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Guru A, Lite C, Freddy AJ, Issac PK, Pasupuleti M, Saraswathi NT, Arasu MV, Al-Dhabi NA, Arshad A, Arockiaraj J. Intracellular ROS scavenging and antioxidant regulation of WL15 from cysteine and glycine-rich protein 2 demonstrated in zebrafish in vivo model. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 114:103863. [PMID: 32918928 DOI: 10.1016/j.dci.2020.103863] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/24/2020] [Accepted: 09/04/2020] [Indexed: 05/02/2023]
Abstract
Antioxidant peptides are naturally present in food, especially in fishes, and are considered to contain rich source of various bioactive compounds that are structurally heterogeneous. This study aims to identify and characterize the antioxidant property of the WL15 peptide, derived from Cysteine and glycine-rich protein 2 (CSRP2) identified from the transcriptome of a freshwater food fish, Channa striatus. C. striatus is already studied to contain high levels of amino acids and fatty acids, besides traditionally known for its pharmacological benefits in the Southeast Asian region. In our study, in vitro analysis of WL15 peptide exhibited strong free radical scavenging activity in 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2'-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS), superoxide anion radical and hydrogen peroxide (H2O2) scavenging assay. Further, to evaluate the cytotoxicity and dose-response, the Human dermal fibroblast (HDF) cells were used. Results showed that the treatment of HDF cells with varying concentrations (10, 20, 30, 40 and 50 μM) of WL15 peptide was not cytotoxic. However, the treatment concentrations showed enhanced antioxidant properties by significantly inhibiting the levels of free radicals. For in vivo assessment, we have used zebrafish larvae for evaluating the developmental toxicity and for determining the antioxidant property of the WL15 peptide. Zebrafish embryos were treated with the WL15 peptide from 4 h of post-fertilization (hpf) to 96 hpf covering the embryo-larval developmental period. At the end of the exposure period, the larvae were exposed to H2O2 (1 mM) for inducing generic oxidative stress. The exposure of WL15 peptide during the embryo-larval period showed no developmental toxicity even in higher concentrations of the peptide. Besides, the WL15 peptide considerably decreased the intracellular reactive oxygen species (ROS) levels induced by H2O2 exposure. WL15 peptide also inhibited the H2O2-induced caspase 3-dependent apoptotic response in zebrafish larvae was observed using the whole-mount immunofluorescence staining. Overall results from our study showed that the pre-treatment of WL15 (50 μM) in the H2O2-exposed zebrafish larvae, attenuated the expression of activated caspase 3 expressions, reduced Malondialdehyde (MDA) levels, and enhanced antioxidant enzymes, including superoxide dismutase (SOD) and catalase (CAT). The gene expression of antioxidant enzymes such as glutathione S-transferase (GST), glutathione peroxide (GPx) and γ-glutamyl cysteine synthetase (GCS) was found to be upregulated. In conclusion, it can be conceived that pre-treatment with WL15 could mitigate H2O2-induced oxidative injury by elevating the activity and expression of antioxidant enzymes, thereby decreasing MDA levels and cellular apoptosis by enhancing the antioxidant response, demonstrated by the in vitro and in vivo experiments.
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Affiliation(s)
- Ajay Guru
- SRM Research Institute, SRM Institute of Science and Technology, Kattankulathur, 603 203, Chennai, Tamil Nadu, India
| | - Christy Lite
- Endocrine and Exposome Laboratory, Department of Zoology, Madras Christian College, Tambaram, Chennai, 600 059, Tamil Nadu, India
| | - Allen J Freddy
- Endocrine and Exposome Laboratory, Department of Zoology, Madras Christian College, Tambaram, Chennai, 600 059, Tamil Nadu, India
| | - Praveen Kumar Issac
- SRM Research Institute, SRM Institute of Science and Technology, Kattankulathur, 603 203, Chennai, Tamil Nadu, India
| | - Mukesh Pasupuleti
- Lab PCN 206, Microbiology Division, CSIR-Central Drug Research Institute, B.S. 10/1 Sector 10 Jankipuram Extension Sitapur Road, Lucknow, 226 031, Uttar Pradesh, India
| | - N T Saraswathi
- Molecular Biophysics Lab, School of Chemical and Biotechnology, SASTRA Deemed to Be University, Thanjavur, 613 401, Tamil Nadu, India
| | - Mariadhas Valan Arasu
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Naif Abdullah Al-Dhabi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Aziz Arshad
- International Institute of Aquaculture and Aquatic Sciences (I-AQUAS), Universiti Putra Malaysia, 71050, Port Dickson, Negeri Sembilan, Malaysia; Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Jesu Arockiaraj
- SRM Research Institute, SRM Institute of Science and Technology, Kattankulathur, 603 203, Chennai, Tamil Nadu, India.
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Hoffmann C, Mao X, Dieterle M, Moreau F, Al Absi A, Steinmetz A, Oudin A, Berchem G, Janji B, Thomas C. CRP2, a new invadopodia actin bundling factor critically promotes breast cancer cell invasion and metastasis. Oncotarget 2017; 7:13688-705. [PMID: 26883198 PMCID: PMC4924671 DOI: 10.18632/oncotarget.7327] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 01/27/2016] [Indexed: 01/11/2023] Open
Abstract
A critical process underlying cancer metastasis is the acquisition by tumor cells of an invasive phenotype. At the subcellular level, invasion is facilitated by actin-rich protrusions termed invadopodia, which direct extracellular matrix (ECM) degradation. Here, we report the identification of a new cytoskeletal component of breast cancer cell invadopodia, namely cysteine-rich protein 2 (CRP2). We found that CRP2 was not or only weakly expressed in epithelial breast cancer cells whereas it was up-regulated in mesenchymal/invasive breast cancer cells. In addition, high expression of the CRP2 encoding gene CSRP2 was associated with significantly increased risk of metastasis in basal-like breast cancer patients. CRP2 knockdown significantly reduced the invasive potential of aggressive breast cancer cells, whereas it did not impair 2D cell migration. In keeping with this, CRP2-depleted breast cancer cells exhibited a reduced capacity to promote ECM degradation, and to secrete and express MMP-9, a matrix metalloproteinase repeatedly associated with cancer progression and metastasis. In turn, ectopic expression of CRP2 in weakly invasive cells was sufficient to stimulate cell invasion. Both GFP-fused and endogenous CRP2 localized to the extended actin core of invadopodia, a structure primarily made of actin bundles. Purified recombinant CRP2 autonomously crosslinked actin filaments into thick bundles, suggesting that CRP2 contributes to the formation/maintenance of the actin core. Finally, CRP2 depletion significantly reduced the incidence of lung metastatic lesions in two xenograft mouse models of breast cancer. Collectively, our data identify CRP2 as a new cytoskeletal component of invadopodia that critically promotes breast cancer cell invasion and metastasis.
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Affiliation(s)
- Céline Hoffmann
- Laboratory of Experimental Cancer Research, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Xianqing Mao
- Laboratory of Experimental Cancer Research, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Monika Dieterle
- Laboratory of Experimental Cancer Research, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg.,NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Flora Moreau
- Laboratory of Experimental Cancer Research, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Antoun Al Absi
- Laboratory of Experimental Cancer Research, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - André Steinmetz
- Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Anaïs Oudin
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Guy Berchem
- Laboratory of Experimental Cancer Research, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Bassam Janji
- Laboratory of Experimental Cancer Research, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Clément Thomas
- Laboratory of Experimental Cancer Research, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
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Kihara T, Sugimoto Y, Shinohara S, Takaoka S, Miyake J. Cysteine-rich protein 2 accelerates actin filament cluster formation. PLoS One 2017; 12:e0183085. [PMID: 28813482 PMCID: PMC5558965 DOI: 10.1371/journal.pone.0183085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/29/2017] [Indexed: 12/22/2022] Open
Abstract
Filamentous actin (F-actin) forms many types of structures and dynamically regulates cell morphology and movement, and plays a mechanosensory role for extracellular stimuli. In this study, we determined that the smooth muscle-related transcription factor, cysteine-rich protein 2 (CRP2), regulates the supramolecular networks of F-actin. The structures of CRP2 and F-actin in solution were analyzed by small-angle X-ray solution scattering (SAXS). The general shape of CRP2 was partially unfolded and relatively ellipsoidal in structure, and the apparent cross sectional radius of gyration (Rc) was about 15.8 Å. The predicted shape, derived by ab initio modeling, consisted of roughly four tandem clusters: LIM domains were likely at both ends with the middle clusters being an unfolded linker region. From the SAXS analysis, the Rc of F-actin was about 26.7 Å, and it was independent of CRP2 addition. On the other hand, in the low angle region of the CRP2-bound F-actin scattering, the intensities showed upward curvature with the addition of CRP2, which indicates increasing branching of F-actin following CRP2 binding. From biochemical analysis, the actin filaments were augmented and clustered by the addition of CRP2. This F-actin clustering activity of CRP2 was cooperative with α-actinin. Thus, binding of CRP2 to F-actin accelerates actin polymerization and F-actin cluster formation.
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Affiliation(s)
- Takanori Kihara
- Department of Life and Environment Engineering, Faculty of Environmental Engineering, The University of Kitakyushu, Hibikino, Wakamatsu, Kitakyushu, Fukuoka, Japan
| | - Yasunobu Sugimoto
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Satoko Shinohara
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, Machikaneyama, Toyonaka, Osaka, Japan
| | - Shunpei Takaoka
- Department of Life and Environment Engineering, Faculty of Environmental Engineering, The University of Kitakyushu, Hibikino, Wakamatsu, Kitakyushu, Fukuoka, Japan
| | - Jun Miyake
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, Machikaneyama, Toyonaka, Osaka, Japan
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The molecular interaction of heart LIM protein (HLP) with RyR2 and caveolin-3 is essential for Ca 2+ -induced Ca 2+ release in the heart. Biochem Biophys Res Commun 2015; 463:975-81. [DOI: 10.1016/j.bbrc.2015.06.045] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 06/06/2015] [Indexed: 11/20/2022]
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NMR spectroscopy on domain dynamics in biomacromolecules. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 112:58-117. [DOI: 10.1016/j.pbiomolbio.2013.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 05/06/2013] [Accepted: 05/07/2013] [Indexed: 12/22/2022]
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Domain interactions of the transcription–translation coupling factor Escherichia coli NusG are intermolecular and transient. Biochem J 2011; 435:783-9. [DOI: 10.1042/bj20101679] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The bacterial transcription factor NusG (N-utilization substance G) is suggested to act as a key coupling factor between transcription and translation [Burmann, Schweimer, Luo, Wahl, Stitt, Gottesman and Rösch (2010) Science 328, 501–504] and contributes to phage λ-mediated antitermination in Escherichia coli that enables read-through of early transcription termination sites. E. coli NusG consists of two structurally and functionally distinct domains that are connected through a flexible linker. The homologous Aquifex aeolicus NusG, with a secondary structure that is highly similar to E. coli NusG shows direct interaction between its N- and C-terminal domains in a domain-swapped dimer. In the present study, we performed NMR paramagnetic relaxation enhancement measurements and identified interdomain interactions that were concentration dependent and thus probably not only weak and transient, but also predominantly intermolecular. This notion of two virtually independent domains in a monomeric protein was supported by 15N-relaxation measurements. Thus we suggest that a regulatory role of NusG interdomain interactions is highly unlikely.
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Boëda B, Knowles PP, Briggs DC, Murray-Rust J, Soriano E, Garvalov BK, McDonald NQ, Way M. Molecular recognition of the Tes LIM2-3 domains by the actin-related protein Arp7A. J Biol Chem 2011; 286:11543-54. [PMID: 21278383 PMCID: PMC3064208 DOI: 10.1074/jbc.m110.171264] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 12/15/2010] [Indexed: 11/06/2022] Open
Abstract
Actin-related proteins (Arps) are a highly conserved family of proteins that have extensive sequence and structural similarity to actin. All characterized Arps are components of large multimeric complexes associated with chromatin or the cytoskeleton. In addition, the human genome encodes five conserved but largely uncharacterized "orphan" Arps, which appear to be mostly testis-specific. Here we show that Arp7A, which has 43% sequence identity with β-actin, forms a complex with the cytoskeletal proteins Tes and Mena in the subacrosomal layer of round spermatids. The N-terminal 65-residue extension to the actin-like fold of Arp7A interacts directly with Tes. The crystal structure of the 1-65(Arp7A)·LIM2-3(Tes)·EVH1(Mena) complex reveals that residues 28-49 of Arp7A contact the LIM2-3 domains of Tes. Two alanine residues from Arp7A that occupy equivalent apolar pockets in both LIM domains as well as an intervening GPAK linker that binds the LIM2-3 junction are critical for the Arp7A-Tes interaction. Equivalent occupied apolar pockets are also seen in the tandem LIM domain structures of LMO4 and Lhx3 bound to unrelated ligands. Our results indicate that apolar pocket interactions are a common feature of tandem LIM domain interactions, but ligand specificity is principally determined by the linker sequence.
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Affiliation(s)
- Batiste Boëda
- From the Cell Motility and
- the Cell Polarity and Migration Group, CNRS 2582, Institut Pasteur, 75724 Paris, France, and
| | - Phillip P. Knowles
- Structural Biology Laboratories, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, United Kingdom
| | - David C. Briggs
- Structural Biology Laboratories, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, United Kingdom
- the Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Judith Murray-Rust
- Structural Biology Laboratories, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, United Kingdom
| | - Erika Soriano
- Structural Biology Laboratories, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, United Kingdom
| | - Boyan K. Garvalov
- the Institute of Neuropathology, Justus Liebig University, Aulweg 123, 35392 Giessen, Germany
| | - Neil Q. McDonald
- Structural Biology Laboratories, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, United Kingdom
- the Institute of Structural and Molecular Biology, University College London and Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom
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Schallus T, Fehér K, Ulrich AS, Stier G, Muhle-Goll C. Structure and dynamics of the human muscle LIM protein. FEBS Lett 2009; 583:1017-22. [PMID: 19230835 DOI: 10.1016/j.febslet.2009.02.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Revised: 02/10/2009] [Accepted: 02/11/2009] [Indexed: 12/01/2022]
Abstract
The family of cysteine rich proteins (CRP) comprises three closely homologous members that have been reported to interact with alpha-actinin. Muscular LIM protein (MLP/CRP3), the skeletal muscle variant, was originally discovered as a positive regulator of myogenesis and is suggested to be part of the stretch sensor of the myofibril through its interaction with telethonin (T-Cap). We determined the structure of both LIM domains of human MLP by nuclear magnetic resonance spectroscopy. We confirm by (15)N relaxation measurements that both LIM domains act as independent units and that the adjacent linker regions are fully flexible. With the published structures of CRP1 and CRP2, the complete family has now been structurally characterized.
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Affiliation(s)
- Thomas Schallus
- Department of Biomolecular Mechanisms, Max-Planck-Institute for Medical Research, Heidelberg, Germany
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9
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Sagave JF, Moser M, Ehler E, Weiskirchen S, Stoll D, Günther K, Büttner R, Weiskirchen R. Targeted disruption of the mouse Csrp2 gene encoding the cysteine- and glycine-rich LIM domain protein CRP2 result in subtle alteration of cardiac ultrastructure. BMC DEVELOPMENTAL BIOLOGY 2008; 8:80. [PMID: 18713466 PMCID: PMC2529283 DOI: 10.1186/1471-213x-8-80] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Accepted: 08/19/2008] [Indexed: 11/23/2022]
Abstract
Background The cysteine and glycine rich protein 2 (CRP2) encoded by the Csrp2 gene is a LIM domain protein expressed in the vascular system, particularly in smooth muscle cells. It exhibits a bimodal subcellular distribution, accumulating at actin-based filaments in the cytosol and in the nucleus. In order to analyze the function of CRP2 in vivo, we disrupted the Csrp2 gene in mice and analysed the resulting phenotype. Results A ~17.3 kbp fragment of the murine Csrp2 gene containing exon 3 through 6 was isolated. Using this construct we confirmed the recently determined chromosomal localization (Chromosome 10, best fit location between markers D10Mit203 proximal and D10Mit150 central). A gene disruption cassette was cloned into exon 4 and a mouse strain lacking functional Csrp2 was generated. Mice lacking CRP2 are viable and fertile and have no obvious deficits in reproduction and survival. However, detailed histological and electron microscopic studies reveal that CRP2-deficient mice have subtle alterations in their cardiac ultrastructure. In these mice, the cardiomyocytes display a slight increase in their thickness, indicating moderate hypertrophy at the cellular level. Although the expression of several intercalated disc-associated proteins such as β-catenin, N-RAP and connexin-43 were not affected in these mice, the distribution of respective proteins was changed within heart tissue. Conclusion We conclude that the lack of CRP2 is associated with alterations in cardiomyocyte thickness and hypertrophy.
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Affiliation(s)
- Julia F Sagave
- Institute of Clinical Chemistry and Pathobiochemistry, RWTH- University Hospital Aachen, Germany.
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Alleyne AT, O'Garro LW. Host selectivity of a 40kDa phytotoxic extract fromColletotrichum gloeosporioides(Phyllachoraceae) on yamDioscorea alata(Dioscoreace). CARIBB J SCI 2008. [DOI: 10.18475/cjos.v44i1.a2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Thomas C, Moreau F, Dieterle M, Hoffmann C, Gatti S, Hofmann C, Van Troys M, Ampe C, Steinmetz A. The LIM domains of WLIM1 define a new class of actin bundling modules. J Biol Chem 2007; 282:33599-33608. [PMID: 17827159 DOI: 10.1074/jbc.m703691200] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Actin filament bundling, i.e. the formation of actin cables, is an important process that relies on proteins able to directly bind and cross-link subunits of adjacent actin filaments. Animal cysteine-rich proteins and their plant counterparts are two LIM domain-containing proteins that were recently suggested to define a new family of actin cytoskeleton regulators involved in actin filament bundling. We here identified the LIM domains as responsible for F-actin binding and bundling activities of the tobacco WLIM1. The deletion of one of the two LIM domains reduced significantly, but did not entirely abolish, the ability of WLIM1 to bind actin filaments. Individual LIM domains were found to interact directly with actin filaments, although with a reduced affinity compared with the native protein. Variants lacking the C-terminal or the inter-LIM domain were only weakly affected in their F-actin stabilizing and bundling activities and trigger the formation of thick cables containing tightly packed actin filaments as does the native protein. In contrast, the deletion of one of the two LIM domains negatively impacted both activities and resulted in the formation of thinner and wavier cables. In conclusion, we demonstrate that the LIM domains of WLIM1 are new autonomous actin binding and bundling modules that cooperate to confer WLIM1 high actin binding and bundling activities.
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Affiliation(s)
- Clément Thomas
- Centre de Recherche Public-Santé, Luxembourg, L-1526 Luxembourg.
| | - Flora Moreau
- Centre de Recherche Public-Santé, Luxembourg, L-1526 Luxembourg
| | - Monika Dieterle
- Centre de Recherche Public-Santé, Luxembourg, L-1526 Luxembourg
| | - Céline Hoffmann
- Centre de Recherche Public-Santé, Luxembourg, L-1526 Luxembourg
| | - Sabrina Gatti
- Centre de Recherche Public-Santé, Luxembourg, L-1526 Luxembourg
| | - Christina Hofmann
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, F-67084 Strasbourg, France
| | - Marleen Van Troys
- VIB Department of Medical Protein Research, Ugent and Department of Biochemistry, Faculty of Medicine and Health Sciences, B-9052 Ghent, Belgium
| | - Christophe Ampe
- VIB Department of Medical Protein Research, Ugent and Department of Biochemistry, Faculty of Medicine and Health Sciences, B-9052 Ghent, Belgium
| | - André Steinmetz
- Centre de Recherche Public-Santé, Luxembourg, L-1526 Luxembourg
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Jarymowycz VA, Stone MJ. Fast time scale dynamics of protein backbones: NMR relaxation methods, applications, and functional consequences. Chem Rev 2007; 106:1624-71. [PMID: 16683748 DOI: 10.1021/cr040421p] [Citation(s) in RCA: 312] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Virginia A Jarymowycz
- Department of Chemistry and Interdisciplinary Biochemistry Program, Indiana University, Bloomington, Indiana 47405-0001, USA
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Baminger B, Ludwiczek ML, Kontaxis G, Knapp S, Konrat R. Protein-protein interaction site mapping using NMR-detected mutational scanning. JOURNAL OF BIOMOLECULAR NMR 2007; 38:133-7. [PMID: 17447011 DOI: 10.1007/s10858-007-9154-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Accepted: 03/12/2007] [Indexed: 05/15/2023]
Abstract
We demonstrate a novel NMR method for the mapping of protein-protein interaction sites. In our approach protein-protein binding sites are mapped by competition binding experiments using indirect NMR reporter technology and Ala positional scanning. The methodology provides high sensitivity, ease of implementation and high-throughput capabilities. The feasibility of the technique is demonstrated with an application to the beta-Catenin/Tcf4 complex.
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Affiliation(s)
- Bettina Baminger
- Department of Biomolecular Structural Chemistry, Max F. Perutz Laboratories, University of Vienna, Vienna, 1030, Austria
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Jin L, Kern MJ, Otey CA, Wamhoff BR, Somlyo AV. Angiotensin II, focal adhesion kinase, and PRX1 enhance smooth muscle expression of lipoma preferred partner and its newly identified binding partner palladin to promote cell migration. Circ Res 2007; 100:817-25. [PMID: 17322171 DOI: 10.1161/01.res.0000261351.54147.de] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Lipoma preferred partner (LPP) is a proline rich LIM domain family protein highly expressed at plasma membrane dense bodies and focal adhesions in smooth muscle cells.(1) Using the C-terminus of LPP as bait in a yeast two hybrid system, palladin, an actin-associated protein was identified. The palladin interacting region of LPP was mapped to the first and second LIM domains. The N-terminus of palladin interacted with LPP both in vitro and in vivo, but not solely through its FPLPPP and FPPPP motifs. Like LPP, palladin, is highly expressed in differentiated smooth muscle, colocalized at focal adhesions, at isolated lamellipodia and at dense bodies in smooth muscle tissue. Both LPP and palladin enhanced cell migration and spreading. LPP and palladin expression was markedly decreased, in contrast to vinculin or paxillin, in migration defective focal adhesion kinase null cells, but was restored by expression of the paired-related homeobox gene-1 protein. We have previously shown in focal adhesion kinase null cells, that tetracycline induced expression of focal adhesion kinase upregulated expression of LPP(2) and now show upregulation of palladin, and paired-related homeobox gene-1 protein. The expression of both LPP and palladin, like smooth muscle alpha-actin, was increased by angiotensin II, regulated by actin dynamics, upregulated by myocardin and expressed in the neointima of injured aorta. Overall, the data suggest that the function of LPP and palladin is context dependent, that they play a critical role in cytoskeletal remodeling, respond to signals induced by vascular injury as well as signals that induce smooth muscle cell hypertrophy, such as angiotension II.
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Affiliation(s)
- Li Jin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
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Haynes C, Iakoucheva LM. Serine/arginine-rich splicing factors belong to a class of intrinsically disordered proteins. Nucleic Acids Res 2006; 34:305-12. [PMID: 16407336 PMCID: PMC1326245 DOI: 10.1093/nar/gkj424] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Serine/arginine-rich (SR) splicing factors play an important role in constitutive and alternative splicing as well as during several steps of RNA metabolism. Despite the wealth of functional information about SR proteins accumulated to-date, structural knowledge about the members of this family is very limited. To gain a better insight into structure-function relationships of SR proteins, we performed extensive sequence analysis of SR protein family members and combined it with ordered/disordered structure predictions. We found that SR proteins have properties characteristic of intrinsically disordered (ID) proteins. The amino acid composition and sequence complexity of SR proteins were very similar to those of the disordered protein regions. More detailed analysis showed that the SR proteins, and their RS domains in particular, are enriched in the disorder-promoting residues and are depleted in the order-promoting residues as compared to the entire human proteome. Moreover, disorder predictions indicated that RS domains of SR proteins were completely unstructured. Two different classification methods, the charge-hydropathy measure and the cumulative distribution function (CDF) of the disorder scores, were in agreement with each other, and they both strongly predicted members of the SR protein family to be disordered. This study emphasizes the importance of the disordered structure for several functions of SR proteins, such as for spliceosome assembly and for interaction with multiple partners. In addition, it demonstrates the usefulness of order/disorder predictions for inferring protein structure from sequence.
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Affiliation(s)
| | - Lilia M. Iakoucheva
- To whom correspondence should be addressed. Tel: +1 212 327 7989; Fax: +1 212 327 7996;
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van den Berk LCJ, van Ham MA, te Lindert MM, Walma T, Aelen J, Vuister GW, Hendriks WJAJ. The interaction of PTP-BL PDZ domains with RIL: An enigmatic role for the RIL LIM domain. Mol Biol Rep 2005; 31:203-15. [PMID: 15663004 DOI: 10.1007/s11033-005-1407-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PDZ domains are protein-protein interaction modules that are crucial for the assembly of structural and signaling complexes. PDZ domains specifically bind short carboxyl-terminal peptides and occasionally internal sequences that structurally resemble peptide termini. Previously, using yeast two-hybrid methodology, we studied the interaction of two PDZ domains present in the large submembranous protein tyrosine phosphatase PTP-BL with' the C-terminal half of the LIM domain-containing protein RIL. Deletion of the extreme RIL C-terminus did not eliminate binding, suggesting the presence of a PDZ binding site within the RIL LIM moiety. We have now performed experiments in mammalian cell lysates and found that the RIL C-terminus proper, but not the RIL LIM domain, can interact with PTP-BL, albeit very weakly. However, this interaction with PTP-BL PDZ domains is greatly enhanced when the combined RIL LIM domain and C-terminus is used, pointing to synergistic effects. NMR titration experiments and site-directed mutagenesis indicate that this result is not dependent on specific interactions that require surface exposed residues on the RIL LIM domain, suggesting a stabilizing role in the association with PTP-BL.
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Affiliation(s)
- Lieke C J van den Berk
- Department of Cell Biology, Nijmegen Center for Molecular Life Sciences, University of Nijmegen, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
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18
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Kadrmas JL, Beckerle MC. The LIM domain: from the cytoskeleton to the nucleus. Nat Rev Mol Cell Biol 2004; 5:920-31. [PMID: 15520811 DOI: 10.1038/nrm1499] [Citation(s) in RCA: 560] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
First described 15 years ago as a cysteine-rich sequence that was common to a small group of homeodomain transcription factors, the LIM domain is now recognized as a tandem zinc-finger structure that functions as a modular protein-binding interface. LIM domains are present in many proteins that have diverse cellular roles as regulators of gene expression, cytoarchitecture, cell adhesion, cell motility and signal transduction. An emerging theme is that LIM proteins might function as biosensors that mediate communication between the cytosolic and the nuclear compartments.
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Affiliation(s)
- Julie L Kadrmas
- Huntsman Cancer Institute and the Department of Biology, University of Utah, 2000 East, Circle of Hope, Salt Lake City, Utah 84112, USA
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19
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Casrouge A, Veitia R, Kirchner J, Bevan MJ, Kanellopoulos J. The human and mouse orthologous LIM-only proteins respectively encoded in chromosome 6 and 17 show a different expression pattern. Microbes Infect 2004; 6:1063-72. [PMID: 15380775 PMCID: PMC2778486 DOI: 10.1016/j.micinf.2004.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2004] [Accepted: 06/04/2004] [Indexed: 01/15/2023]
Abstract
Thymocytes interact with various subpopulations of thymic epithelial cells (TECs) at different stages of their development. To identify new molecules specifically expressed in TECs and/or thymic nurse cells (TNCs), we used representational difference analysis. We identified a LIM protein located on mouse chromosome 17 (m17TLP) and belonging to the family of the LIM-only proteins (LIMo). We found a new splice variant in addition to the two described A and B isoforms. The three alternative species of m17TLP are found strictly in the thymic stroma. This protein is expressed on a subpopulation of TECs and TNCs. Strikingly, we found that the human ortholog of m17TLP, located on chromosome 6 (h6LIMo), is expressed in most tissues, but not in skeletal muscle. We have identified four human splice variants of h6LIMo which differ in their carboxy-terminal regions. The sequence comprising the genomic structure suggests that CRP2 is the closest known relative of m17TLP. Although the human and mouse nucleotide sequences are 88-97% homologous, this homology is reduced to 47% in the promoter regions, which strongly suggests that their differential expression is related to their promoter regulatory activity.
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Affiliation(s)
- Armanda Casrouge
- Laboratoire de Biologie Moléculaire du Gène, Inserm U277-Institut Pasteur, 75724-Paris cedex 15, France
| | - Reiner Veitia
- Immunogénétique humaine, Institut Pasteur, Université Denis Diderot, Paris, France
| | - Jacqueline Kirchner
- Department of Immunology, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Michael. J. Bevan
- Department of Immunology, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Jean Kanellopoulos
- Laboratoire Activation Cellulaire et Transduction des Signaux, IBBMC, CNRS-UMR 8619, Université Paris-Sud Centre d’Orsay, 91405 Orsay cedex, France
- Corresponding author. Tel.: +33-1-69-15-48-25; fax: +33-1-69-85-37-15. (J. Kanellopoulos)
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20
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Velyvis A, Vaynberg J, Yang Y, Vinogradova O, Zhang Y, Wu C, Qin J. Structural and functional insights into PINCH LIM4 domain-mediated integrin signaling. Nat Struct Mol Biol 2003; 10:558-64. [PMID: 12794636 DOI: 10.1038/nsb938] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2003] [Accepted: 05/09/2003] [Indexed: 11/09/2022]
Abstract
PINCH is an adaptor protein found in focal adhesions, large cellular complexes that link extracellular matrix to the actin cytoskeleton. PINCH, which contains an array of five LIM domains, has been implicated as a platform for multiple protein-protein interactions that mediate integrin signaling within focal adhesions. We had previously characterized the LIM1 domain of PINCH, which functions in focal adhesions by binding specifically to integrin-linked kinase. Using NMR spectroscopy, we show here that the PINCH LIM4 domain, while maintaining the conserved LIM scaffold, recognizes the third SH3 domain of another adaptor protein, Nck2 (also called Nckbeta or Grb4), in a manner distinct from that of the LIM1 domain. Point mutation of LIM residues in the SH3-binding interface disrupted LIM-SH3 interaction and substantially impaired localization of PINCH to focal adhesions. These data provide novel structural insight into LIM domain-mediated protein-protein recognition and demonstrate that the PINCH-Nck2 interaction is an important component of the focal adhesion assembly during integrin signaling.
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Affiliation(s)
- Algirdas Velyvis
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10500 Euclid Avenue, Cleveland, Ohio 44102, USA
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21
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Deane JE, Mackay JP, Kwan AHY, Sum EYM, Visvader JE, Matthews JM. Structural basis for the recognition of ldb1 by the N-terminal LIM domains of LMO2 and LMO4. EMBO J 2003; 22:2224-33. [PMID: 12727888 PMCID: PMC156068 DOI: 10.1093/emboj/cdg196] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2003] [Revised: 02/27/2003] [Accepted: 03/05/2003] [Indexed: 01/29/2023] Open
Abstract
LMO2 and LMO4 are members of a small family of nuclear transcriptional regulators that are important for both normal development and disease processes. LMO2 is essential for hemopoiesis and angiogenesis, and inappropriate overexpression of this protein leads to T-cell leukemias. LMO4 is developmentally regulated in the mammary gland and has been implicated in breast oncogenesis. Both proteins comprise two tandemly repeated LIM domains. LMO2 and LMO4 interact with the ubiquitous nuclear adaptor protein ldb1/NLI/CLIM2, which associates with the LIM domains of LMO and LIM homeodomain proteins via its LIM interaction domain (ldb1-LID). We report the solution structures of two LMO:ldb1 complexes (PDB: 1M3V and 1J2O) and show that ldb1-LID binds to the N-terminal LIM domain (LIM1) of LMO2 and LMO4 in an extended conformation, contributing a third strand to a beta-hairpin in LIM1 domains. These findings constitute the first molecular definition of LIM-mediated protein-protein interactions and suggest a mechanism by which ldb1 can bind a variety of LIM domains that share low sequence homology.
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Affiliation(s)
- Janet E Deane
- School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia
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22
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Chang DF, Belaguli NS, Iyer D, Roberts WB, Wu SP, Dong XR, Marx JG, Moore MS, Beckerle MC, Majesky MW, Schwartz RJ. Cysteine-rich LIM-only proteins CRP1 and CRP2 are potent smooth muscle differentiation cofactors. Dev Cell 2003; 4:107-18. [PMID: 12530967 DOI: 10.1016/s1534-5807(02)00396-9] [Citation(s) in RCA: 197] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cysteine-rich LIM-only proteins, CRP1 and CRP2, expressed during cardiovascular development act as bridging molecules that associate with serum response factor and GATA proteins. SRF-CRP-GATA complexes strongly activated smooth muscle gene targets. CRP2 was found in the nucleus during early stages of coronary smooth muscle differentiation from proepicardial cells. A dominant-negative CRP2 mutant blocked proepicardial cells from differentiating into smooth muscle cells. Together with SRF and GATA proteins, CRP1 and CRP2 converted pluripotent 10T1/2 fibroblasts into smooth muscle cells, while muscle LIM protein CRP3 inhibited the conversion. Thus, LIM-only proteins of the CRP family play important roles in organizing multiprotein complexes, both in the cytoplasm, where they participate in cytoskeletal remodeling, and in the nucleus, where they strongly facilitate smooth muscle differentiation.
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Affiliation(s)
- David F Chang
- The Center for Cardiovascular Development, Baylor College of Medicine, Houston, TX 77030, USA
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23
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Midorikawa Y, Tsutsumi S, Taniguchi H, Ishii M, Kobune Y, Kodama T, Makuuchi M, Aburatani H. Identification of genes associated with dedifferentiation of hepatocellular carcinoma with expression profiling analysis. Jpn J Cancer Res 2002; 93:636-43. [PMID: 12079511 PMCID: PMC5927043 DOI: 10.1111/j.1349-7006.2002.tb01301.x] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
To identify the genes associated with dedifferentiation of hepatocellular carcinoma (HCC), gene expression profiles of HCCs of well-and moderately differentiated grades were compared by means of oligonucleotide arrays. One tumor showed a nodule-in-nodule appearance (NIN), which is occasionally observed in the course of progression of HCC from well to less differentiated grade, when an inner, moderately differentiated tumor (MD) develops sequentially from the outer, well-differentiated tumor (WD). Seventy-six genes were identified to be up-regulated more than 3-fold and 33 genes were down-regulated in the inner nodule in NIN. By statistical analysis of the profiles from 10 individual additional liver tumors, 5 WDs and 5 MDs, we were able to identify 12 genes, LAMA3, PPIB, ADAR, PSMD4, NDUFS8, D9SVA, CCT3, GBAP, ARD1, RDBP, CSRP2, and TLE1, with significantly elevated expression, and 4 genes, CP, IL7R, CD48, and PLGL, with decreased expression in MD. These selected genes were further validated using another 12 tumors, 5 WDs and 7 MDs, with semi-quantitative RT-PCR. We also applied neighborhood analysis to list the genes with high predictability values as most closely correlated with WD-MD distinction. Seven genes, ADAR, PSMD4, D9SVA, CCT3, GBAP, RDBP, and CSRP2, whose expression was elevated and one gene, IL7R, whose expression was decreased, were included among the top 50 predictor genes. These genes are likely to be associated with dedifferentiation of HCC and their identification may help to elucidate the mechanism of liver cancer progression.
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Affiliation(s)
- Yutaka Midorikawa
- Genome Science Division, Research Center for Advanced Science and Technology, University of Tokyo, Meguro-ku, Tokyo 153-8904
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24
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Weiskirchen R, Moser M, Weiskirchen S, Erdel M, Dahmen S, Buettner R, Gressner AM. LIM-domain protein cysteine- and glycine-rich protein 2 (CRP2) is a novel marker of hepatic stellate cells and binding partner of the protein inhibitor of activated STAT1. Biochem J 2001; 359:485-96. [PMID: 11672422 PMCID: PMC1222169 DOI: 10.1042/0264-6021:3590485] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Activation of hepatic stellate cells is considered to be the main step in the development of liver fibrosis, which is characterized by the transition of quiescent vitamin-A-rich cells to proliferative, fibrogenic and contractile myofibroblasts. The identification of regulatory genes during early cell activation and transdifferentiation is essential to extend our knowledge of hepatic fibrogenesis. In liver, the gene CSRP2 is exclusively expressed by stellate cells, whereas no transcripts are detectable in hepatocytes, sinusoidal endothelial cells or Kupffer cells. The early activation of stellate cells induced by platelet-derived growth factor is accompanied by an enhanced expression of CSRP2. During later stages of transdifferentiation, the expression of CSRP2 in these cells is suppressed in vitro and in vivo. The CSRP2-encoded cysteine- and glycine-rich double-LIM-domain protein (CRP)2 is proposed to function as a molecular adapter, arranging two or more as yet unidentified protein constituents into a macromolecular complex. To identify these proteins and assign a cellular function to CRP2, a human cDNA library was screened with full-length CRP2 as bait in a yeast two-hybrid screen. The protein inhibitor of activated STAT1 ('PIAS1') was shown to associate selectively with the C-terminal LIM domain of CRP2. Physical interaction of both proteins in the cellular environment was confirmed by co-localization experiments with confocal laser scanning microscopy and co-immunoprecipitation analysis. These results establish CRP2 as a potential new factor in the JAK/STAT-signalling pathway and suggest that the suppression of CSRP2 might be a prerequisite for the myofibroblastic transition of hepatic stellate cells.
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Affiliation(s)
- R Weiskirchen
- Institute of Clinical Chemistry and Pathobiochemistry, RWTH-University Hospital, Pauwelsstrasse 30, D-52074 Aachen, Germany.
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25
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Schüler W, Kloiber K, Matt T, Bister K, Konrat R. Application of cross-correlated NMR spin relaxation to the zinc-finger protein CRP2(LIM2): evidence for collective motions in LIM domains. Biochemistry 2001; 40:9596-604. [PMID: 11583159 DOI: 10.1021/bi010509m] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The solution structure of quail CRP2(LIM2) was significantly improved by using an increased number of NOE constraints obtained from a 13C,15N-labeled protein sample and by applying a recently developed triple-resonance cross-correlated relaxation experiment for the determination of the backbone dihedral angle psi. Additionally, the relative orientation of the 15N(i)-1HN(i) dipole and the 13CO(i) CSA tensor, which is related to both backbone angles phi and psi, was probed by nitrogen-carbonyl multiple-quantum relaxation and used as an additional constraint for the refinement of the local geometry of the metal-coordination sites in CRP2(LIM2). The backbone dynamics of residues located in the folded part of CRP2(LIM2) have been characterized by proton-detected 13C'(i-1)-15N(i) and 15N(i)-1HN(i) multiple-quantum relaxation, respectively. We show that regions having cross-correlated time modulation of backbone isotropic chemical shifts on the millisecond to microsecond time scale correlate with residues that are structurally altered in the mutant protein CRP2(LIM2)R122A (disruption of the CCHC zinc-finger stabilizing side-chain hydrogen bond) and that these residues are part of an extended hydrogen-bonding network connecting the two zinc-binding sites. This indicates the presence of long-range collective motions in the two zinc-binding subdomains. The conformational plasticity of the LIM domain may be of functional relevance for this important protein recognition motif.
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Affiliation(s)
- W Schüler
- Institute of Organic Chemistry and Institute of Biochemistry, University of Innsbruck, Austria
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26
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Deane JE, Sum E, Mackay JP, Lindeman GJ, Visvader JE, Matthews JM. Design, production and characterization of FLIN2 and FLIN4: the engineering of intramolecular ldb1:LMO complexes. PROTEIN ENGINEERING 2001; 14:493-9. [PMID: 11522923 DOI: 10.1093/protein/14.7.493] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The nuclear LIM-only (LMO) transcription factors LMO2 and LMO4 play important roles in both normal and leukemic T-cell development. LIM domains are cysteine/histidine-rich domains that contain two structural zinc ions and that function as protein-protein adaptors; members of the LMO family each contain two closely spaced LIM domains. These LMO proteins all bind with high affinity to the nuclear protein LIM domain binding protein 1 (ldb1). The LMO-ldb1 interaction is mediated through the N-terminal LIM domain (LIM1) of LMO proteins and a 38-residue region towards the C-terminus of ldb1 [ldb1(LID)]. Unfortunately, recombinant forms of LMO2 and LMO4 have limited solubility and stability, effectively preventing structural analysis. Therefore, we have designed and constructed a fusion protein in which ldb1(LID) and LIM1 of LMO2 can form an intramolecular complex. The engineered protein, FLIN2 (fusion of the LIM interacting domain of ldb1 and the N-terminal LIM domain of LMO2) has been expressed and purified in milligram quantities. FLIN2 is monomeric, contains significant levels of secondary structure and yields a sharp and well-dispersed one-dimensional (1)H NMR spectrum. The analogous LMO4 protein, FLIN4, has almost identical properties. These data suggest that we will be able to obtain high-resolution structural information about the LMO-ldb1 interactions.
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Affiliation(s)
- J E Deane
- Department of Biochemistry, University of Sydney, Sydney, NSW 2006, Australia
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27
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Fieber W, Schneider ML, Matt T, Kräutler B, Konrat R, Bister K. Structure, function, and dynamics of the dimerization and DNA-binding domain of oncogenic transcription factor v-Myc. J Mol Biol 2001; 307:1395-410. [PMID: 11292350 DOI: 10.1006/jmbi.2001.4537] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The protein product (c-Myc) of the protooncogene c-myc is a transcriptional regulator playing a key role in cellular growth, differentiation, and apoptosis. Deregulated myc genes, like the transduced retroviral v-myc allele, are oncogenic and cause cell transformation. The C-terminal bHLHZip domain of v-Myc, encompassing protein dimerization (helix-loop-helix, leucine zipper) and DNA contact (basic region) surfaces, was expressed in bacteria as a highly soluble p15(v-myc )recombinant protein. Dissociation constants (K(d)) for the heterodimer formed with the recombinant bHLHZip domain of the Myc binding partner Max (p14(max)) and for the Myc-Max-DNA complex were estimated using circular dichroism (CD) spectroscopy and quantitative electrophoretic mobility shift assay (EMSA). Multi-dimensional NMR spectroscopy was used to characterize the solution structural and dynamic properties of the v-Myc bHLHZip domain. Significant secondary chemical shifts indicate the presence of two separated alpha-helical regions. The C-terminal leucine zipper region forms a compact alpha-helix, while the N-terminal basic region exhibits conformational averaging with substantial alpha-helical content. Both helices lack stabilizing tertiary side-chain interactions and represent exceptional examples for loosely coupled secondary structural segments in a native protein. These results and CD thermal denaturation data indicate a monomeric state of the v-Myc bHLHZip domain. The (15)N relaxation data revealed backbone mobilities which corroborate the existence of a partially folded state, and suggest a "beads-on-a-string" motional behaviour of the v-Myc bHLHZip domain in solution. The preformation of alpha-helical regions was confirmed by CD thermal denaturation studies, and quantification of the entropy changes caused by the hydrophobic effect and the reduction of conformational entropy upon protein dimerization. The restricted conformational space of the v-Myc bHLHZip domain reduces the entropy penalty associated with heterodimerization and allows rapid and accurate recognition by the authentic Myc binding partner Max.
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Affiliation(s)
- W Fieber
- Institute of Organic Chemistry and
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28
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Beglova N, North CL, Blacklow SC. Backbone dynamics of a module pair from the ligand-binding domain of the LDL receptor. Biochemistry 2001; 40:2808-15. [PMID: 11258891 DOI: 10.1021/bi0027276] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ligand-binding domain of the LDL receptor consists of seven contiguous LDL-A modules. The fifth of these ligand-binding modules is absolutely required for recognition of both LDL and beta-VLDL particles. A four-residue linker of variable sequence connects each pair of modules, except for modules four and five, which are connected by a 12-residue linker. To provide a more detailed understanding of the structural relationship in a typical pair of functionally important LDL-A repeats of the LDLR, we investigated the backbone dynamics of repeats five (LR5) and six (LR6) alone and in the context of the covalently connected LR5-6 pair. Our results reveal substantial flexibility in the four-residue linker connecting the two repeats in the LR5-6 pair. The intrinsic dynamic behavior of each repeat is essentially unchanged when the repeats are covalently connected. These observations indicate that the relative orientation of repeats in LR5-6 is not fixed. Modeled in an extended conformation, the linker can separate LR5 and LR6 by up to 15 A, a distance that would allow substantial freedom of motion of each repeat with respect to the other in the pair.
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Affiliation(s)
- N Beglova
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, Massachusetts 02115, USA
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29
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Wixler V, Geerts D, Laplantine E, Westhoff D, Smyth N, Aumailley M, Sonnenberg A, Paulsson M. The LIM-only protein DRAL/FHL2 binds to the cytoplasmic domain of several alpha and beta integrin chains and is recruited to adhesion complexes. J Biol Chem 2000; 275:33669-78. [PMID: 10906324 DOI: 10.1074/jbc.m002519200] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
LIM proteins contain one or more double zinc finger structures (LIM domains) mediating specific contacts between proteins that participate in the formation of multiprotein complexes. We report that the LIM-only protein DRAL/FHL2, with four and a half LIM domains, can associate with alpha(3A), alpha(3B), alpha(7A), and several beta integrin subunits as shown in yeast two-hybrid assays as well as after overexpression in human cells. The amino acid sequence immediately following the conserved membrane-proximal region in the integrin alpha subunits or the C-terminal region with the conserved NXXY motif of the integrin beta subunits are critical for binding DRAL/FHL2. Furthermore, the DRAL/FHL2 associates with itself and with other molecules that bind to the cytoplasmic domain of integrin alpha subunits. Deletion analysis of DRAL/FHL2 revealed that particular LIM domains or LIM domain combinations bind the different proteins. These results, together with the fact that full-length DRAL/FHL2 is found in cell adhesion complexes, suggest that it is an adaptor/docking protein involved in integrin signaling pathways.
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Affiliation(s)
- V Wixler
- Institute for Biochemistry II, Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 52, 50931 Cologne, Germany
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30
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Weiskirchen R, Gressner AM. The cysteine- and glycine-rich LIM domain protein CRP2 specifically interacts with a novel human protein (CRP2BP). Biochem Biophys Res Commun 2000; 274:655-63. [PMID: 10924333 DOI: 10.1006/bbrc.2000.3187] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We used the interaction trap to isolate a novel human protein that specifically interacts with the double LIM domain protein CRP2. This protein, designated CRP2BP (for CRP2 binding partner), was previously postulated by sequencing contigs of human chromosome 20. The observed interaction is mediated via the LIM1 domain of CRP2 and is of functional relevance in cellular environment. This novel single copy gene spans approximately 45-bp and is organized into at least ten exons. CRP2BP is expressed in all human tissues tested, with a major mRNA of 4-kb in size and an additional 3.2-kb transcript in placenta.
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Affiliation(s)
- R Weiskirchen
- Central Laboratory, Institute of Clinical Chemistry and Pathobiochemistry, RWTH-University Hospital, Pauwelstrasse 30, Aachen, D-52074, Germany.
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31
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Abstract
Lim1, also known as Lhx1, encodes a LIM homeodomain transcription factor that is essential for head development in the mouse. As with other LIM homeodomain proteins, LIM1 has two LIM domains located N-terminal to the homeodomain, with each LIM domain containing two zinc finger motifs. LIM domains can physically interact with other proteins to form protein complexes that regulate transcription. Previous studies have suggested that LIM domains negatively regulate the transcriptional activity of their associated homeodomains. To investigate the requirement of LIM domains for LIM1 activity, we have mutated the Lim1 gene to alter the conserved amino acid residues that are required for zinc finger structure within both of the LIM domains. Although mice homozygous for this Lim1 allele express the mutant mRNA and protein appropriately, they are a phenocopy for Lim1-null mice. These results suggest that the integrity of the LIM domains is essential for LIM1 activity in mouse head development. genesis 27:12-21, 2000.
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Affiliation(s)
- S S Cheah
- Department of Molecular Genetics, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, USA
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32
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Kloiber K, Weiskirchen R, Kräutler B, Bister K, Konrat R. Mutational analysis and NMR spectroscopy of quail cysteine and glycine-rich protein CRP2 reveal an intrinsic segmental flexibility of LIM domains. J Mol Biol 1999; 292:893-908. [PMID: 10525413 DOI: 10.1006/jmbi.1999.3118] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The LIM domain is a conserved cysteine and histidine-containing structural module of two tandemly arranged zinc fingers. It has been identified in single or multiple copies in a variety of regulatory proteins, either in combination with defined functional domains, like homeodomains, or alone, like in the CRP family of LIM proteins. Structural studies of CRP proteins have allowed a detailed evaluation of interactions in LIM-domains at the molecular level. The packing interactions in the hydrophobic core have been identified as a significant contribution to the LIM domain fold, whereas hydrogen bonding within each single zinc binding site stabilizes zinc finger geometry in a so-called "outer" or "indirect" coordination sphere. Here we report the solution structure of a point-mutant of the carboxyl-terminal LIM domain of quail cysteine and glycine-rich protein CRP2, CRP2(LIM2)R122A, and discuss the structural consequences of the disruption of the hydrogen bond formed between the guanidinium side-chain of Arg122 and the zinc-coordinating cysteine thiolate group in the CCHC rubredoxin-knuckle. The structural analysis revealed that the three-dimensional structure of the CCHC zinc binding site in CRP2(LIM2)R122A is adapted as a consequence of the modified hydrogen bonding pattern. Additionally, as a result of the conformational rearrangement of the zinc binding site, the packing interactions in the hydrophobic core region are altered, leading to a change in the relative orientation of the two zinc fingers with a concomitant change in the solvent accessibilities of hydrophobic residues located at the interface of the two modules. The backbone dynamics of residues located in the folded part of CRP2(LIM2)R122A have been characterized by proton-detected(15)N NMR spectroscopy. Analysis of the R2/R1ratios revealed a rotational correlation time of approximately 6.2 ns and tumbling with an axially symmetric diffusion tensor (D parallel/D perpendicular=1.43). The relaxation data were also analyzed using a reduced spectral density mapping approach. As in wild-type CRP2(LIM2), significant mobility on a picosecond/nanosecond time-scale was detected, and conformational exchange on a microsecond time-scale was identified for residues located in loop regions between secondary structure elements. In summary, the relative orientation of the two zinc binding sites and the accessibility of hydrophobic residues is not only determined by hydrophobic interactions, but can also be modified by the formation and/or breakage of hydrogen bonds. This may be important for the molecular interactions of an adaptor-type LIM domain protein in macromolecular complexes, particularly for the modulation of protein-protein interactions.
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