. In Arabidopsis thaliana, one of the most central members of this family is SEPALLATA3 (SEP3), which is involved in many aspects of plant reproduction, including floral meristem and floral organ development. SEP3 has been shown to form homo and heterooligomeric complexes with other MADS domain transcription factors through its intervening (I) and keratin-like (K) domains. SEP3 function depends on its ability to form specific protein-protein complexes; however, the atomic level determinants of oligomerization are poorly understood. Here, we report the 2.5-Å crystal structure of a small portion of the intervening and the complete keratin-like domain of SEP3. The domains form two amphipathic alpha helices separated by a rigid kink, which prevents intramolecular association and presents separate dimerization and tetramerization interfaces comprising predominantly hydrophobic patches. Mutations to the tetramerization interface demonstrate the importance of highly conserved hydrophobic residues for tetramer stability. Atomic force microscopy was used to show SEP3-DNA interactions and the role of oligomerization in DNA binding and conformation. Based on these data, the oligomerization patterns of the larger family of MADS domain transcription factors can be predicted and manipulated based on the primary sequence.
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Affiliation(s)
- Sriharsha Puranik
- European Synchrotron Radiation Facility, Structural Biology Group, 38042 Grenoble, France
| | - Samira Acajjaoui
- European Synchrotron Radiation Facility, Structural Biology Group, 38042 Grenoble, France
| | - Simon Conn
- Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide SA 5000, Australia
| | - Luca Costa
- European Synchrotron Radiation Facility, Structural Biology Group, 38042 Grenoble, France
| | - Vanessa Conn
- Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide SA 5000, Australia
| | - Anthony Vial
- European Synchrotron Radiation Facility, Structural Biology Group, 38042 Grenoble, France
| | - Romain Marcellin
- European Synchrotron Radiation Facility, Structural Biology Group, 38042 Grenoble, France Faculté des Sciences de Montpellier, place Eugène Bataillon, 34095 Montpellier, France
| | - Rainer Melzer
- Department of Genetics, Friedrich Schiller University, 07737 Jena, Germany
| | - Elizabeth Brown
- European Synchrotron Radiation Facility, Structural Biology Group, 38042 Grenoble, France
| | - Darren Hart
- Université Grenoble Alpes, CNRS, Integrated Structural Biology Grenoble, Unit of Virus Host Cell Interactions, Unité Mixte Internationale 3265 (CNRS-EMBL-UJF), UMS 3518 (CNRS-CEA-UJF-EMBL), 38042 Grenoble, France
| | - Günter Theißen
- Department of Genetics, Friedrich Schiller University, 07737 Jena, Germany
| | - Catarina S Silva
- CNRS, Laboratoire de Physiologie Cellulaire and Végétale, UMR 5168, 38054 Grenoble, France Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire et Végétale, F-38054 Grenoble, France Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Physiologie Cellulaire et Végétale, F-38054 Grenoble, France INRA, Laboratoire de Physiologie Cellulaire et Végétale, USC1359, F-38054 Grenoble, France
| | - François Parcy
- CNRS, Laboratoire de Physiologie Cellulaire and Végétale, UMR 5168, 38054 Grenoble, France Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire et Végétale, F-38054 Grenoble, France Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Physiologie Cellulaire et Végétale, F-38054 Grenoble, France INRA, Laboratoire de Physiologie Cellulaire et Végétale, USC1359, F-38054 Grenoble, France
| | - Renaud Dumas
- CNRS, Laboratoire de Physiologie Cellulaire and Végétale, UMR 5168, 38054 Grenoble, France Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire et Végétale, F-38054 Grenoble, France Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Physiologie Cellulaire et Végétale, F-38054 Grenoble, France INRA, Laboratoire de Physiologie Cellulaire et Végétale, USC1359, F-38054 Grenoble, France
| | - Max Nanao
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, France Unit for Virus Host-Cell Interactions, Université Grenoble Alpes-EMBL-CNRS, 38042 Grenoble, France
| | - Chloe Zubieta
- CNRS, Laboratoire de Physiologie Cellulaire and Végétale, UMR 5168, 38054 Grenoble, France Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire et Végétale, F-38054 Grenoble, France Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Physiologie Cellulaire et Végétale, F-38054 Grenoble, France INRA, Laboratoire de Physiologie Cellulaire et Végétale, USC1359, F-38054 Grenoble, France
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22
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Shrivastava T, Mino K, Babayeva ND, Baranovskaya OI, Rizzino A, Tahirov TH. Structural basis of Ets1 activation by Runx1. Leukemia 2014; 28:2040-8. [PMID: 24646888 PMCID: PMC4169772 DOI: 10.1038/leu.2014.111] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 03/11/2014] [Accepted: 03/13/2014] [Indexed: 11/23/2022]
Abstract
Runx1 is required for definitive hematopoiesis and is well-known for its frequent chromosomal translocations and point mutations in leukemia. Runx1 regulates a variety of genes via Ets1 activation on an Ets1•Runx1 composite DNA sequence. The structural basis of such regulation remains unresolved. To address this problem, we determined the crystal structure of the ternary complex containing Runx11-242 and Ets1296-441 bound to T cell receptor alpha (TCRα) enhancer DNA. In the crystal, an Ets1-interacting domain of Runx1 is bound to the Ets1 DNA-binding domain and displaced an entire autoinhibitory module of Ets1, revealing a novel mechanism of Ets1 activation. The DNA binding and transcriptional studies with a variety of structure-guided Runx1 mutants confirmed a critical role of direct Ets1•Runx1 interaction in Ets1 activation. More importantly, the discovered mechanism provides a plausible explanation for how the Ets1•Runx1 interaction effectively activates not only a wild-type Ets1, but also a highly inhibited phosphorylated form of Ets1.
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Affiliation(s)
- T Shrivastava
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - K Mino
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - N D Babayeva
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - O I Baranovskaya
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - A Rizzino
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - T H Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
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23
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Profantová B, Profant V, Zíma V, Kopecký V, Bednárová L, Zentz C, Baumruk V, Turpin PY, Štěpánek J. Protonation Effect of Tyrosine in a Segment of the SRF Transcription Factor: A Combined Optical Spectroscopy, Molecular Dynamics, and Density Functional Theory Calculation Study. J Phys Chem B 2013; 117:16086-95. [DOI: 10.1021/jp4099864] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Barbora Profantová
- Institute
of Physics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
- Laboratoire
Jean Perrin, FRE 3231, Université Pierre et Marie Curie, place Jussieu 4, 75252 Paris CEDEX 5, France
| | - Václav Profant
- Institute
of Physics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
| | - Vlastimil Zíma
- Institute
of Physics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
| | - Vladimír Kopecký
- Institute
of Physics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
| | - Lucie Bednárová
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Christian Zentz
- ER12, Université Pierre et Marie Curie, Place Jussieu 4, 75252 Paris CEDEX 5, France
| | - Vladimír Baumruk
- Institute
of Physics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
| | - Pierre-Yves Turpin
- Laboratoire
Jean Perrin, FRE 3231, Université Pierre et Marie Curie, place Jussieu 4, 75252 Paris CEDEX 5, France
| | - Josef Štěpánek
- Institute
of Physics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
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24
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Munde M, Poon GMK, Wilson WD. Probing the electrostatics and pharmacological modulation of sequence-specific binding by the DNA-binding domain of the ETS family transcription factor PU.1: a binding affinity and kinetics investigation. J Mol Biol 2013; 425:1655-69. [PMID: 23416556 DOI: 10.1016/j.jmb.2013.02.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 02/07/2013] [Indexed: 10/27/2022]
Abstract
Members of the ETS family of transcription factors regulate a functionally diverse array of genes. All ETS proteins share a structurally conserved but sequence-divergent DNA-binding domain, known as the ETS domain. Although the structure and thermodynamics of the ETS-DNA complexes are well known, little is known about the kinetics of sequence recognition, a facet that offers potential insight into its molecular mechanism. We have characterized DNA binding by the ETS domain of PU.1 by biosensor-surface plasmon resonance (SPR). SPR analysis revealed a striking kinetic profile for DNA binding by the PU.1 ETS domain. At low salt concentrations, it binds high-affinity cognate DNA with a very slow association rate constant (≤10(5)M(-)(1)s(-)(1)), compensated by a correspondingly small dissociation rate constant. The kinetics are strongly salt dependent but mutually balance to produce a relatively weak dependence in the equilibrium constant. This profile contrasts sharply with reported data for other ETS domains (e.g., Ets-1, TEL) for which high-affinity binding is driven by rapid association (>10(7)M(-)(1)s(-)(1)). We interpret this difference in terms of the hydration properties of ETS-DNA binding and propose that at least two mechanisms of sequence recognition are employed by this family of DNA-binding domain. Additionally, we use SPR to demonstrate the potential for pharmacological inhibition of sequence-specific ETS-DNA binding, using the minor groove-binding distamycin as a model compound. Our work establishes SPR as a valuable technique for extending our understanding of the molecular mechanisms of ETS-DNA interactions as well as developing potential small-molecule agents for biotechnological and therapeutic purposes.
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Affiliation(s)
- Manoj Munde
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
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25
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Poon GMK. DNA Binding Regulates the Self-Association of the ETS Domain of PU.1 in a Sequence-Dependent Manner. Biochemistry 2012; 51:4096-107. [DOI: 10.1021/bi300331v] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Gregory M. K. Poon
- Department of Pharmaceutical
Sciences, Washington State University,
Pullman, Washington 99164-6534, United States
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26
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Odrowaz Z, Sharrocks AD. ELK1 uses different DNA binding modes to regulate functionally distinct classes of target genes. PLoS Genet 2012; 8:e1002694. [PMID: 22589737 PMCID: PMC3349735 DOI: 10.1371/journal.pgen.1002694] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 03/22/2012] [Indexed: 12/13/2022] Open
Abstract
Eukaryotic transcription factors are grouped into families and, due to their similar DNA binding domains, often have the potential to bind to the same genomic regions. This can lead to redundancy at the level of DNA binding, and mechanisms are required to generate specific functional outcomes that enable distinct gene expression programmes to be controlled by a particular transcription factor. Here we used ChIP–seq to uncover two distinct binding modes for the ETS transcription factor ELK1. In one mode, other ETS transcription factors can bind regulatory regions in a redundant fashion; in the second, ELK1 binds in a unique fashion to another set of genomic targets. Each binding mode is associated with different binding site features and also distinct regulatory outcomes. Furthermore, the type of binding mode also determines the control of functionally distinct subclasses of genes and hence the phenotypic response elicited. This is demonstrated for the unique binding mode where a novel role for ELK1 in controlling cell migration is revealed. We have therefore uncovered an unexpected link between the type of binding mode employed by a transcription factor, the subsequent gene regulatory mechanisms used, and the functional categories of target genes controlled. One of the major outstanding questions in eukaryotic gene regulation is how transcription factors with seemingly very similar DNA binding specificities elicit specific biological responses. The ETS transcription factor family provides a paradigm for investigating this phenomenon. Here, we have focused on the ETS transcription factor ELK1, and by combining genome-wide binding analysis coupled with gene expression analysis we have dissected two distinct gene regulatory activities for this transcription factor. In each of these regulatory modes, ELK1 exhibits distinct DNA binding characteristics which correlate with either positive or negative transcriptional activities and give rise to functionally distinct gene expression programmes. We demonstrate a novel function for ELK1 in controlling cell migration through one of these regulatory modes. Thus, we have demonstrated a clear link between the types of regulatory region bound by a transcription factor and its ability to control gene expression (i.e. in a positive or negative manner) and the functional downstream consequences of its target gene cohort. This work has implications for understanding how members of other multi-protein transcription factor families might function to generate different downstream functional consequences through engaging with different types of regulatory regions.
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Affiliation(s)
| | - Andrew D. Sharrocks
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail:
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27
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Hollenhorst PC, McIntosh LP, Graves BJ. Genomic and biochemical insights into the specificity of ETS transcription factors. Annu Rev Biochem 2011; 80:437-71. [PMID: 21548782 DOI: 10.1146/annurev.biochem.79.081507.103945] [Citation(s) in RCA: 365] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
ETS proteins are a group of evolutionarily related, DNA-binding transcriptional factors. These proteins direct gene expression in diverse normal and disease states by binding to specific promoters and enhancers and facilitating assembly of other components of the transcriptional machinery. The highly conserved DNA-binding ETS domain defines the family and is responsible for specific recognition of a common sequence motif, 5'-GGA(A/T)-3'. Attaining specificity for biological regulation in such a family is thus a conundrum. We present the current knowledge of routes to functional diversity and DNA binding specificity, including divergent properties of the conserved ETS and PNT domains, the involvement of flanking structured and unstructured regions appended to these dynamic domains, posttranslational modifications, and protein partnerships with other DNA-binding proteins and coregulators. The review emphasizes recent advances from biochemical and biophysical approaches, as well as insights from genomic studies that detect ETS-factor occupancy in living cells.
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Affiliation(s)
- Peter C Hollenhorst
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana 47405, USA.
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28
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Fuxreiter M, Simon I, Bondos S. Dynamic protein-DNA recognition: beyond what can be seen. Trends Biochem Sci 2011; 36:415-23. [PMID: 21620710 DOI: 10.1016/j.tibs.2011.04.006] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2011] [Revised: 04/15/2011] [Accepted: 04/15/2011] [Indexed: 12/28/2022]
Abstract
Traditionally, specific DNA recognition is thought to rely on static contacts with the bases or phosphates. Recent results, however, indicate that residues far outside the binding context can crucially influence selectivity or binding affinity via transient, dynamic interactions with the DNA binding interface. These regions usually do not adopt a well-defined structure, even when bound to DNA, and thus form a fuzzy complex. Here, we propose the existence of a dynamic DNA readout mechanism, wherein distant segments modulate conformational preferences, flexibility or spacing of the DNA binding motifs or serve as competitive partners. Despite their low sequence similarity, these intrinsically disordered regions are often conserved at the structural level, and exploited for regulation of the transcription machinery via protein-protein interactions, post-translational modifications or alternative splicing.
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Affiliation(s)
- Monika Fuxreiter
- Department of Biological Chemistry, Weizmann Institute of Science, 7600 Rehovot, Israel.
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29
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Evans EL, Saxton J, Shelton SJ, Begitt A, Holliday ND, Hipskind RA, Shaw PE. Dimer formation and conformational flexibility ensure cytoplasmic stability and nuclear accumulation of Elk-1. Nucleic Acids Res 2011; 39:6390-402. [PMID: 21543455 PMCID: PMC3159454 DOI: 10.1093/nar/gkr266] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The ETS (E26) protein Elk-1 serves as a paradigm for mitogen-responsive transcription factors. It is multiply phosphorylated by mitogen-activated protein kinases (MAPKs), which it recruits into pre-initiation complexes on target gene promoters. However, events preparatory to Elk-1 phosphorylation are less well understood. Here, we identify two novel, functional elements in Elk-1 that determine its stability and nuclear accumulation. One element corresponds to a dimerization interface in the ETS domain and the second is a cryptic degron adjacent to the serum response factor (SRF)-interaction domain that marks dimerization-defective Elk-1 for rapid degradation by the ubiquitin–proteasome system. Dimerization appears to be crucial for Elk-1 stability only in the cytoplasm, as latent Elk-1 accumulates in the nucleus and interacts dynamically with DNA as a monomer. These findings define a novel role for the ETS domain of Elk-1 and demonstrate that nuclear accumulation of Elk-1 involves conformational flexibility prior to its phosphorylation by MAPKs.
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Affiliation(s)
- Emma L Evans
- School of Biomedical Sciences, Queen's Medical Centre, Nottingham, NG7 2UH, UK
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30
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Majesky MW, Dong XR, Regan JN, Hoglund VJ. Vascular smooth muscle progenitor cells: building and repairing blood vessels. Circ Res 2011; 108:365-77. [PMID: 21293008 DOI: 10.1161/circresaha.110.223800] [Citation(s) in RCA: 149] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Molecular pathways that control the specification, migration, and number of available smooth muscle progenitor cells play key roles in determining blood vessel size and structure, capacity for tissue repair, and progression of age-related disorders. Defects in these pathways produce malformations of developing blood vessels, depletion of smooth muscle progenitor cell pools for vessel wall maintenance and repair, and aberrant activation of alternative differentiation pathways in vascular disease. A better understanding of the molecular mechanisms that uniquely specify and maintain vascular smooth muscle cell precursors is essential if we are to use advances in stem and progenitor cell biology and somatic cell reprogramming for applications directed to the vessel wall.
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Affiliation(s)
- Mark W Majesky
- Seattle Children's Research Institute, University of Washington, 1900 Ninth Ave, M/S C9S-5, Seattle, WA 98101, USA.
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31
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32
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van Dijk ADJ, van Ham RCHJ. Conserved and variable correlated mutations in the plant MADS protein network. BMC Genomics 2010; 11:607. [PMID: 20979667 PMCID: PMC3017862 DOI: 10.1186/1471-2164-11-607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Accepted: 10/28/2010] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Plant MADS domain proteins are involved in a variety of developmental processes for which their ability to form various interactions is a key requisite. However, not much is known about the structure of these proteins or their complexes, whereas such knowledge would be valuable for a better understanding of their function. Here, we analyze those proteins and the complexes they form using a correlated mutation approach in combination with available structural, bioinformatics and experimental data. RESULTS Correlated mutations are affected by several types of noise, which is difficult to disentangle from the real signal. In our analysis of the MADS domain proteins, we apply for the first time a correlated mutation analysis to a family of interacting proteins. This provides a unique way to investigate the amount of signal that is present in correlated mutations because it allows direct comparison of mutations in various family members and assessing their conservation. We show that correlated mutations in general are conserved within the various family members, and if not, the variability at the respective positions is less in the proteins in which the correlated mutation does not occur. Also, intermolecular correlated mutation signals for interacting pairs of proteins display clear overlap with other bioinformatics data, which is not the case for non-interacting protein pairs, an observation which validates the intermolecular correlated mutations. Having validated the correlated mutation results, we apply them to infer the structural organization of the MADS domain proteins. CONCLUSION Our analysis enables understanding of the structural organization of the MADS domain proteins, including support for predicted helices based on correlated mutation patterns, and evidence for a specific interaction site in those proteins.
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Affiliation(s)
- Aalt DJ van Dijk
- Applied Bioinformatics, PRI, Wageningen UR, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Roeland CHJ van Ham
- Applied Bioinformatics, PRI, Wageningen UR, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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33
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Lee SM, Vasishtha M, Prywes R. Activation and repression of cellular immediate early genes by serum response factor cofactors. J Biol Chem 2010; 285:22036-49. [PMID: 20466732 DOI: 10.1074/jbc.m110.108878] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The induction of expression of many cellular immediate early genes (IEG) involves the transcription factor serum response factor (SRF). Two families of SRF coactivators have also been implicated in IEG induction, the ternary complex factors (TCFs), ELK1, Sap1, and Net, and the myocardin-related factors, MKL1 and MKL2. We found that serum induction of some SRF target genes is preferentially regulated by MKL1/2, whereas others are redundantly activated by both TCFs and MKL1/2. Yet ELK1 can also repress transcription. Binding of ELK1 and MKL1 to SRF has been found to be mutually exclusive in vitro, suggesting that ELK1 could repress expression of IEGs by blocking MKL1 binding. We characterized the in vivo binding of MKL1 and ELK1 to target genes and found an inverse relationship of serum-induced MKL1 binding and serum-decreased ELK1 binding. However, experiments with short hairpin RNA-mediated MKL1/2 depletion and expression of a nuclear MKL1 (N100) variant in stably transfected cells failed to alter ELK1 binding, suggesting that ELK1 binding to target genes is regulated independently of MKL1/2. Nevertheless, we found that short interfering RNA-mediated depletion of TCFs increased target gene expression in cells containing the N100 MKL1 activator, most notably in cells under continuous growth conditions. These results indicate that the TCFs can function both as activators and repressors of target gene expression depending upon the cellular growth conditions.
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Affiliation(s)
- Seung-Min Lee
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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34
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A competitive transcription factor binding mechanism determines the timing of late cell cycle-dependent gene expression. Mol Cell 2010; 38:29-40. [PMID: 20385087 PMCID: PMC3566586 DOI: 10.1016/j.molcel.2010.02.030] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2009] [Revised: 12/10/2009] [Accepted: 02/21/2010] [Indexed: 12/28/2022]
Abstract
Transcriptional control is exerted by the antagonistic activities of activator and repressor proteins. In Saccharomyces cerevisiae, transcription factor complexes containing the MADS box protein Mcm1p are key regulators of cell cycle-dependent transcription at both the G2/M and M/G1 transitions. The homeodomain repressor protein Yox1p acts in a complex with Mcm1p to control the timing of gene expression. Here, we show that Yox1p interacts with Mcm1p through a motif located N terminally to its homeodomain. Yox1p functions as a transcriptional repressor by competing with the forkhead transcription activator protein Fkh2p for binding to Mcm1p through protein-protein interactions at promoters of a subset of Mcm1p-regulated genes. Importantly, this competition is not through binding the same DNA site that is commonly observed. Thus, this study describes a different mechanism for determining the timing of cell cycle-dependent gene expression that involves competition between short peptide motifs in repressor and activator proteins for interaction with a common binding partner.
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35
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Boros J, O’Donnell A, Donaldson IJ, Kasza A, Zeef L, Sharrocks AD. Overlapping promoter targeting by Elk-1 and other divergent ETS-domain transcription factor family members. Nucleic Acids Res 2009; 37:7368-80. [PMID: 19789270 PMCID: PMC2794171 DOI: 10.1093/nar/gkp804] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 09/10/2009] [Accepted: 09/11/2009] [Indexed: 01/07/2023] Open
Abstract
ETS-domain transcription factors play important roles in controlling gene expression in a variety of different contexts; however, these proteins bind to very similar sites and it is unclear how in vivo specificity is achieved. In silico analysis is unlikely to reveal specific targets for individual family members and direct experimental approaches are therefore required. Here, we take advantage of an inducible dominant-negative expression system to identify a group of novel target genes for the ETS-domain transcription factor Elk-1. Elk-1 is thought to mainly function through cooperation with a second transcription factor SRF, but the targets we identify are largely SRF-independent. Furthermore, we demonstrate that there is a high degree of overlapping, cell type-specific, target gene binding by Elk-1 and other ETS-domain transcription factors. Our results are therefore consistent with the notion that there is a high degree of functional redundancy in target gene regulation by ETS-domain transcription factors in addition to the specific target gene regulation that can be dictated through heterotypic interactions exemplified by the Elk-1-SRF complex.
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Affiliation(s)
| | | | | | | | | | - Andrew D. Sharrocks
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
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36
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Blaker AL, Taylor JM, Mack CP. PKA-dependent phosphorylation of serum response factor inhibits smooth muscle-specific gene expression. Arterioscler Thromb Vasc Biol 2009; 29:2153-60. [PMID: 19778940 DOI: 10.1161/atvbaha.109.197285] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE Our goal was to identify phosphorylation sites that regulate serum response factor (SRF) activity to gain a better understanding of the signaling mechanisms that regulate SRF's involvement in smooth muscle cell (SMC)-specific and early response gene expression. METHODS AND RESULTS By screening phosphorylation-deficient and mimetic mutations in SRF(-/-) embryonic stem cells, we identified T159 as a phosphorylation site that significantly inhibits SMC-specific gene expression in an embryonic stem cell model of SMC differentiation. This residue conforms to a highly conserved consensus cAMP-dependent protein kinase (PKA) site, and in vitro and in vivo labeling studies demonstrated that it was phosphorylated by PKA. Results from gel shift and chromatin immunoprecipitation assays demonstrated that T159 phosphorylation inhibited SRF binding to SMC-specific CArG elements. Interestingly, the myocardin factors could at least partially rescue the effects of the T159D mutation under some conditions, but this response was promoter specific. Finally, PKA signaling had much less of an effect on c-fos promoter activity and SRF binding to the c-fos CArG. CONCLUSIONS Our results indicate that phosphorylation of SRF by PKA inhibits SMC-specific transcription suggesting a novel signaling mechanism for the control of SMC phenotype.
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Affiliation(s)
- Alicia L Blaker
- Department of Pathology, University of North Carolina, Chapel Hill, NC 27599-7525, USA
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37
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Elucidation of the ELK1 target gene network reveals a role in the coordinate regulation of core components of the gene regulation machinery. Genome Res 2009; 19:1963-73. [PMID: 19687146 DOI: 10.1101/gr.093047.109] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Transcription factors play an important role in orchestrating the activation of specific networks of genes through targeting their proximal promoter and distal enhancer regions. However, it is unclear how the specificity of downstream responses is maintained by individual members of transcription-factor families and, in most cases, what their target repertoire is. We have used ChIP-chip analysis to identify the target genes of the ETS-domain transcription factor ELK1. Two distinct modes of ELK1 target gene selection are identified; the first involves redundant promoter binding with other ETS-domain family members; the second occurs through combinatorial binding with a second transcription factor SRF, which specifies a unique group of target genes. One of the most prominent groups of genes forming the ELK1 target network includes classes involved in core gene expression control, namely, components of the basal transcriptional machinery, the spliceosome and the ribosome. Amongst the set of genes encoding the basal transcription machinery components, are a functionally linked subset of GTFs and TAFs. Our study, therefore, reveals an unsuspected level of coordinate regulation of components of the core gene expression control machinery and also identifies two different modes of promoter targeting through binding with a second transcription factor or redundant binding with other ETS-domain family members.
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38
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Balamotis MA, Pennella MA, Stevens JL, Wasylyk B, Belmont AS, Berk AJ. Complexity in transcription control at the activation domain-mediator interface. Sci Signal 2009; 2:ra20. [PMID: 19417216 DOI: 10.1126/scisignal.1164302] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Transcript elongation by polymerase II paused at the Egr1 promoter is activated by mitogen-activated protein kinase phosphorylation of the ternary complex factor (TCF) ELK1 bound at multiple upstream sites and subsequent phospho-ELK1 interaction with mediator through the MED23 subunit. Consequently, Med23 knockout (KO) nearly eliminates Egr1 (early growth response factor 1) transcription in embryonic stem (ES) cells, leaving a paused polymerase at the promoter. Med23 KO did not, however, eliminate Egr1 transcription in fibroblasts. Chromatin immunoprecipitation analysis and direct visualization of fluorescently labeled TCF derivatives and mediator subunits revealed that three closely related TCFs bound to the same control regions. The relative amounts of these TCFs, which responded differently to the loss of MED23, differed in ES cells and fibroblasts. Transcriptome analysis suggests that most genes expressed in both cell types, such as Egr1, are regulated by alternative transcription factors in the two cell types that respond differently to the same signal transduction pathways.
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Affiliation(s)
- Michael A Balamotis
- Department of Microbiology, Immunology and Molecular Genetics, Molecular Biology Institute, University of California-Los Angeles, Los Angeles, CA 90095, USA
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39
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Kamberaj H, van der Vaart A. Correlated motions and interactions at the onset of the DNA-induced partial unfolding of Ets-1. Biophys J 2009; 96:1307-17. [PMID: 19217849 DOI: 10.1016/j.bpj.2008.11.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Accepted: 11/05/2008] [Indexed: 11/26/2022] Open
Abstract
The binding of the Ets-1 transcription factor to its target DNA sequence is characterized by a highly unusual conformational change consisting of the unfolding of inhibitory helix 1 (HI-1). To probe the interactions that lead to this unfolding, we performed molecular dynamics simulations of the folded states of apo-Ets-1 and the Ets-1-DNA complex. The simulations showed large differences in correlated motions between helix 4 (H4) and HI-1. In apo-Ets-1, H4 and HI-1 moved in-phase and stabilized each other by hydrogen bonding and macrodipolar interactions, whereas in the DNA-bound state, the motion was out-of-phase, with a disruption of the stabilizing interactions. This change in motion was due to hydrogen-bonding interactions between helix 1 (H1) and the DNA. The dipolar energy between H1 and H4 was modulated by hydrogen bonds between H1 and DNA, and, in accordance with experiments, elimination of the hydrogen bonds increased the stability of HI-1. The simulations confirm that the hydrogen bonds between H1 and DNA act as a conformational switch and show that the presence of DNA is communicated from H1 to H4, destabilizing HI-1. The calculations reveal a critical role for correlated motions at the onset of the DNA-induced unfolding.
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Affiliation(s)
- Hiqmet Kamberaj
- Center for Biological Physics, Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, USA
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40
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Lamber EP, Vanhille L, Textor LC, Kachalova GS, Sieweke MH, Wilmanns M. Regulation of the transcription factor Ets-1 by DNA-mediated homo-dimerization. EMBO J 2008; 27:2006-17. [PMID: 18566588 PMCID: PMC2486274 DOI: 10.1038/emboj.2008.117] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Accepted: 05/23/2008] [Indexed: 01/07/2023] Open
Abstract
The function of the Ets-1 transcription factor is regulated by two regions that flank its DNA-binding domain. A previously established mechanism for auto-inhibition of monomeric Ets-1 on DNA response elements with a single ETS-binding site, however, has not been observed for the stromelysin-1 promoter containing two palindromic ETS-binding sites. We present the structure of Ets-1 on this promoter element, revealing a ternary complex in which protein homo-dimerization is mediated by the specific arrangement of the two ETS-binding sites. In this complex, the N-terminal-flanking region is required for ternary protein-DNA assembly. Ets-1 variants, in which residues from this region are mutated, loose the ability for DNA-mediated dimerization and stromelysin-1 promoter transactivation. Thus, our data unravel the molecular basis for relief of auto-inhibition and the ability of Ets-1 to function as a facultative dimeric transcription factor on this site. Our findings may also explain previous data of Ets-1 function in the context of heterologous transcription factors, thus providing a molecular model that could also be valid for Ets-1 regulation by hetero-oligomeric assembly.
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Affiliation(s)
| | - Laurent Vanhille
- Centre d'Immunologie de Marseille-Luminy, Université de la Méditerranée, Marseille, France,Institut National de la Santé et de la Recherche Médicale, Marseille, France,Centre National de la Recherche Scientifique, Parc scientifique de Luminy, Marseille, France
| | | | - Galina S Kachalova
- Max-Planck Unit for Structural Molecular Biology, c/o DESY, Hamburg, Germany
| | - Michael H Sieweke
- Centre d'Immunologie de Marseille-Luminy, Université de la Méditerranée, Marseille, France,Institut National de la Santé et de la Recherche Médicale, Marseille, France,Centre National de la Recherche Scientifique, Parc scientifique de Luminy, Marseille, France
| | - Matthias Wilmanns
- EMBL-Hamburg, c/o DESY, Hamburg, Germany,EMBL Hamburg Outstation, EMBL c/o DESY, Notkestrasse 85, Building 25A, Hamburg D-22603, Germany. Tel.: +49 40 899 021 26; Fax: +49 40 899 021 49; E-mail:
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41
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Zhang Y, Fillmore RA, Zimmer WE. Structural and functional analysis of domains mediating interaction between the bagpipe homologue, Nkx3.1 and serum response factor. Exp Biol Med (Maywood) 2008; 233:297-309. [PMID: 18296735 DOI: 10.3181/0709-rm-236] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Nkx3.1 is a member of the NK2 class of homeodomain proteins and is expressed in development, being an early marker of the sclerotome and prostate gland. It has been shown to be a critical factor for prostate differentiation and function. Previous studies suggested that Nkx3.1 interacts with Serum Response Factor (SRF) to transactivate the Smooth Muscle gamma-Actin (SMGA) promoter. In studies presented here, we examined the molecular mechanisms underlying the functional synergy of these factors upon SMGA transcription. We demonstrate that full length Nkx3.1 physically interacts with SRF in the absence of DNA and that these factors are able to co-associate in cellular context using a mammalian two-hybrid system. The segment of SRF responsible for Nkx3.1 interaction was mapped to a approximately 30 amino acid region (AAs 142-171) at the N-terminal segment of the MADS box. Two separate regions of Nkx3.1 were found to mediate interactions with SRF. Interestingly, recognized domains of NK2 proteins, namely the TN, homeodomain DNA binding segment, and the NK2-SD do not participate in SRF interactions. One of the Nkx3.1 SRF binding domains was mapped to the N-terminal of the protein consistent with recent studies of these proteins using NMR spectroscopy by Gelmann and colleagues (1). A second SRF binding region was mapped to amino acids C-terminal to the homeodomain. Structural predictions indicate that both of the SRF interacting segments are largely hydrophobic in character and beta-strand in structure. With co-transfection transcriptional analyses we found that interaction between SRF and Nkx3.1 as well as DNA binding by both factors was required for the observed transcriptional synergy. Thus our studies have identified novel protein-protein interacting domains within Nkx3.1 and SRF that operate in concert with their respective DNA binding domains to mediate functional transcriptional synergy of these factors to regulate SMGA gene activation.
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Affiliation(s)
- Yan Zhang
- Department of Systems Biology and Translational Medicine, College of Medicine, Texas A&M Health Science Center, College Station, TX 77843-1114, USA
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Hollenhorst PC, Shah AA, Hopkins C, Graves BJ. Genome-wide analyses reveal properties of redundant and specific promoter occupancy within the ETS gene family. Genes Dev 2007; 21:1882-94. [PMID: 17652178 PMCID: PMC1935027 DOI: 10.1101/gad.1561707] [Citation(s) in RCA: 225] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The conservation of in vitro DNA-binding properties within families of transcription factors presents a challenge for achieving in vivo specificity. To uncover the mechanisms regulating specificity within the ETS gene family, we have used chromatin immunoprecipitation coupled with genome-wide promoter microarrays to query the occupancy of three ETS proteins in a human T-cell line. Unexpectedly, redundant occupancy was frequently detected, while specific occupancy was less likely. Redundant binding correlated with housekeeping classes of genes, whereas specific binding examples represented more specialized genes. Bioinformatics approaches demonstrated that redundant binding correlated with consensus ETS-binding sequences near transcription start sites. In contrast, specific binding sites diverged dramatically from the consensus and were found further from transcription start sites. One route to specificity was found--a highly divergent binding site that facilitates ETS1 and RUNX1 cooperative DNA binding. The specific and redundant DNA-binding modes suggest two distinct roles for members of the ETS transcription factor family.
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Affiliation(s)
- Peter C. Hollenhorst
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Atul A. Shah
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | | | - Barbara J. Graves
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
- Corresponding author.E-MAIL ; FAX (801) 585-1980
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Abstract
The origins of vascular smooth muscle are far more diverse than previously thought. Lineage mapping studies show that the segmental organization of early vertebrate embryos leaves footprints on the adult vascular system in the form of a mosaic pattern of different smooth muscle types. Moreover, evolutionarily conserved tissue forming pathways produce vascular smooth muscle from a variety of unanticipated sources. A closer look at the diversity of smooth muscle origins in vascular development provides new perspectives about how blood vessels differ from one another and why they respond in disparate ways to common risk factors associated with vascular disease. The origins of vascular smooth muscle are far more diverse than previously thought. A closer look at the diversity of smooth muscle origins in vascular development provides new perspectives about how blood vessels differ from one another and why they respond in disparate ways to common risk factors associated with vascular disease.
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Affiliation(s)
- Mark W Majesky
- Department of Medicine, Carolina Cardiovascular Biology Center, University of North Carolina, Chapel Hill, NC 27599-7126, USA.
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Nakazawa Y, Suzuki M, Manabe N, Yamada T, Kihara-Negishi F, Sakurai T, Tenen DG, Iwama A, Mochizuki M, Oikawa T. Cooperative interaction between ETS1 and GFI1 transcription factors in the repression of Bax gene expression. Oncogene 2007; 26:3541-50. [PMID: 17213822 DOI: 10.1038/sj.onc.1210140] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The proto-oncoproteins ETS1 and growth factor independent-1 (GFI1) are implicated in cell growth and differentiation in various types of cells, and their deregulated expression is involved in malignant transformation. Here, we report that ETS1 and GFI1 interact and affect gene expression through their cross-talk. Co-immunoprecipitation analyses and glutathione-S-transferase pull-down assays revealed that ETS1 bound directly to GFI1 via its Ets domain, and GFI1 bound to ETS1 via its zinc-finger domain. Luciferase (Luc) assays using artificial reporters showed that GFI1 repressed ETS1-mediated transcriptional activation and ETS1 repressed GFI1-mediated transcriptional activation, in a dose-dependent manner. However, in the Bax promoter where the Ets- and Gfi-binding sites (EBS and GBS) are adjacent, ETS1 and GFI1 cooperatively reduced activation. Site-directed mutagenesis on the EBS and GBS of the Bax promoter showed that both binding sites were necessary for full repression. Chromatin immunoprecipitation analyses confirmed that an ETS1-GFI1 complex formed on the Bax promoter even when either EBS or GBS was mutated. Introduction of small interfering RNA against ETS1 and/or GFI1 enhanced endogenous Bax gene expression. Our results suggest that the interaction between ETS1 and GFI1 facilitates their binding to specific sites on the Bax promoter and represses Bax expression in vivo.
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Affiliation(s)
- Y Nakazawa
- Department of Cell Genetics, Sasaki Institute, Tokyo, Japan
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45
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Anbanandam A, Albarado DC, Nguyen CT, Halder G, Gao X, Veeraraghavan S. Insights into transcription enhancer factor 1 (TEF-1) activity from the solution structure of the TEA domain. Proc Natl Acad Sci U S A 2006; 103:17225-30. [PMID: 17085591 PMCID: PMC1859914 DOI: 10.1073/pnas.0607171103] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transcription enhancer factor 1 is essential for cardiac, skeletal, and smooth muscle development and uses its N-terminal TEA domain (TEAD) to bind M-CAT elements. Here, we present the first structure of TEAD and show that it is a three-helix bundle with a homeodomain fold. Structural data reveal how TEAD binds DNA. Using structure-function correlations, we find that the L1 loop is essential for cooperative loading of TEAD molecules on to tandemly duplicated M-CAT sites. Furthermore, using a microarray chip-based assay, we establish that known binding sites of the full-length protein are only a subset of DNA elements recognized by TEAD. Our results provide a model for understanding the regulation of genome-wide gene expression during development by TEA/ATTS family of transcription factors.
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Affiliation(s)
- Asokan Anbanandam
- *Department of Biochemistry & Molecular Biology, University of Texas Medical School, Houston, TX 77030
| | - Diana C. Albarado
- *Department of Biochemistry & Molecular Biology, University of Texas Medical School, Houston, TX 77030
| | - Catherine T. Nguyen
- *Department of Biochemistry & Molecular Biology, University of Texas Medical School, Houston, TX 77030
| | - Georg Halder
- Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, TX 77030; and
| | - Xiaolian Gao
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204
| | - Sudha Veeraraghavan
- *Department of Biochemistry & Molecular Biology, University of Texas Medical School, Houston, TX 77030
- To whom correspondence should be addressed. E-mail:
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46
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Posern G, Treisman R. Actin’ together: serum response factor, its cofactors and the link to signal transduction. Trends Cell Biol 2006; 16:588-96. [DOI: 10.1016/j.tcb.2006.09.008] [Citation(s) in RCA: 416] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Revised: 08/29/2006] [Accepted: 09/25/2006] [Indexed: 11/30/2022]
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47
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Zaromytidou AI, Miralles F, Treisman R. MAL and ternary complex factor use different mechanisms to contact a common surface on the serum response factor DNA-binding domain. Mol Cell Biol 2006; 26:4134-48. [PMID: 16705166 PMCID: PMC1489092 DOI: 10.1128/mcb.01902-05] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The transcription factor serum response factor (SRF) interacts with its cofactor, MAL/MKL1, a member of the myocardin-related transcription factor (MRTF) family, through its DNA-binding domain. We define a seven-residue sequence within the conserved MAL B1 region essential and sufficient for complex formation. The neighboring Q-box sequence facilitates this interaction. The B1 and Q-box regions also have antagonistic effects on MAL nuclear import, but the residues involved are largely distinct. Both MAL and the ternary complex factor (TCF) family of SRF cofactors interact with a hydrophobic groove and pocket on the SRF DNA-binding domain. Unlike the TCFs, however, interaction of MAL with SRF is impaired by SRF alphaI-helix mutations that reduce DNA bending in the SRF-DNA complex. A clustered SRF alphaI-helix mutation strongly impairs MAL-SRF complex formation but does not affect DNA distortion in the MAL-SRF complex. MAL-SRF complex formation is facilitated by DNA binding. DNase I footprinting indicates that in the SRF-MAL complex MAL directly contacts DNA. These contacts, which flank the DNA sequences protected from DNase I by SRF, are required for effective MAL-SRF complex formation in gel mobility shift assays. We propose a model of MAL-SRF complex formation in which MAL interacts with SRF by the addition of a beta-strand to the SRF DNA-binding domain beta-sheet region, while SRF-induced DNA bending facilitates MAL-DNA contact.
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Affiliation(s)
- Alexia-Ileana Zaromytidou
- Transcription Laboratory, Lincoln's Inn Fields Laboratories, Cancer Research UK London Research Institute, Room 401, 44 Lincoln's Inn Fields, London WC2A 3PX, United Kingdom
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48
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Kim S, Denny CT, Wisdom R. Cooperative DNA binding with AP-1 proteins is required for transformation by EWS-Ets fusion proteins. Mol Cell Biol 2006; 26:2467-78. [PMID: 16537893 PMCID: PMC1430316 DOI: 10.1128/mcb.26.7.2467-2478.2006] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A key molecular event in the genesis of Ewing's sarcoma is the consistent presence of chromosomal translocations that result in the formation of proteins in which the amino terminus of EWS is fused to the carboxyl terminus, including the DNA binding domain, of one of five different Ets family proteins. These fusion proteins function as deregulated transcription factors, resulting in aberrant control of gene expression. Recent data indicate that some EWS-Ets target promoters, including the uridine phosphorylase (UPP) promoter, harbor tandem binding sites for Ets and AP-1 proteins. Here we show that those Ets family proteins that participate in Ewing's sarcoma, including Fli1, ERG, and ETV1, cooperatively bind these tandem elements with Fos-Jun while other Ets family members do not. Analysis of this cooperativity in vitro shows that (i) many different spatial arrangements of the Ets and AP-1 sites support cooperative binding, (ii) the bZIP motifs of Fos and Jun are sufficient to support this cooperativity, and (iii) both the Ets domain and carboxy-terminal sequences of Fli1 are important for cooperative DNA binding. EWS-Fli1 activates the expression of UPP mRNA, is directly bound to the UPP promoter, and transforms 3T3 fibroblasts; in contrast, a C-terminally truncated mutant form of EWS-Fli1 that cannot cooperatively bind DNA with Fos-Jun is defective in all of these properties. The results show that the ability of EWS-Ets proteins to cooperatively bind DNA with Fos-Jun is critical to the biologic activities of these proteins. The results have implications for understanding the pathogenesis of Ewing's sarcoma. In addition, they may be relevant to the mechanisms of Ras-dependent activation of genes that harbor tandem Ets and AP-1 binding sites.
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Affiliation(s)
- Sungeun Kim
- Division of Hematology/Oncology and UC Davis Cancer Center, University of California at Davis, USA
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49
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Iyer D, Chang D, Marx J, Wei L, Olson EN, Parmacek MS, Balasubramanyam A, Schwartz RJ. Serum response factor MADS box serine-162 phosphorylation switches proliferation and myogenic gene programs. Proc Natl Acad Sci U S A 2006; 103:4516-21. [PMID: 16537394 PMCID: PMC1450203 DOI: 10.1073/pnas.0505338103] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phosphorylation of a cluster of amino acids in the serum response factor (SRF) "MADS box" alphaI coil DNA binding domain regulated the transcription of genes associated with proliferation or terminal muscle differentiation. Mimicking phosphorylation of serine-162, a target of protein kinase C-alpha, with an aspartic acid substitution (SRF-S162D) completely inhibited SRF-DNA binding and blocked alpha-actin gene transcription even in the presence of potent myogenic cofactors, while preserving c-fos promoter activity because of stabilization of the ternary complex via Elk-1. Introduction of SRF-S162D into SRF null ES cells permitted transcription of the c-fos gene but was unable to rescue expression of myogenic contractile genes. Transition of proliferating C2C12 myoblasts to postfusion myocytes after serum withdrawal was associated with a progressive decline in SRF-S162 phosphorylation and an increase in alpha-actin gene expression. Hence, the phosphorylation status of serine-162 in the alphaI coil may constitute a novel switch that directs target gene expression into proliferation or differentiation programs.
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Affiliation(s)
- Dinakar Iyer
- *Department of Medicine
- Division of Diabetes, Endocrinology, and Metabolism
| | - David Chang
- *Department of Medicine
- Center for Cardiovascular Development, and Departments of
| | - Joe Marx
- Molecular and Cellular Biology and
| | - Lei Wei
- *Department of Medicine
- Center for Cardiovascular Development, and Departments of
| | - Eric N. Olson
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148
| | - Michael S. Parmacek
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and
| | - Ashok Balasubramanyam
- *Department of Medicine
- Division of Diabetes, Endocrinology, and Metabolism
- Molecular and Cellular Biology and
- **Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030
- To whom correspondence may be addressed. E-mail:
or
| | - Robert J. Schwartz
- *Department of Medicine
- Center for Cardiovascular Development, and Departments of
- Molecular and Cellular Biology and
- **Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030
- Center for Molecular Development and Diseases, Institute of Biosciences and Technology, Texas A&M University System Health Science Center, Houston, TX 77030
- To whom correspondence may be addressed. E-mail:
or
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Abstract
Adenovirus continues to be an important model system for investigating basic aspects of cell biology. Interactions of several cellular proteins with E1A conserved regions (CR) 1 and 2, and inhibition of apoptosis by E1B proteins are required for oncogenic transformation. CR2 binds RB family members, de-repressing E2F transcription factors, thus activating genes required for cell cycling. E1B-19K is a BCL2 homolog that binds and inactivates proapoptotic BAK and BAX. E1B-55K binds p53, inhibiting its transcriptional activation function. In productively infected cells, E1B-55K and E4orf6 assemble a ubiquitin ligase with cellular proteins Elongins B and C, Cullin 5 and RBX1 that polyubiquitinates p53 and one or more subunits of the MRN complex involved in DNA double-strand break repair, directing them to proteosomal degradation. E1A CR3 activates viral transcription by interacting with the MED23 Mediator subunit, stimulating preinitiation complex assembly on early viral promoters and probably also the rate at which they initiate transcription. The viral E1B-55K/E4orf6 ubiquitin ligase is also required for efficient viral late protein synthesis in many cell types, but the mechanism is not understood. E1A CR1 binds several chromatin-modifying complexes, but how this contributes to stimulation of cellular DNA synthesis and transformation is not clear. E1A CR4 binds the CtBP corepressor, but the mechanism by which this modulates the frequency of transformation remains to be determined. Clearly, adenovirus has much left to teach us about fundamental cellular processes.
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Affiliation(s)
- Arnold J Berk
- Department of Microbiology, Immunology and Molecular Genetics, Molecular Biology Institute, University of California, Los Angeles (UCLA), 90095-1570, USA.
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