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1.
Cell ; 152(3): 492-503, 2013 Jan 31.
Article in English | MEDLINE | ID: mdl-23374345

ABSTRACT

In peripheral tissues circadian gene expression can be driven either by local oscillators or by cyclic systemic cues controlled by the master clock in the brain's suprachiasmatic nucleus. In the latter case, systemic signals can activate immediate early transcription factors (IETFs) and thereby control rhythmic transcription. In order to identify IETFs induced by diurnal blood-borne signals, we developed an unbiased experimental strategy, dubbed Synthetic TAndem Repeat PROMoter (STAR-PROM) screening. This technique relies on the observation that most transcription factor binding sites exist at a relatively high frequency in random DNA sequences. Using STAR-PROM we identified serum response factor (SRF) as an IETF responding to oscillating signaling proteins present in human and rodent sera. Our data suggest that in mouse liver SRF is regulated via dramatic diurnal changes of actin dynamics, leading to the rhythmic translocation of the SRF coactivator Myocardin-related transcription factor-B (MRTF-B) into the nucleus.


Subject(s)
Actins/metabolism , Circadian Rhythm , Gene Expression Regulation , Genetic Techniques , Serum Response Factor/metabolism , Signal Transduction , Active Transport, Cell Nucleus , Animals , Blood Proteins/analysis , Blood Proteins/metabolism , Cell Line , Cell Nucleus/metabolism , Humans , Male , Mice , Period Circadian Proteins/metabolism , Rats , Transcription Factors/metabolism
2.
Mol Cell ; 65(6): 1081-1095.e5, 2017 Mar 16.
Article in English | MEDLINE | ID: mdl-28286024

ABSTRACT

We investigated the relationship among ERK signaling, histone modifications, and transcription factor activity, focusing on the ERK-regulated ternary complex factor family of SRF partner proteins. In MEFs, activation of ERK by TPA stimulation induced a common pattern of H3K9acS10ph, H4K16ac, H3K27ac, H3K9acK14ac, and H3K4me3 at hundreds of transcription start site (TSS) regions and remote regulatory sites. The magnitude of the increase in histone modification correlated well with changes in transcription. H3K9acS10ph preceded the other modifications. Most induced changes were TCF dependent, but TCF-independent TSSs exhibited the same hierarchy, indicating that it reflects gene activation per se. Studies with TCF Elk-1 mutants showed that TCF-dependent ERK-induced histone modifications required Elk-1 to be phosphorylated and competent to activate transcription. Analysis of direct TCF-SRF target genes and chromatin modifiers confirmed this and showed that H3S10ph required only Elk-1 phosphorylation. Induction of histone modifications following ERK stimulation is thus directed by transcription factor activation and transcription.


Subject(s)
Chromatin Assembly and Disassembly , Chromatin/enzymology , Extracellular Signal-Regulated MAP Kinases/metabolism , Histones/metabolism , Serum Response Factor/metabolism , TCF Transcription Factors/metabolism , Transcription, Genetic , Animals , Cell Line , Chromatin/drug effects , Chromatin/genetics , Chromatin Assembly and Disassembly/drug effects , Early Growth Response Protein 1/genetics , Early Growth Response Protein 1/metabolism , Enzyme Activation , Mice , Mice, Knockout , Mutation , Phosphorylation , RNA Interference , Serum Response Factor/genetics , Signal Transduction , TCF Transcription Factors/genetics , Tetradecanoylphorbol Acetate/pharmacology , Transcription Initiation Site , Transcription, Genetic/drug effects , Transfection , ets-Domain Protein Elk-1/genetics , ets-Domain Protein Elk-1/metabolism
3.
Genes Dev ; 31(23-24): 2361-2375, 2017 12 01.
Article in English | MEDLINE | ID: mdl-29317486

ABSTRACT

Both the MRTF-SRF and the YAP-TEAD transcriptional regulatory networks respond to extracellular signals and mechanical stimuli. We show that the MRTF-SRF pathway is activated in cancer-associated fibroblasts (CAFs). The MRTFs are required in addition to the YAP pathway for CAF contractile and proinvasive properties. We compared MRTF-SRF and YAP-TEAD target gene sets and identified genes directly regulated by one pathway, the other, or both. Nevertheless, the two pathways exhibit mutual dependence. In CAFs, expression of direct MRTF-SRF genomic targets is also dependent on YAP-TEAD activity, and, conversely, YAP-TEAD target gene expression is also dependent on MRTF-SRF signaling. In normal fibroblasts, expression of activated MRTF derivatives activates YAP, while activated YAP derivatives activate MRTF. Cross-talk between the pathways requires recruitment of MRTF and YAP to DNA via their respective DNA-binding partners (SRF and TEAD) and is therefore indirect, arising as a consequence of activation of their target genes. In both CAFs and normal fibroblasts, we found that YAP-TEAD activity is sensitive to MRTF-SRF-induced contractility, while MRTF-SRF signaling responds to YAP-TEAD-dependent TGFß signaling. Thus, the MRF-SRF and YAP-TEAD pathways interact indirectly through their ability to control cytoskeletal dynamics.


Subject(s)
Adaptor Proteins, Signal Transducing/metabolism , Cancer-Associated Fibroblasts/physiology , Cytoskeleton/metabolism , DNA-Binding Proteins/metabolism , Mammary Neoplasms, Animal/physiopathology , Phosphoproteins/metabolism , Trans-Activators/metabolism , Transcription Factors/metabolism , Adaptor Proteins, Signal Transducing/genetics , Animals , Cell Cycle Proteins , Cell Line, Tumor , Female , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Humans , Mice , Phosphoproteins/genetics , Signal Transduction , TEA Domain Transcription Factors , Trans-Activators/genetics , Transcriptional Activation/genetics , Transforming Growth Factor beta1/metabolism , YAP-Signaling Proteins
4.
Mol Cell ; 64(6): 1048-1061, 2016 12 15.
Article in English | MEDLINE | ID: mdl-27867007

ABSTRACT

The ERK-regulated ternary complex factors (TCFs) act with the transcription factor serum response factor (SRF) to activate mitogen-induced transcription. However, the extent of their involvement in the immediate-early transcriptional response, and their wider functional significance, has remained unclear. We show that, in MEFs, TCF inactivation significantly inhibits over 60% of TPA-inducible gene transcription and impairs cell proliferation. Using integrated SRF ChIP-seq and Hi-C data, we identified over 700 TCF-dependent SRF direct target genes involved in signaling, transcription, and proliferation. These also include a significant number of cytoskeletal gene targets for the Rho-regulated myocardin-related transcription factor (MRTF) SRF cofactor family. The TCFs act as general antagonists of MRTF-dependent SRF target gene expression, competing directly with the MRTFs for access to SRF. As a result, TCF-deficient MEFs exhibit hypercontractile and pro-invasive behavior. Thus, competition between TCFs and MRTFs for SRF determines the balance between antagonistic proliferative and contractile programs of gene expression.


Subject(s)
Fibroblasts/metabolism , Gene Expression Regulation , Serum Response Factor/genetics , Ternary Complex Factors/genetics , Animals , Base Sequence , Cell Line , Cell Proliferation/drug effects , Extracellular Signal-Regulated MAP Kinases/genetics , Extracellular Signal-Regulated MAP Kinases/metabolism , Fibroblasts/cytology , Fibroblasts/drug effects , Gene Expression Profiling , Genetic Complementation Test , Humans , Mice , Serum Response Factor/metabolism , Signal Transduction , Ternary Complex Factors/antagonists & inhibitors , Ternary Complex Factors/metabolism , Tetradecanoylphorbol Acetate/pharmacology , Trans-Activators/genetics , Trans-Activators/metabolism , Transcription, Genetic , ets-Domain Protein Elk-1/genetics , ets-Domain Protein Elk-1/metabolism
5.
Genes Dev ; 28(9): 943-58, 2014 May 01.
Article in English | MEDLINE | ID: mdl-24732378

ABSTRACT

The transcription factor SRF (serum response factor) recruits two families of coactivators, the MRTFs (myocardin-related transcription factors) and the TCFs (ternary complex factors), to couple gene transcription to growth factor signaling. Here we investigated the role of the SRF network in the immediate transcriptional response of fibroblasts to serum stimulation. SRF recruited its cofactors in a gene-specific manner, and virtually all MRTF binding was directed by SRF. Much of SRF DNA binding was serum-inducible, reflecting a requirement for MRTF-SRF complex formation in nucleosome displacement. We identified 960 serum-responsive SRF target genes, which were mostly MRTF-controlled, as assessed by MRTF chromatin immunoprecipitation (ChIP) combined with deep sequencing (ChIP-seq) and/or sensitivity to MRTF-linked signals. MRTF activation facilitates RNA polymerase II (Pol II) recruitment or promoter escape according to gene context. MRTF targets encode regulators of the cytoskeleton, transcription, and cell growth, underpinning the role of SRF in cytoskeletal dynamics and mechanosensing. Finally, we show that specific activation of either MRTFs or TCFs can reset the circadian clock.


Subject(s)
Actins/metabolism , Fibroblasts/physiology , Serum/metabolism , Signal Transduction , Transcription, Genetic/genetics , Animals , CLOCK Proteins/genetics , Circadian Clocks/genetics , Mice , Mitogen-Activated Protein Kinases/metabolism , Period Circadian Proteins/genetics , Period Circadian Proteins/metabolism , Serum Response Factor/metabolism
6.
Clin Genet ; 99(5): 673-683, 2021 05.
Article in English | MEDLINE | ID: mdl-33463715

ABSTRACT

A young boy with multifocal epilepsy with infantile spasms and hypsarrhythmia with minimal organic lesions of brain structures underwent DNA diagnosis using whole-exome sequencing. A heterozygous amino-acid substitution p.L519R in a PHACTR1 gene was identified. PHACTR1 belongs to a protein family of G-actin binding protein phosphatase 1 (PP1) cofactors and was not previously associated with a human disease. The missense single nucleotide variant in the proband was shown to occur de novo in the paternal allele. The mutation was shown in vitro to reduce the affinity of PHACTR1 for G-actin, and to increase its propensity to form complexes with the catalytic subunit of PP1. These properties are associated with altered subcellular localization of PHACTR1 and increased ability to induce cytoskeletal rearrangements. Although the molecular role of the PHACTR1 in neuronal excitability and differentiation remains to be defined, PHACTR1 has been previously shown to be involved in Slack channelopathy pathogenesis, consistent with our findings. We conclude that this activating mutation in PHACTR1 causes a severe type of sporadic multifocal epilepsy in the patient.


Subject(s)
Epilepsy/genetics , Microfilament Proteins/genetics , Mutation , Spasms, Infantile/genetics , Actins/metabolism , Animals , Child, Preschool , Humans , Infant , Male , Mice , NIH 3T3 Cells , Exome Sequencing
7.
J Immunol ; 201(6): 1681-1691, 2018 09 15.
Article in English | MEDLINE | ID: mdl-30068599

ABSTRACT

In mouse thymocyte development, signaling by the TCR through the ERK pathway is required for positive selection of conventional naive T cells. The Ets transcription factor ELK4 (SAP-1), an ERK-regulated cofactor of the SRF transcription factor, plays an important role in positive selection by activating immediate-early genes such as the Egr transcription factor family. The role of ELK4-SRF signaling in development of other T cell types dependent on ERK signaling has been unclear. In this article, we show that ELK4, and its close relative ELK1, act cell autonomously in the thymus to control the generation of innate-like αß CD8+ T cells with memory-like characteristics. Mice lacking ELK4 and ELK1 develop increased numbers of innate-like αß CD8+ T cells, which populate the periphery. These cells develop cell autonomously rather than through expansion of PLZF+ thymocytes and concomitantly increased IL-4 signaling. Their development is associated with reduced TCR-mediated activation of ELK4-SRF target genes and can be partially suppressed by overexpression of the ELK4-SRF target gene EGR2. Consistent with this, partial inhibition of ERK signaling in peripheral CD8+T cells promotes the generation of cells with innate-like characteristics. These data establish that low-level ERK signaling through ELK4 (and ELK1) promotes innate-like αß CD8+ T cell differentiation, tuning conventional versus innate-like development.


Subject(s)
CD8-Positive T-Lymphocytes/immunology , Cell Differentiation/immunology , MAP Kinase Signaling System/immunology , Thymus Gland/immunology , ets-Domain Protein Elk-1/immunology , ets-Domain Protein Elk-4/immunology , Animals , CD8-Positive T-Lymphocytes/cytology , Cell Differentiation/genetics , Immunity, Innate , MAP Kinase Signaling System/genetics , Mice , Mice, Knockout , Receptors, Antigen, T-Cell/genetics , Receptors, Antigen, T-Cell/immunology , Thymus Gland/cytology , ets-Domain Protein Elk-1/genetics , ets-Domain Protein Elk-4/genetics
8.
EMBO J ; 34(11): 1554-71, 2015 Jun 03.
Article in English | MEDLINE | ID: mdl-25896507

ABSTRACT

Oncogenic levels of Myc expression sensitize cells to multiple apoptotic stimuli, and this protects long-lived organisms from cancer development. How cells discriminate physiological from supraphysiological levels of Myc is largely unknown. Here, we show that induction of apoptosis by Myc in breast epithelial cells requires association of Myc with Miz1. Gene expression and ChIP-Sequencing experiments show that high levels of Myc invade target sites that lack consensus E-boxes in a complex with Miz1 and repress transcription. Myc/Miz1-repressed genes encode proteins involved in cell adhesion and migration and include several integrins. Promoters of repressed genes are enriched for binding sites of the serum-response factor (SRF). Restoring SRF activity antagonizes Myc repression of SRF target genes, attenuates Myc-induced apoptosis, and reverts a Myc-dependent decrease in Akt phosphorylation and activity, a well-characterized suppressor of Myc-induced apoptosis. We propose that high levels of Myc engage Miz1 in repressive DNA binding complexes and suppress an SRF-dependent transcriptional program that supports survival of epithelial cells.


Subject(s)
Apoptosis/physiology , Epithelial Cells/metabolism , Mammary Glands, Human/metabolism , Proto-Oncogene Proteins c-myc/metabolism , Serum Response Factor/metabolism , Transcription, Genetic/physiology , Cell Adhesion/physiology , Cell Line, Tumor , Cell Movement/physiology , Epithelial Cells/cytology , Female , Humans , Kruppel-Like Transcription Factors/genetics , Kruppel-Like Transcription Factors/metabolism , Mammary Glands, Human/cytology , Proto-Oncogene Proteins c-akt/genetics , Proto-Oncogene Proteins c-akt/metabolism , Proto-Oncogene Proteins c-myc/genetics , Serum Response Factor/genetics
9.
Trends Biochem Sci ; 38(8): 376-7, 2013 Aug.
Article in English | MEDLINE | ID: mdl-23810602

ABSTRACT

The functions of nuclear actin have been a mystery for many years. Recent papers demonstrate that the nuclear and cytoplasmic actin pools are in dynamic communication, but that not all nuclear actin freely exchanges. Extracellular signals can induce changes in nuclear actin dynamics, affecting activity of the myocardin-related transcription factor (MRTF) transcriptional coactivators, which reversibly bind G-actin. By contrast, actin is stably associated with the Ino80 chromatin remodelling complex, where it plays a role in the recognition of nucleosome linker DNA.


Subject(s)
Actin Cytoskeleton/metabolism , Actins/metabolism , Cell Nucleus/metabolism , Models, Biological , Animals , Chromatin Assembly and Disassembly , Cytoplasm/genetics , Humans , Protein Transport , Signal Transduction
10.
Blood ; 125(8): 1244-55, 2015 Feb 19.
Article in English | MEDLINE | ID: mdl-25573994

ABSTRACT

Chemokine signaling is important for the seeding of different sites by hematopoietic stem cells (HSCs) during development. Serum response factor (SRF) controls multiple genes governing adhesion and migration, mainly by recruiting members of the myocardin-related transcription factor (MRTF) family of G-actin-regulated cofactors. We used vav-iCre to inactivate MRTF-SRF signaling early during hematopoietic development. In both Srf- and Mrtf-deleted animals, hematopoiesis in fetal liver and spleen is intact but does not become established in fetal bone marrow. Srf-null HSC progenitor cells (HSC/Ps) fail to effectively engraft in transplantation experiments, exhibiting normal proximal signaling responses to SDF-1, but reduced adhesiveness, F-actin assembly, and reduced motility. Srf-null HSC/Ps fail to polarize in response to SDF-1 and cannot migrate through restrictive membrane pores to SDF-1 or Scf in vitro. Mrtf-null HSC/Ps were also defective in chemotactic responses to SDF-1. Srf-null HSC/Ps exhibit substantial deficits in cytoskeletal gene expression. MRTF-SRF signaling is thus critical for expression of genes required for the response to chemokine signaling during hematopoietic development.


Subject(s)
Bone Marrow/embryology , Bone Marrow/physiology , Hematopoietic Stem Cells/physiology , Serum Response Factor/physiology , Stem Cell Niche , Trans-Activators/physiology , Transcription Factors/physiology , Animals , Bone Marrow/growth & development , Cell Movement/genetics , Cells, Cultured , Gene Expression Regulation, Developmental , Hematopoiesis/genetics , Mice , Mice, Inbred C57BL , Mice, Knockout , Signal Transduction/genetics , Stem Cell Niche/genetics
11.
EMBO J ; 29(20): 3448-58, 2010 Oct 20.
Article in English | MEDLINE | ID: mdl-20818336

ABSTRACT

Myocardin-related transcription factors (MRTFs) are actin-regulated transcriptional coactivators, which bind G-actin through their N-terminal RPEL domains. In response to signal-induced actin polymerisation and concomitant G-actin depletion, MRTFs accumulate in the nucleus and activate target gene transcription through their partner protein SRF. Nuclear accumulation of MRTFs in response to signal is inhibited by increased G-actin level. Here, we study the mechanism by which MRTF-A enters the nucleus. We show that MRTF-A contains an unusually long bipartite nuclear localisation signal (NLS), comprising two basic elements separated by 30 residues, embedded within the RPEL domain. Using siRNA-mediated protein depletion in vivo, and nuclear import assays in vitro, we show that the MRTF-A extended bipartite NLS uses the importin (Imp)α/ß-dependent import pathway, and that import is inhibited by G-actin. Interaction of the NLS with the Impα-Impß heterodimer requires both NLS basic elements, and is dependent on the Impα major and minor binding pockets. Binding of the Impα-Impß heterodimer to the intact MRTF-A RPEL domain occurs competitively with G-actin. Thus, MRTF-A contains an actin-sensitive nuclear import signal.


Subject(s)
Actins/metabolism , Active Transport, Cell Nucleus/physiology , Nuclear Localization Signals/genetics , Nuclear Localization Signals/metabolism , Trans-Activators/metabolism , alpha Karyopherins/metabolism , beta Karyopherins/metabolism , Amino Acid Sequence , Animals , Cell Nucleus/metabolism , Mice , Molecular Sequence Data , NIH 3T3 Cells , RNA Interference , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Trans-Activators/genetics , alpha Karyopherins/genetics , beta Karyopherins/genetics
12.
J Cell Sci ; 125(Pt 23): 5860-72, 2012 Dec 01.
Article in English | MEDLINE | ID: mdl-22976292

ABSTRACT

The Phactr family of PP1-binding proteins is implicated in human diseases including Parkinson's, cancer and myocardial infarction. Each Phactr protein contains four G-actin binding RPEL motifs, including an N-terminal motif, abutting a basic element, and a C-terminal triple RPEL repeat, which overlaps a conserved C-terminus required for interaction with PP1. RPEL motifs are also found in the regulatory domains of the MRTF transcriptional coactivators, where they control MRTF subcellular localisation and activity by sensing signal-induced changes in G-actin concentration. However, whether G-actin binding controls Phactr protein function - and its relation to signalling - has not been investigated. Here, we show that Rho-actin signalling induced by serum stimulation promotes the nuclear accumulation of Phactr1, but not other Phactr family members. Actin binding by the three Phactr1 C-terminal RPEL motifs is required for Phactr1 cytoplasmic localisation in resting cells. Phactr1 nuclear accumulation is importin α-ß dependent. G-actin and importin α-ß bind competitively to nuclear import signals associated with the N- and C-terminal RPEL motifs. All four motifs are required for the inhibition of serum-induced Phactr1 nuclear accumulation when G-actin is elevated. G-actin and PP1 bind competitively to the Phactr1 C-terminal region, and Phactr1 C-terminal RPEL mutants that cannot bind G-actin induce aberrant actomyosin structures dependent on their nuclear accumulation and on PP1 binding. In CHL-1 melanoma cells, Phactr1 exhibits actin-regulated subcellular localisation and is required for stress fibre assembly, motility and invasiveness. These data support a role for Phactr1 in actomyosin assembly and suggest that Phactr1 G-actin sensing allows its coordination with F-actin availability.


Subject(s)
Actins/metabolism , Actomyosin/metabolism , Microfilament Proteins/metabolism , Animals , Cell Adhesion Molecules/metabolism , Cell Line, Tumor , Humans , Mice , Microscopy, Fluorescence , NIH 3T3 Cells , Protein Binding
13.
Nat Commun ; 15(1): 7956, 2024 Sep 11.
Article in English | MEDLINE | ID: mdl-39261466

ABSTRACT

Paracrine IL-2 signalling drives the CD8 + T cell expansion and differentiation that allow protection against viral infections, but the underlying molecular events are incompletely understood. Here we show that the transcription factor SRF, a master regulator of cytoskeletal gene expression, is required for effective IL-2 signalling during L. monocytogenes infection. Acting cell-autonomously with its actin-regulated cofactors MRTF-A and MRTF-B, SRF is dispensible for initial TCR-mediated CD8+ T cell proliferation, but is required for sustained IL-2 dependent CD8+ effector T cell expansion, and persistence of memory cells. Following TCR activation, Mrtfab-null CD8+ T cells produce IL-2 normally, but homotypic clustering is impaired both in vitro and in vivo. Expression of cytoskeletal structural and regulatory genes, most notably actins, is defective in Mrtfab-null CD8+ T cells. Activation-induced cell clustering in vitro requires F-actin assembly, and Mrtfab-null cell clusters are small, contain less F-actin, and defective in IL-2 retention. Clustering of Mrtfab-null cells can be partially restored by exogenous actin expression. IL-2 mediated CD8+ T cell proliferation during infection thus depends on the control of cytoskeletal dynamics and actin gene expression by MRTF-SRF signalling.


Subject(s)
CD8-Positive T-Lymphocytes , Cytoskeleton , Interleukin-2 , Mice, Inbred C57BL , Serum Response Factor , Trans-Activators , CD8-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/metabolism , Interleukin-2/metabolism , Interleukin-2/genetics , Animals , Trans-Activators/metabolism , Trans-Activators/genetics , Cytoskeleton/metabolism , Mice , Serum Response Factor/metabolism , Serum Response Factor/genetics , Listeria monocytogenes/immunology , Listeriosis/immunology , Listeriosis/genetics , Listeriosis/microbiology , Actins/metabolism , Gene Expression Regulation , Signal Transduction , Mice, Knockout , Cell Proliferation , Lymphocyte Activation
14.
EMBO Rep ; 12(9): 963-70, 2011 Sep 01.
Article in English | MEDLINE | ID: mdl-21799516

ABSTRACT

The serum response factor (SRF) coactivator myocardin-related transcription factor A (MAL/MKL1/MRTF-A), the nuclear transport and activity of which is regulated by monomeric actin, has been implicated in tension-based regulation of SRF-mediated transcriptional activity. However, the mechanisms involved remain unclear. We used fibroblasts grown within collagen matrices to explore whether MRTF-A transport is regulated by tissue tension. We show that MRTF-A nuclear accumulation following stimulation with serum, actin drugs or acute mechanical stress is prevented within mechanically loaded, anchored matrices at tensional homeostasis. This is accompanied by a higher G/F actin ratio, defective nuclear import and increased cofilin expression. We propose that tension regulates MRTF-A/SRF activity through cofilin-mediated modulation of actin dynamics.


Subject(s)
Homeostasis , Serum Response Factor/metabolism , Trans-Activators/genetics , Trans-Activators/metabolism , Actins/genetics , Actins/metabolism , Active Transport, Cell Nucleus , Animals , Cell Line , Cofilin 1/biosynthesis , Cofilin 1/metabolism , DNA-Binding Proteins/metabolism , Down-Regulation , Mice , NIH 3T3 Cells , Serum Response Factor/genetics , Signal Transduction , Stress, Physiological , Transcription Factors/metabolism
15.
EMBO J ; 27(23): 3198-208, 2008 Dec 03.
Article in English | MEDLINE | ID: mdl-19008859

ABSTRACT

Serum response factor transcriptional activity is controlled through interactions with regulatory cofactors such as the coactivator MAL/MRTF-A (myocardin-related transcription factor A). MAL is itself regulated in vivo by changes in cellular actin dynamics, which alter its interaction with G-actin. The G-actin-sensing mechanism of MAL/MRTF-A resides in its N-terminal domain, which consists of three tandem RPEL repeats. We describe the first molecular insights into RPEL function obtained from structures of two independent RPEL(MAL) peptide:G-actin complexes. Both RPEL peptides bind to the G-actin hydrophobic cleft and to subdomain 3. These RPEL(MAL):G-actin structures explain the sequence conservation defining the RPEL motif, including the invariant arginine. Characterisation of the RPEL(MAL):G-actin interaction by fluorescence anisotropy and cell reporter-based assays validates the significance of actin-binding residues for proper MAL localisation and regulation in vivo. We identify important differences in G-actin engagement between the two RPEL(MAL) structures. Comparison with other actin-binding proteins reveals an unexpected similarity to the vitamin-D-binding protein, extending the G-actin-binding protein repertoire.


Subject(s)
Actins/chemistry , Actins/metabolism , DNA-Binding Proteins/chemistry , DNA-Binding Proteins/metabolism , Oncogene Proteins, Fusion/chemistry , Oncogene Proteins, Fusion/metabolism , Protein Structure, Quaternary , Amino Acid Sequence , Binding Sites , Circular Dichroism , Crystallography, X-Ray , Fluorescence Polarization , Genes, Reporter , Luciferases/genetics , Luciferases/metabolism , Models, Molecular , Molecular Sequence Data , Protein Binding , Sequence Alignment , Trans-Activators
16.
J Immunol ; 185(2): 1082-92, 2010 Jul 15.
Article in English | MEDLINE | ID: mdl-20554967

ABSTRACT

The ternary complex factors (TCFs; SAP-1, Elk-1, and Net) are serum response factor cofactors that share many functional properties and are coexpressed in many tissues. SAP-1, the predominant thymus TCF, is required for thymocyte positive selection. In this study, we assessed whether the different TCFs are functionally equivalent. Elk-1 deletion, but not the hypomorphic Net(delta) mutation, exacerbated the SAP-1 positive selection phenotype, but triply deficient thymocytes were no more defective than SAP-1(-/-) Elk-1(-/-) cells. Inactivation of the other TCFs did not affect SAP-1-independent processes, including beta-selection, regulatory T cell selection, and negative selection, although reduced marginal zone B cells were observed in SAP-1(-/-) Elk-1(-/-) animals. Ectopic expression of Elk-1, but not Net, rescued positive selection of SAP-1(-/-) thymocytes; thus, SAP-1 and Elk-1 are functionally equivalent in this system, and the SAP-1 null selection phenotype reflects only its high expression in the thymus. Array analysis of TCR-stimulated double-positive cells identified SAP-1-dependent inducible genes whose transcription was further impaired in SAP-1(-/-) Elk-1(-/-) cells; thus, these genes, which include Egr-1 and Egr-2, represent candidate mediators of positive selection. Chromatin immunoprecipitation revealed subtly different promoter targeting between the different TCFs. Ectopic expression of Egr-1 restored positive selection in SAP-1 null thymocytes, establishing it (and possibly other Egr family members) as the major effector for ERK-SAP-1 signaling in thymocyte positive selection.


Subject(s)
Proto-Oncogene Proteins c-ets/immunology , Thymus Gland/immunology , ets-Domain Protein Elk-1/immunology , ets-Domain Protein Elk-4/immunology , Animals , Cell Differentiation/genetics , Cell Differentiation/immunology , Cells, Cultured , Chromatin Immunoprecipitation , Female , Flow Cytometry , Gene Expression Profiling , Male , Mice , Mice, Inbred C57BL , Mice, Knockout , Oligonucleotide Array Sequence Analysis , Proto-Oncogene Proteins c-ets/genetics , Proto-Oncogene Proteins c-ets/metabolism , Retroviridae/genetics , Thymus Gland/cytology , Thymus Gland/metabolism , Transduction, Genetic , ets-Domain Protein Elk-1/genetics , ets-Domain Protein Elk-1/metabolism , ets-Domain Protein Elk-4/genetics , ets-Domain Protein Elk-4/metabolism
17.
Elife ; 92020 09 25.
Article in English | MEDLINE | ID: mdl-32975518

ABSTRACT

PPP-family phosphatases such as PP1 have little intrinsic specificity. Cofactors can target PP1 to substrates or subcellular locations, but it remains unclear how they might confer sequence-specificity on PP1. The cytoskeletal regulator Phactr1 is a neuronally enriched PP1 cofactor that is controlled by G-actin. Structural analysis showed that Phactr1 binding remodels PP1's hydrophobic groove, creating a new composite surface adjacent to the catalytic site. Using phosphoproteomics, we identified mouse fibroblast and neuronal Phactr1/PP1 substrates, which include cytoskeletal components and regulators. We determined high-resolution structures of Phactr1/PP1 bound to the dephosphorylated forms of its substrates IRSp53 and spectrin αII. Inversion of the phosphate in these holoenzyme-product complexes supports the proposed PPP-family catalytic mechanism. Substrate sequences C-terminal to the dephosphorylation site make intimate contacts with the composite Phactr1/PP1 surface, which are required for efficient dephosphorylation. Sequence specificity explains why Phactr1/PP1 exhibits orders-of-magnitude enhanced reactivity towards its substrates, compared to apo-PP1 or other PP1 holoenzymes.


Specific arrangements of atoms such as bulky phosphate groups can change the activity of a protein and how it interacts with other molecules. Enzymes called kinases are responsible for adding these groups onto a protein, while phosphatases remove them. Kinases are generally specific for a small number of proteins, adding phosphate groups only at sites embedded in a particular sequence in the target protein. Phosphatases, however, are generalists: only a few different types exist, which exhibit little target sequence specificity. Partner proteins can attach to phosphatases to bring the enzymes to specific locations in the cell, or to deliver target proteins to them; yet, it is unclear whether partner binding could also change the structure of the enzyme so the phosphatase can recognise only a restricted set of targets. To investigate this, Fedoryshchak, Prechová et al. studied a phosphatase called PP1 and its partner, Phactr1. First, the structure of the Phactr1/PP1 complex was examined using biochemistry approaches and X-ray crystallography. This showed that binding of Phactr1 to PP1 creates a new surface pocket, which comprised elements of both proteins. In particular, this composite pocket is located next to the part of the PP1 enzyme responsible for phosphate removal. Next, mass spectrometry and genetics methods were harnessed to identify and characterise the targets of the Phactr1/PP1 complex. Structural analysis of the proteins most susceptible to Phactr1/PP1 activity showed that they had particular sequences that could interact with Phactr1/PP1's composite pocket. Further experiments revealed that, compared to PP1 acting alone, the pocket increased the binding efficiency and reactivity of the complex 100-fold. This work demonstrates that a partner protein can make phosphatases more sequence-specific, suggesting that future studies could adopt a similar approach to examine how other enzymes in this family perform their role. In addition, the results suggest that it will be possible to design Phactr1/PP1-specific drugs that act on the composite pocket. This would represent an important proof of principle, since current phosphatase-specific drugs do not target particular phosphatase complexes.


Subject(s)
Microfilament Proteins/metabolism , Animals , Catalytic Domain , Crystallization , Cytoskeleton/metabolism , Holoenzymes/chemistry , Holoenzymes/metabolism , Mice , Microfilament Proteins/chemistry , Nerve Tissue Proteins/metabolism , Phosphates/metabolism , Protein Conformation , Spectrin/metabolism , Substrate Specificity
18.
J Cell Biol ; 157(5): 831-8, 2002 May 27.
Article in English | MEDLINE | ID: mdl-12034774

ABSTRACT

The small GTPase RhoA controls activity of serum response factor (SRF) by inducing changes in actin dynamics. We show that in PC12 cells, activation of SRF after serum stimulation is RhoA dependent, requiring both actin polymerization and the Rho kinase (ROCK)-LIM kinase (LIMK)-cofilin signaling pathway, previously shown to control F-actin turnover. Activation of SRF by overexpression of wild-type LIMK or ROCK-insensitive LIMK mutants also requires functional RhoA, indicating that a second RhoA-dependent signal is involved. This is provided by the RhoA effector mDia: dominant interfering mDia1 derivatives inhibit both serum- and LIMK-induced SRF activation and reduce the ability of LIMK to induce F-actin accumulation. These results demonstrate a role for LIMK in SRF activation, and functional cooperation between RhoA-controlled LIMK and mDia effector pathways.


Subject(s)
Actins/metabolism , Carrier Proteins/metabolism , Neurons/enzymology , Protein Kinases/metabolism , Serum Response Factor/metabolism , Actin Depolymerizing Factors , Animals , Intracellular Signaling Peptides and Proteins , Lim Kinases , Microfilament Proteins/metabolism , Neurons/cytology , PC12 Cells , Phosphorylation , Protein Serine-Threonine Kinases/metabolism , Rats , rho-Associated Kinases , rhoA GTP-Binding Protein/metabolism
19.
Mol Cell Biol ; 26(11): 4134-48, 2006 Jun.
Article in English | MEDLINE | ID: mdl-16705166

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.


Subject(s)
DNA-Binding Proteins/metabolism , Serum Response Factor/chemistry , Serum Response Factor/metabolism , Ternary Complex Factors/metabolism , Trans-Activators/metabolism , Active Transport, Cell Nucleus , Amino Acid Sequence , Animals , Cell Nucleus/metabolism , DNA/metabolism , Hydrophobic and Hydrophilic Interactions , Mice , Models, Molecular , Molecular Sequence Data , Mutation/genetics , NIH 3T3 Cells , Protein Binding , Protein Structure, Secondary , Protein Structure, Tertiary
20.
Nat Cell Biol ; 21(7): 845-855, 2019 07.
Article in English | MEDLINE | ID: mdl-31209295

ABSTRACT

RPEL proteins, which contain the G-actin-binding RPEL motif, coordinate cytoskeletal processes with actin dynamics. We show that the ArhGAP12- and ArhGAP32-family GTPase-activating proteins (GAPs) are RPEL proteins. We determine the structure of the ArhGAP12/G-actin complex, and show that G-actin contacts the RPEL motif and GAP domain sequences. G-actin inhibits ArhGAP12 GAP activity, and this requires the G-actin contacts identified in the structure. In B16 melanoma cells, ArhGAP12 suppresses basal Rac and Cdc42 activity, F-actin assembly, invadopodia formation and experimental metastasis. In this setting, ArhGAP12 mutants defective for G-actin binding exhibit more effective downregulation of Rac GTP loading following HGF stimulation and enhanced inhibition of Rac-dependent processes, including invadopodia formation. Potentiation or disruption of the G-actin/ArhGAP12 interaction, by treatment with the actin-binding drugs latrunculin B or cytochalasin D, has corresponding effects on Rac GTP loading. The interaction of G-actin with RPEL-family rhoGAPs thus provides a negative feedback loop that couples Rac activity to actin dynamics.


Subject(s)
Actins/metabolism , GTPase-Activating Proteins/metabolism , cdc42 GTP-Binding Protein/metabolism , Actins/drug effects , Animals , Bridged Bicyclo Compounds, Heterocyclic/pharmacology , Cytochalasin D/pharmacology , GTPase-Activating Proteins/drug effects , GTPase-Activating Proteins/genetics , Guanosine Triphosphate/metabolism , Humans , Mice , Protein Binding/drug effects , Protein Binding/genetics , Rabbits , Thiazolidines/pharmacology , cdc42 GTP-Binding Protein/drug effects , rac GTP-Binding Proteins/metabolism
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