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Aboreden NG, Lam JC, Goel VY, Wang S, Wang X, Midla SC, Quijano A, Keller CA, Giardine BM, Hardison RC, Zhang H, Hansen AS, Blobel GA. LDB1 establishes multi-enhancer networks to regulate gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.23.609430. [PMID: 39229045 PMCID: PMC11370584 DOI: 10.1101/2024.08.23.609430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
How specific enhancer-promoter pairing is established is still mostly unclear. Besides the CTCF/cohesin machinery, only a few nuclear factors have been studied for a direct role in physically connecting regulatory elements. Here, we show via acute degradation experiments that LDB1 directly and broadly promotes enhancer-promoter loops. Most LDB1-mediated contacts, even those spanning hundreds of kb, can form in the absence of CTCF, cohesin, or YY1 as determined via the use of multiple degron systems. Moreover, an engineered LDB1-driven chromatin loop is cohesin independent. Cohesin-driven loop extrusion does not stall at LDB1 occupied sites but may aid the formation of a subset of LDB1 anchored loops. Leveraging the dynamic reorganization of nuclear architecture during the transition from mitosis to G1-phase, we establish a relationship between LDB1-dependent interactions in the context of TAD organization and gene activation. Lastly, Tri-C and Region Capture Micro-C reveal that LDB1 organizes multi-enhancer networks to activate transcription. This establishes LDB1 as a direct driver of regulatory network inter-connectivity.
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Affiliation(s)
- Nicholas G Aboreden
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jessica C Lam
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Viraat Y Goel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Siqing Wang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Xiaokang Wang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Susannah C Midla
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Alma Quijano
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Belinda M Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Haoyue Zhang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Anders S Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Gerd A Blobel
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
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2
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Kim DS, Cheah JS, Lai TW, Zhao KX, Foust SR, Julie Lee YR, Lo SH, Heinrich V, Yamada S. Tandem LIM domain-containing proteins, LIMK1 and LMO1, directly bind to force-bearing keratin intermediate filaments. Cell Rep 2024; 43:114480. [PMID: 39003737 DOI: 10.1016/j.celrep.2024.114480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 05/10/2024] [Accepted: 06/25/2024] [Indexed: 07/16/2024] Open
Abstract
The cytoskeleton of the cell is constantly exposed to physical forces that regulate cellular functions. Selected members of the LIM (Lin-11, Isl-1, and Mec-3) domain-containing protein family accumulate along force-bearing actin fibers, with evidence supporting that the LIM domain is solely responsible for this force-induced interaction. However, LIM domain's force-induced interactions are not limited to actin. LIMK1 and LMO1, both containing only two tandem LIM domains, are recruited to force-bearing keratin fibers in epithelial cells. This unique recruitment is mediated by their LIM domains and regulated by the sequences outside the LIM domains. Based on in vitro reconstitution of this interaction, LIMK1 and LMO1 directly interact with stretched keratin 8/18 fibers. These results show that LIM domain's mechano-sensing abilities extend to the keratin cytoskeleton, highlighting the diverse role of LIM proteins in force-regulated signaling.
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Affiliation(s)
- Dah Som Kim
- Biomedical Engineering Department, University of California, Davis, Davis CA 95616, USA
| | - Joleen S Cheah
- Biomedical Engineering Department, University of California, Davis, Davis CA 95616, USA
| | - Tzu Wei Lai
- Biomedical Engineering Department, University of California, Davis, Davis CA 95616, USA
| | - Karen X Zhao
- Biomedical Engineering Department, University of California, Davis, Davis CA 95616, USA
| | - Skylar R Foust
- Biomedical Engineering Department, University of California, Davis, Davis CA 95616, USA
| | - Yuh-Ru Julie Lee
- Department of Plant Biology, University of California, Davis, Davis CA 95616, USA
| | - Su Hao Lo
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis CA 95616 USA
| | - Volkmar Heinrich
- Biomedical Engineering Department, University of California, Davis, Davis CA 95616, USA
| | - Soichiro Yamada
- Biomedical Engineering Department, University of California, Davis, Davis CA 95616, USA.
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3
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Healy MD, Collins BM. The PDLIM family of actin-associated proteins and their emerging role in membrane trafficking. Biochem Soc Trans 2023; 51:2005-2016. [PMID: 38095060 PMCID: PMC10754285 DOI: 10.1042/bst20220804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/29/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023]
Abstract
The PDZ and LIM domain (PDLIM) proteins are associated with the actin cytoskeleton and have conserved in roles in metazoan actin organisation and function. They primarily function as scaffolds linking various proteins to actin and its binding partner α-actinin via two conserved domains; an N-terminal postsynaptic density 95, discs large and zonula occludens-1 (PDZ) domain, and either single or multiple C-terminal LIN-11, Isl-1 and MEC-3 (LIM) domains in the actinin-associated LIM protein (ALP)- and Enigma-related proteins, respectively. While their role in actin organisation, such as in stress fibres or in the Z-disc of muscle fibres is well known, emerging evidence also suggests a role in actin-dependent membrane trafficking in the endosomal system. This is mediated by a recently identified interaction with the sorting nexin 17 (SNX17) protein, an adaptor for the trafficking complex Commander which is itself intimately linked to actin-directed formation of endosomal recycling domains. In this review we focus on the currently understood structural basis for PDLIM function. The PDZ domains mediate direct binding to distinct classes of PDZ-binding motifs (PDZbms), including α-actinin and other actin-associated proteins, and a highly specific interaction with the type III PDZbm such as the one found in the C-terminus of SNX17. The structures of the LIM domains are less well characterised and how they engage with their ligands is completely unknown. Despite the lack of experimental structural data, we find that recently developed machine learning-based structure prediction methods provide insights into their potential interactions and provide a template for further studies of their molecular functions.
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Affiliation(s)
- Michael D. Healy
- The University of Queensland, Institute for Molecular Bioscience, St Lucia, Queensland 4072, Australia
| | - Brett M. Collins
- The University of Queensland, Institute for Molecular Bioscience, St Lucia, Queensland 4072, Australia
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4
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El Omari K, Duman R, Mykhaylyk V, Orr CM, Latimer-Smith M, Winter G, Grama V, Qu F, Bountra K, Kwong HS, Romano M, Reis RI, Vogeley L, Vecchia L, Owen CD, Wittmann S, Renner M, Senda M, Matsugaki N, Kawano Y, Bowden TA, Moraes I, Grimes JM, Mancini EJ, Walsh MA, Guzzo CR, Owens RJ, Jones EY, Brown DG, Stuart DI, Beis K, Wagner A. Experimental phasing opportunities for macromolecular crystallography at very long wavelengths. Commun Chem 2023; 6:219. [PMID: 37828292 PMCID: PMC10570326 DOI: 10.1038/s42004-023-01014-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/26/2023] [Indexed: 10/14/2023] Open
Abstract
Despite recent advances in cryo-electron microscopy and artificial intelligence-based model predictions, a significant fraction of structure determinations by macromolecular crystallography still requires experimental phasing, usually by means of single-wavelength anomalous diffraction (SAD) techniques. Most synchrotron beamlines provide highly brilliant beams of X-rays of between 0.7 and 2 Å wavelength. Use of longer wavelengths to access the absorption edges of biologically important lighter atoms such as calcium, potassium, chlorine, sulfur and phosphorus for native-SAD phasing is attractive but technically highly challenging. The long-wavelength beamline I23 at Diamond Light Source overcomes these limitations and extends the accessible wavelength range to λ = 5.9 Å. Here we report 22 macromolecular structures solved in this extended wavelength range, using anomalous scattering from a range of elements which demonstrate the routine feasibility of lighter atom phasing. We suggest that, in light of its advantages, long-wavelength crystallography is a compelling option for experimental phasing.
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Affiliation(s)
- Kamel El Omari
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Ramona Duman
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Vitaliy Mykhaylyk
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Christian M Orr
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | | | - Graeme Winter
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
| | - Vinay Grama
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
| | - Feng Qu
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Kiran Bountra
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Hok Sau Kwong
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Maria Romano
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Institute of Biostructures and Bioimaging, IBB, CNR, 80131, Naples, Italy
- Department of Pharmacy, University of Naples "Federico II", 80131, Naples, Italy
| | - Rosana I Reis
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Lutz Vogeley
- Charles River Discovery Research Services UK, Chesterford Research Park, Saffron Walden, CB10 1XL, UK
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Luca Vecchia
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - C David Owen
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Sina Wittmann
- Department of Biochemistry, University of Oxford, Oxford, UK
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Max Renner
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden
| | - Miki Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
| | - Naohiro Matsugaki
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
- Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University of Advanced Studies (Soken-dai), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Yoshiaki Kawano
- Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo, 679-5148, Japan
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Isabel Moraes
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Jonathan M Grimes
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Erika J Mancini
- School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - Martin A Walsh
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Cristiane R Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, 05508-000, Brazil
| | - Raymond J Owens
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- The Rosalind Franklin Institute, Harwell Campus, Oxford, OX11 0FA, UK
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - David G Brown
- Charles River Discovery Research Services UK, Chesterford Research Park, Saffron Walden, CB10 1XL, UK
| | - Dave I Stuart
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Konstantinos Beis
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Armin Wagner
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK.
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK.
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5
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Imdad MJ, Khan MN, Alam HS, Khan AB, Mirani ZA, Khan A, Ahmed F. Design and in silico analysis of mRNA vaccine construct against Salmonella. J Biomol Struct Dyn 2023; 41:7248-7264. [PMID: 36093938 DOI: 10.1080/07391102.2022.2119280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/24/2022] [Indexed: 10/14/2022]
Abstract
Salmonella infections are continuously growing. Causative serovars have gained enhanced drug resistance and virulence. Current vaccines have fallen short of providing sufficient protection. mRNA vaccines have come up with huge success against SARS-CoV-2; Pfizer-BioNTech and Moderna vaccines have resulted in >90% efficacy with efficient translocation, expression, and presentation of antigen to the host immune system. Herein, based on the same approach a mRNA vaccine construct has been designed and analyzed against Salmonella by joining regions of genes of outer membrane proteins C and F of S. Typhi through a flexible linker. Construct was flanked by regulatory regions that have previously shown better expression and translocation of encoded protein. GC content of the construct was improved to attain structural and thermodynamic stability and smooth translation. Sites of strong binding miRNAs were removed through codon optimization. Protein encoded by this construct is structurally plausible, highly antigenic, non-allergen to humans, and does not cross-react to the human proteome. It is enriched in potent, highly antigenic, and conserved linear and conformational epitopes. Most conserved conformational epitopes of core protein lie on extended beta hairpins exposed to the cellular exterior. Stability and thermodynamic attributes of the final construct were found highly comparable to the Pfizer-BioNTech vaccine construct. Both contain a stable stem-loop structure downstream of the start codon and do not offer destabilizing secondary structures upstream of the start codon. Given structural and thermodynamic stability, effective immune response, and epitope composition the construct is expected to provide broad-spectrum protection against clinically important Salmonella serovars.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muhammad Janees Imdad
- Department of Microbiology, University of Karachi, Karachi, Pakistan
- Microbiology Section, FMRRC, Pakistan Council of Scientific and Industrial Research Laboratories Complex, Karachi, Pakistan
| | - Muhammad Naseem Khan
- Microbiology Section, FMRRC, Pakistan Council of Scientific and Industrial Research Laboratories Complex, Karachi, Pakistan
| | | | - Abdul Basit Khan
- Microbiology Section, FMRRC, Pakistan Council of Scientific and Industrial Research Laboratories Complex, Karachi, Pakistan
| | - Zulfiqar Ali Mirani
- Microbiology Section, FMRRC, Pakistan Council of Scientific and Industrial Research Laboratories Complex, Karachi, Pakistan
| | - Adnan Khan
- Department of Microbiology, University of Karachi, Karachi, Pakistan
| | - Faraz Ahmed
- Microbiology Section, FMRRC, Pakistan Council of Scientific and Industrial Research Laboratories Complex, Karachi, Pakistan
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6
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Grochowska KM, Gomes GM, Raman R, Kaushik R, Sosulina L, Kaneko H, Oelschlegel AM, Yuanxiang P, Reyes‐Resina I, Bayraktar G, Samer S, Spilker C, Woo MS, Morawski M, Goldschmidt J, Friese MA, Rossner S, Navarro G, Remy S, Reissner C, Karpova A, Kreutz MR. Jacob-induced transcriptional inactivation of CREB promotes Aβ-induced synapse loss in Alzheimer's disease. EMBO J 2023; 42:e112453. [PMID: 36594364 PMCID: PMC9929644 DOI: 10.15252/embj.2022112453] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 01/04/2023] Open
Abstract
Synaptic dysfunction caused by soluble β-amyloid peptide (Aβ) is a hallmark of early-stage Alzheimer's disease (AD), and is tightly linked to cognitive decline. By yet unknown mechanisms, Aβ suppresses the transcriptional activity of cAMP-responsive element-binding protein (CREB), a master regulator of cell survival and plasticity-related gene expression. Here, we report that Aβ elicits nucleocytoplasmic trafficking of Jacob, a protein that connects a NMDA-receptor-derived signalosome to CREB, in AD patient brains and mouse hippocampal neurons. Aβ-regulated trafficking of Jacob induces transcriptional inactivation of CREB leading to impairment and loss of synapses in mouse models of AD. The small chemical compound Nitarsone selectively hinders the assembly of a Jacob/LIM-only 4 (LMO4)/ Protein phosphatase 1 (PP1) signalosome and thereby restores CREB transcriptional activity. Nitarsone prevents impairment of synaptic plasticity as well as cognitive decline in mouse models of AD. Collectively, the data suggest targeting Jacob protein-induced CREB shutoff as a therapeutic avenue against early synaptic dysfunction in AD.
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Affiliation(s)
- Katarzyna M Grochowska
- RG NeuroplasticityLeibniz Institute for NeurobiologyMagdeburgGermany
- Leibniz Group ‘Dendritic Organelles and Synaptic Function’, Center for Molecular Neurobiology (ZMNH)University Medical Center Hamburg‐EppendorfHamburgGermany
| | - Guilherme M Gomes
- RG NeuroplasticityLeibniz Institute for NeurobiologyMagdeburgGermany
- Center for Behavioral Brain SciencesOtto von Guericke UniversityMagdeburgGermany
| | - Rajeev Raman
- RG NeuroplasticityLeibniz Institute for NeurobiologyMagdeburgGermany
| | - Rahul Kaushik
- RG NeuroplasticityLeibniz Institute for NeurobiologyMagdeburgGermany
| | - Liudmila Sosulina
- Department of Cellular NeuroscienceLeibniz Institute for NeurobiologyMagdeburgGermany
- German Center for Neurodegenerative Diseases (DZNE)MagdeburgGermany
| | - Hiroshi Kaneko
- Department of Cellular NeuroscienceLeibniz Institute for NeurobiologyMagdeburgGermany
- German Center for Neurodegenerative Diseases (DZNE)MagdeburgGermany
| | | | - PingAn Yuanxiang
- RG NeuroplasticityLeibniz Institute for NeurobiologyMagdeburgGermany
| | | | - Gonca Bayraktar
- RG NeuroplasticityLeibniz Institute for NeurobiologyMagdeburgGermany
| | - Sebastian Samer
- RG NeuroplasticityLeibniz Institute for NeurobiologyMagdeburgGermany
| | - Christina Spilker
- RG NeuroplasticityLeibniz Institute for NeurobiologyMagdeburgGermany
| | - Marcel S Woo
- Institute of Neuroimmunology and Multiple Sclerosis, Center for Molecular Neurobiology (ZMNH)University Medical Center Hamburg‐EppendorfHamburgGermany
| | - Markus Morawski
- Molecular Imaging in NeurosciencesPaul Flechsig Institute of Brain ResearchLeipzigGermany
| | - Jürgen Goldschmidt
- Department of Systems Physiology of Learning and MemoryLeibniz Institute for NeurobiologyMagdeburgGermany
| | - Manuel A Friese
- Institute of Neuroimmunology and Multiple Sclerosis, Center for Molecular Neurobiology (ZMNH)University Medical Center Hamburg‐EppendorfHamburgGermany
| | - Steffen Rossner
- Molecular Imaging in NeurosciencesPaul Flechsig Institute of Brain ResearchLeipzigGermany
| | - Gemma Navarro
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food ScienceUniversity of BarcelonaBarcelonaSpain
- Institut de Neurociències de la Universitat de BarcelonaBarcelonaSpain
| | - Stefan Remy
- Center for Behavioral Brain SciencesOtto von Guericke UniversityMagdeburgGermany
- Department of Cellular NeuroscienceLeibniz Institute for NeurobiologyMagdeburgGermany
- German Center for Neurodegenerative Diseases (DZNE)MagdeburgGermany
| | - Carsten Reissner
- Institute of Anatomy and Molecular NeurobiologyWestfälische Wilhelms‐UniversityMünsterGermany
| | - Anna Karpova
- RG NeuroplasticityLeibniz Institute for NeurobiologyMagdeburgGermany
- Center for Behavioral Brain SciencesOtto von Guericke UniversityMagdeburgGermany
| | - Michael R Kreutz
- RG NeuroplasticityLeibniz Institute for NeurobiologyMagdeburgGermany
- Leibniz Group ‘Dendritic Organelles and Synaptic Function’, Center for Molecular Neurobiology (ZMNH)University Medical Center Hamburg‐EppendorfHamburgGermany
- Center for Behavioral Brain SciencesOtto von Guericke UniversityMagdeburgGermany
- German Center for Neurodegenerative Diseases (DZNE)MagdeburgGermany
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7
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Babina M, Franke K, Bal G. How "Neuronal" Are Human Skin Mast Cells? Int J Mol Sci 2022; 23:ijms231810871. [PMID: 36142795 PMCID: PMC9505265 DOI: 10.3390/ijms231810871] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/05/2022] [Accepted: 09/14/2022] [Indexed: 11/24/2022] Open
Abstract
Mast cells are evolutionarily old cells and the principal effectors in allergic responses and inflammation. They are seeded from the yolk sac during embryogenesis or are derived from hematopoietic progenitors and are therefore related to other leukocyte subsets, even though they form a separate clade in the hematopoietic system. Herein, we systematically bundle information from several recent high-throughput endeavors, especially those comparing MCs with other cell types, and combine such information with knowledge on the genes’ functions to reveal groups of neuronal markers specifically expressed by MCs. We focus on recent advances made regarding human tissue MCs, but also refer to studies in mice. In broad terms, genes hyper-expressed in MCs, but largely inactive in other myelocytes, can be classified into subcategories such as traffic/lysosomes (MLPH and RAB27B), the dopamine system (MAOB, DRD2, SLC6A3, and SLC18A2), Ca2+-related entities (CALB2), adhesion molecules (L1CAM and NTM) and, as an overall principle, the transcription factors and modulators of transcriptional activity (LMO4, PBX1, MEIS2, and EHMT2). Their function in MCs is generally unknown but may tentatively be deduced by comparison with other systems. MCs share functions with the nervous system, as they express typical neurotransmitters (histamine and serotonin) and a degranulation machinery that shares features with the neuronal apparatus at the synapse. Therefore, selective overlaps are plausible, and they further highlight the uniqueness of MCs within the myeloid system, as well as when compared with basophils. Apart from investigating their functional implications in MCs, a key question is whether their expression in the lineage is due to the specific reactivation of genes normally silenced in leukocytes or whether the genes are not switched off during mastocytic development from early progenitors.
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Affiliation(s)
- Magda Babina
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology and Allergology IA, 12203 Berlin, Germany
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Allergology, Hindenburgdamm 30, 12203 Berlin, Germany
- Correspondence:
| | - Kristin Franke
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology and Allergology IA, 12203 Berlin, Germany
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Allergology, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Gürkan Bal
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology and Allergology IA, 12203 Berlin, Germany
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Allergology, Hindenburgdamm 30, 12203 Berlin, Germany
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8
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Abstract
The field of molecular embryology started around 1990 by identifying new genes and analyzing their functions in early vertebrate embryogenesis. Those genes encode transcription factors, signaling molecules, their regulators, etc. Most of those genes are relatively highly expressed in specific regions or exhibit dramatic phenotypes when ectopically expressed or mutated. This review focuses on one of those genes, Lim1/Lhx1, which encodes a transcription factor. Lim1/Lhx1 is a member of the LIM homeodomain (LIM-HD) protein family, and its intimate partner, Ldb1/NLI, binds to two tandem LIM domains of LIM-HDs. The most ancient LIM-HD protein and its partnership with Ldb1 were innovated in the metazoan ancestor by gene fusion combining LIM domains and a homeodomain and by creating the LIM domain-interacting domain (LID) in ancestral Ldb, respectively. The LIM domain has multiple interacting interphases, and Ldb1 has a dimerization domain (DD), the LID, and other interacting domains that bind to Ssbp2/3/4 and the boundary factor, CTCF. By means of these domains, LIM-HD-Ldb1 functions as a hub protein complex, enabling more intricate and elaborate gene regulation. The common, ancestral role of LIM-HD proteins is neuron cell-type specification. Additionally, Lim1/Lhx1 serves crucial roles in the gastrula organizer and in kidney development. Recent studies using Xenopus embryos have revealed Lim1/Lhx1 functions and regulatory mechanisms during development and regeneration, providing insight into evolutionary developmental biology, functional genomics, gene regulatory networks, and regenerative medicine. In this review, we also discuss recent progress at unraveling participation of Ldb1, Ssbp, and CTCF in enhanceosomes, long-distance enhancer-promoter interactions, and trans-interactions between chromosomes.
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Affiliation(s)
- Yuuri Yasuoka
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
| | - Masanori Taira
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Bunkyo-ku, Tokyo, Japan.
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9
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Xue W, Zheng X, Hu X, Zhang Y. Research and Clinical Significance of the Differentially Expressed Genes TP63 and LMO4 in Human Immunodeficiency Virus-Related Penile Squamous Cell Carcinoma. Am J Mens Health 2021; 15:15579883211011380. [PMID: 33906487 PMCID: PMC8108076 DOI: 10.1177/15579883211011380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
To study the differential gene expression and clinical significance in human immunodeficiency virus-infected individuals (HIVIIs) with penile squamous cell carcinoma. At our hospital from 2019 to 2020, we selected six samples of HIV-related penile squamous cell carcinoma for the experimental group and six samples of non-HIV-related penile squamous cell carcinoma for the control group. Transcriptome sequencing of sample mRNAs was performed by high-throughput sequencing. Differential gene expression analysis, differential Gene Ontology (GO) enrichment analysis and differential Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were carried out, and the reads per kilobase per million reads (RPKM) value was used as a measure of gene expression. A total of 2418 differentially expressed genes were obtained, of which 663 were upregulated and 1755 were downregulated (absolute value of logFC >1 and p value <.05). On the basis of the significance of the GO enrichment analysis, we found that the tumor protein p63 (TP63) gene was significantly upregulated and that the LIM domain only 4 (LMO4) gene was significantly downregulated in the experimental group compared with the control group. KEGG pathway analysis of the differentially expressed genes revealed that DNA replication was the most significant pathway associated with the upregulated genes and cell adhesion molecule (CAM) metabolism was the most significant pathway associated with the downregulated genes. The gene expression profiles of HIV-related penile squamous cell carcinoma and non-HIV-related penile squamous cell carcinoma are significantly different and involve significant GO enrichment and KEGG metabolic pathways, and this is very meaningful for the study of non-AIDS-defining cancers (NADCs). Differential expression of genes may be an important target for the prevention of penile squamous cell carcinoma in HIVIIs.
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Affiliation(s)
- Wenrui Xue
- Beijing Youan Hospital of Capital Medical University, Fengtai District, Beijing China
| | - Xin Zheng
- Beijing Youan Hospital of Capital Medical University, Fengtai District, Beijing China
| | - Xiaopeng Hu
- Beijing Chaoyang Hospital of Capital Medical University, Chaoyang District, Beijing China
| | - Yu Zhang
- Beijing Youan Hospital of Capital Medical University, Fengtai District, Beijing China
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10
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Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins. Int J Mol Sci 2021; 22:ijms22052647. [PMID: 33808029 PMCID: PMC7961639 DOI: 10.3390/ijms22052647] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 02/07/2023] Open
Abstract
Members of the human Zyxin family are LIM domain-containing proteins that perform critical cellular functions and are indispensable for cellular integrity. Despite their importance, not much is known about their structure, functions, interactions and dynamics. To provide insights into these, we used a set of in-silico tools and databases and analyzed their amino acid sequence, phylogeny, post-translational modifications, structure-dynamics, molecular interactions, and functions. Our analysis revealed that zyxin members are ohnologs. Presence of a conserved nuclear export signal composed of LxxLxL/LxxxLxL consensus sequence, as well as a possible nuclear localization signal, suggesting that Zyxin family members may have nuclear and cytoplasmic roles. The molecular modeling and structural analysis indicated that Zyxin family LIM domains share similarities with transcriptional regulators and have positively charged electrostatic patches, which may indicate that they have previously unanticipated nucleic acid binding properties. Intrinsic dynamics analysis of Lim domains suggest that only Lim1 has similar internal dynamics properties, unlike Lim2/3. Furthermore, we analyzed protein expression and mutational frequency in various malignancies, as well as mapped protein-protein interaction networks they are involved in. Overall, our comprehensive bioinformatic analysis suggests that these proteins may play important roles in mediating protein-protein and protein-nucleic acid interactions.
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11
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Milton-Harris L, Jeeves M, Walker SA, Ward SE, Mancini EJ. Small molecule inhibits T-cell acute lymphoblastic leukaemia oncogenic interaction through conformational modulation of LMO2. Oncotarget 2020; 11:1737-1748. [PMID: 32477463 PMCID: PMC7233811 DOI: 10.18632/oncotarget.27580] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/03/2020] [Indexed: 01/05/2023] Open
Abstract
Ectopic expression in T-cell precursors of LIM only protein 2 (LMO2), a key factor in hematopoietic development, has been linked to the onset of T-cell acute lymphoblastic leukaemia (T-ALL). In the T-ALL context, LMO2 drives oncogenic progression through binding to erythroid-specific transcription factor SCL/TAL1 and sequestration of E-protein transcription factors, normally required for T-cell differentiation. A key requirement for the formation of this oncogenic protein-protein interaction (PPI) is the conformational flexibility of LMO2. Here we identify a small molecule inhibitor of the SCL-LMO2 PPI, which hinders the interaction in vitro through direct binding to LMO2. Biophysical analysis demonstrates that this inhibitor acts through a mechanism of conformational modulation of LMO2. Importantly, this work has led to the identification of a small molecule inhibitor of the SCL-LMO2 PPI, which can provide a starting point for the development of new agents for the treatment of T-ALL. These results suggest that similar approaches, based on the modulation of protein conformation by small molecules, might be used for therapeutic targeting of other oncogenic PPIs.
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Affiliation(s)
- Leanne Milton-Harris
- School of Life Sciences, Biochemistry Department, University of Sussex, Falmer, Brighton, BN1 9QG, United Kingdom
| | - Mark Jeeves
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Sarah A Walker
- Sussex Drug Discovery Centre, University of Sussex, Brighton, BN1 9QJ, United Kingdom
| | - Simon E Ward
- Medicines Discovery Institute, Cardiff University, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Erika J Mancini
- School of Life Sciences, Biochemistry Department, University of Sussex, Falmer, Brighton, BN1 9QG, United Kingdom
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12
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Abstract
The Lim domain binding proteins (LDB1 and LDB2 in human and Chip in Drosophila) play critical roles in cell fate decisions through partnership with multiple Lim-homeobox and Lim-only proteins in diverse developmental systems including cardiogenesis, neurogenesis, and hematopoiesis. In mammalian erythroid cells, LDB1 dimerization supports long-range connections between enhancers and genes involved in erythropoiesis, including the β-globin genes. Single-stranded DNA binding proteins (SSBPs) interact specifically with the LDB/Chip conserved domain (LCCD) of LDB proteins and stabilize LDBs by preventing their proteasomal degradation, thus promoting their functions in gene regulation. The structural basis for LDB1 self-interaction and interface with SSBPs is unclear. Here we report a crystal structure of the human LDB1/SSBP2 complex at 2.8-Å resolution. The LDB1 dimerization domain (DD) contains an N-terminal nuclear transport factor 2 (NTF2)-like subdomain and a small helix 4-helix 5 subdomain, which together form the LDB1 dimerization interface. The 2 LCCDs in the symmetric LDB1 dimer flank the core DDs, with each LCCD forming extensive interactions with an SSBP2 dimer. The conserved linker between LDB1 DD and LCCD covers a potential ligand-binding pocket of the LDB1 NTF2-like subdomain and may serve as a regulatory site for LDB1 structure and function. Our structural and biochemical data provide a much-anticipated structural basis for understanding how LDB1 and the LDB1/SSBP interactions form the structural core of diverse complexes mediating cell choice decisions and long-range enhancer-promoter interactions.
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13
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Rahmani A, Baee M, Rostamtabar M, Karkhah A, Alizadeh S, Tourani M, Nouri HR. Development of a conserved chimeric vaccine based on helper T-cell and CTL epitopes for induction of strong immune response against Schistosoma mansoni using immunoinformatics approaches. Int J Biol Macromol 2019; 141:125-136. [PMID: 31479669 DOI: 10.1016/j.ijbiomac.2019.08.259] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 08/15/2019] [Accepted: 08/30/2019] [Indexed: 01/05/2023]
Abstract
Currently, three recombinant antigens based vaccines are under clinical trials against Schistosomiasis, but there is no vaccine available for prophylaxis or therapeutic. This study was conducted to construct a multi-epitope based vaccine against Schistosoma mansoni via utilizing Sm14, Sm21.7, Sm23, Sm29, Smp80, Sm-CB and SM-TSP-2 antigens. Helper T lymphocyte (HTL), cytotoxic T lymphocyte (CTL) and IFN-γ epitopes were predicted. Furthermore, Pan HLA DR-binding epitope was added to the vaccine. Moreover, 50S ribosomal protein L7/L12 of Mycobacterium tuberculosis as a novel TLR4 agonist was applied. The TAT peptide was added to the vaccine to augment intracellular delivery. The selected epitopes were linked together through appropriate linkers and chimeric vaccine was constructed with 617 amino acids with molecular weight of 65.43 kDa. Physico-chemical properties revealed a soluble protein with antigenic and non-allergic properties. Further analyses validated the stability of the construct that was able to interact with TLR4. Immunoinformatics analysis demonstrated the strong potential of constructed vaccine to stimulate T and B-cell mediated immune responses. In summary, obtained data indicated that the proposed vaccine can properly induce both T and B cells immune responses and could possibly be utilized for prophylactic or therapeutic aims in response to infection caused by S. mansoni.
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Affiliation(s)
- Abolfazl Rahmani
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | - Masoud Baee
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | - Maryam Rostamtabar
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Ahmad Karkhah
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Solmaz Alizadeh
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | - Mehdi Tourani
- Immunoregulation Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Hamid Reza Nouri
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran; Immunoregulation Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
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14
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Liu B, Yang L, Zhu X, Li H, Zhu P, Wu J, Lu T, He L, Liu N, Meng S, Zhou L, Ye B, Tian Y, Fan Z. Yeats4 drives ILC lineage commitment via activation of Lmo4 transcription. J Exp Med 2019; 216:2653-2668. [PMID: 31434684 PMCID: PMC6829595 DOI: 10.1084/jem.20182363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 06/04/2019] [Accepted: 07/22/2019] [Indexed: 12/20/2022] Open
Abstract
Liu et al. show that Yeats4 recruits the Dot1l–RNA Pol II complex onto the Lmo4 promoter by recognizing H3K27ac modification to initiate Lmo4 transcription in α4β7+ CLPs, leading to ILC lineage commitment. Innate lymphoid cells (ILCs) play critical roles in defending infections and maintaining mucosal homeostasis. All ILCs arise from common lymphoid progenitors (CLPs) in bone marrow. However, how CLPs stratify and differentiate into ILC lineages remains elusive. Here, we showed that Yeats4 is highly expressed in ILCs and their progenitors. Yeats4 conditional KO in the hematopoietic system causes decreased numbers of ILCs and impairs their effector functions. Moreover, Yeats4 regulates α4β7+ CLP differentiation toward common helper ILC progenitors (CHILPs). Mechanistically, Yeats4 recruits the Dot1l–RNA Pol II complex onto Lmo4 promoter through recognizing H3K27ac modification to initiate Lmo4 transcription in α4β7+ CLPs. Additionally, Lmo4 deficiency also impairs ILC lineage differentiation and their effector functions. Collectively, the Yeats4–Lmo4 axis is required for ILC lineage commitment.
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Affiliation(s)
- Benyu Liu
- Key Laboratory of Infection and Immunity of the Chinese Academy of Sciences, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Liuliu Yang
- Key Laboratory of Infection and Immunity of the Chinese Academy of Sciences, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoxiao Zhu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Huimu Li
- Key Laboratory of Infection and Immunity of the Chinese Academy of Sciences, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Pingping Zhu
- Key Laboratory of Infection and Immunity of the Chinese Academy of Sciences, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jiayi Wu
- Key Laboratory of Infection and Immunity of the Chinese Academy of Sciences, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Tiankun Lu
- Key Laboratory of Infection and Immunity of the Chinese Academy of Sciences, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Luyun He
- Key Laboratory of Infection and Immunity of the Chinese Academy of Sciences, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Nian Liu
- Key Laboratory of Infection and Immunity of the Chinese Academy of Sciences, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shu Meng
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Liang Zhou
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL
| | - Buqing Ye
- Key Laboratory of Infection and Immunity of the Chinese Academy of Sciences, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yong Tian
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China .,University of Chinese Academy of Sciences, Beijing, China
| | - Zusen Fan
- Key Laboratory of Infection and Immunity of the Chinese Academy of Sciences, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China .,University of Chinese Academy of Sciences, Beijing, China
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15
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Rostamtabar M, Rahmani A, Baee M, Karkhah A, Prajapati VK, Ebrahimpour S, Nouri HR. Development a multi-epitope driven subunit vaccine for immune response reinforcement against Serogroup B of Neisseria meningitidis using comprehensive immunoinformatics approaches. INFECTION GENETICS AND EVOLUTION 2019; 75:103992. [PMID: 31394292 DOI: 10.1016/j.meegid.2019.103992] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 06/22/2019] [Accepted: 08/02/2019] [Indexed: 11/28/2022]
Abstract
Serogroup B of Neisseria meningitidis is the main cause of mortality due to meningococcal meningitis. Despite of many investigations, there is still no effective vaccine to prevent this serious infection. Therefore, this study was conducted to design a multi-epitope based vaccine through immunoinformatics approaches. The T CD4+ and TCD8+ cells along with IFN-γ inducing epitopes were selected from TspA, FHbp, NspA, TbpB, PilQ and NspA antigens form serogroup B of Neisseria meningitidis. Furthermore, to induce strong helper T lymphocytes (HTLs) responses, Pan HLA DR-binding epitope (PADRE) was used. In addition, loop 5 and 7 of the PorB as a TLR2 agonist were added to the vaccine construct. Physico-chemical properties, secondary and tertiary structures of the proposed construct were assessed. Finally, homology modeling, refinement and molecular docking were carried out to evaluated the construct tertiary structure and protein-protein interaction, respectively. By fusing the CTL, HTL and IFN-γ predicted epitopes along with suitable adjuvant and linkers, a multi-epitope vaccine was constructed with a TAT sequence of HIV at the N-terminal. Immunoinformatics analyses confirmed a soluble and non-allergic protein with a molecular weight of 62.5 kDa and high antigenicity. Furthermore, the stability of the multi-epitope construct was established and showed strong potential to generate humoral and cell-mediated immune responses. In addition, through molecular docking and dynamic simulation, the microscopic interaction between the vaccine construct and TLR-2 were verified. In summary, immunoinformatics analysis demonstrated that the constructed multi-epitope vaccine had a strong potential of T and B-cell stimulation and it could possibly be used for prophylactic or therapeutic aims to protect against serogroup B of N. meningitidis.
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Affiliation(s)
- Maryam Rostamtabar
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | - Abolfazl Rahmani
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | - Masoud Baee
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran; Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Ahmad Karkhah
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran; Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan, India
| | - Soheil Ebrahimpour
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Hamid Reza Nouri
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran; Immunoregulation Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
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16
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Enhancer long-range contacts: The multi-adaptor protein LDB1 is the tie that binds. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:625-633. [DOI: 10.1016/j.bbagrm.2019.04.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 11/20/2022]
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17
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Stokes PH, Robertson NO, Silva APG, Estephan T, Trewhella J, Guss JM, Matthews JM. Mutation in a flexible linker modulates binding affinity for modular complexes. Proteins 2019; 87:425-429. [PMID: 30788856 DOI: 10.1002/prot.25675] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/05/2019] [Accepted: 02/17/2019] [Indexed: 11/11/2022]
Abstract
Tandem beta zippers are modular complexes formed between repeated linear motifs and tandemly arrayed domains of partner proteins in which β-strands form upon binding. Studies of such complexes, formed by LIM domain proteins and linear motifs in their intrinsically disordered partners, revealed spacer regions between the linear motifs that are relatively flexible but may affect the overall orientation of the binding modules. We demonstrate that mutation of a solvent exposed side chain in the spacer region of an LHX4-ISL2 complex has no significant effect on the structure of the complex, but decreases binding affinity, apparently by increasing flexibility of the linker.
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Affiliation(s)
- Philippa H Stokes
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Neil O Robertson
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Ana P G Silva
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Tanya Estephan
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Jill Trewhella
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - J Mitchell Guss
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Jacqueline M Matthews
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
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18
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Deciphering RNA-Recognition Patterns of Intrinsically Disordered Proteins. Int J Mol Sci 2018; 19:ijms19061595. [PMID: 29843482 PMCID: PMC6032373 DOI: 10.3390/ijms19061595] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/10/2018] [Accepted: 05/16/2018] [Indexed: 02/06/2023] Open
Abstract
Intrinsically disordered regions (IDRs) and protein (IDPs) are highly flexible owing to their lack of well-defined structures. A subset of such proteins interacts with various substrates; including RNA; frequently adopting regular structures in the final complex. In this work; we have analysed a dataset of protein–RNA complexes undergoing disorder-to-order transition (DOT) upon binding. We found that DOT regions are generally small in size (less than 3 residues) for RNA binding proteins. Like structured proteins; positively charged residues are found to interact with RNA molecules; indicating the dominance of electrostatic and cation-π interactions. However, a comparison of binding frequency shows that interface hydrophobic and aromatic residues have more interactions in only DOT regions than in a protein. Further; DOT regions have significantly higher exposure to water than their structured counterparts. Interactions of DOT regions with RNA increase the sheet formation with minor changes in helix forming residues. We have computed the interaction energy for amino acids–nucleotide pairs; which showed the preference of His–G; Asn–U and Ser–U at for the interface of DOT regions. This study provides insights to understand protein–RNA interactions and the results could also be used for developing a tool for identifying DOT regions in RNA binding proteins.
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19
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Disparate binding kinetics by an intrinsically disordered domain enables temporal regulation of transcriptional complex formation. Proc Natl Acad Sci U S A 2018; 115:4643-4648. [PMID: 29666277 DOI: 10.1073/pnas.1714646115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Intrinsically disordered regions are highly represented among mammalian transcription factors, where they often contribute to the formation of multiprotein complexes that regulate gene expression. An example of this occurs with LIM-homeodomain (LIM-HD) proteins in the developing spinal cord. The LIM-HD protein LHX3 and the LIM-HD cofactor LDB1 form a binary complex that gives rise to interneurons, whereas in adjacent cell populations, LHX3 and LDB1 form a rearranged ternary complex with the LIM-HD protein ISL1, resulting in motor neurons. The protein-protein interactions within these complexes are mediated by ordered LIM domains in the LIM-HD proteins and intrinsically disordered LIM interaction domains (LIDs) in LDB1 and ISL1; however, little is known about how the strength or rates of binding contribute to complex assemblies. We have measured the interactions of LIM:LID complexes using FRET-based protein-protein interaction studies and EMSAs and used these data to model population distributions of complexes. The protein-protein interactions within the ternary complexes are much weaker than those in the binary complex, yet surprisingly slow LDB1:ISL1 dissociation kinetics and a substantial increase in DNA binding affinity promote formation of the ternary complex over the binary complex in motor neurons. We have used mutational and protein engineering approaches to show that allostery and modular binding by tandem LIM domains contribute to the LDB1LID binding kinetics. The data indicate that a single intrinsically disordered region can achieve highly disparate binding kinetics, which may provide a mechanism to regulate the timing of transcriptional complex assembly.
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20
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Bhati M, Llamosas E, Jacques DA, Jeffries CM, Dastmalchi S, Ripin N, Nicholas HR, Matthews JM. Interactions between LHX3- and ISL1-family LIM-homeodomain transcription factors are conserved in Caenorhabditis elegans. Sci Rep 2017; 7:4579. [PMID: 28676648 PMCID: PMC5496915 DOI: 10.1038/s41598-017-04587-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/17/2017] [Indexed: 02/07/2023] Open
Abstract
LIM-Homeodomain (LIM-HD) transcription factors are highly conserved in animals where they are thought to act in a transcriptional ‘LIM code’ that specifies cell types, particularly in the central nervous system. In chick and mammals the interaction between two LIM-HD proteins, LHX3 and Islet1 (ISL1), is essential for the development of motor neurons. Using yeast two-hybrid analysis we showed that the Caenorhabditis elegans orthologs of LHX3 and ISL1, CEH-14 and LIM-7 can physically interact. Structural characterisation of a complex comprising the LIM domains from CEH-14 and a LIM-interaction domain from LIM-7 showed that these nematode proteins assemble to form a structure that closely resembles that of their vertebrate counterparts. However, mutagenic analysis across the interface indicates some differences in the mechanisms of binding. We also demonstrate, using fluorescent reporter constructs, that the two C. elegans proteins are co-expressed in a small subset of neurons. These data show that the propensity for LHX3 and Islet proteins to interact is conserved from C. elegans to mammals, raising the possibility that orthologous cell specific LIM-HD-containing transcription factor complexes play similar roles in the development of neuronal cells across diverse species.
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Affiliation(s)
- Mugdha Bhati
- School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.,Teva Pharmaceuticals Australia Pty Ltd, Macquarie Park, NSW, 2113, Australia
| | - Estelle Llamosas
- School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.,School of Women's and Children's Health, University of New South Wales, NSW, Australia
| | - David A Jacques
- School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.,iThree Institute, University of Technology, NSW, 2007, Australia
| | - Cy M Jeffries
- School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.,European Molecular Biology Laboratory (EMBL) Hamburg Outstation, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Siavoush Dastmalchi
- Biotechnology Research Center and School of Pharmacy, Tabritz Univeristy of Medical Science, Tabritz, Iran
| | - Nina Ripin
- School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.,Department of Biology, ETH, Zurich, 8093, Switzerland
| | - Hannah R Nicholas
- School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.
| | - Jacqueline M Matthews
- School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.
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21
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Chen XY, Li DZ, Zhong XZ, Chen B, Duan ZL, Wen JS. Induction of multiple cytotoxic T lymphocyte responses in mice by a multiepitope DNA vaccine against dengue virus serotype 1. Microbiol Immunol 2017; 60:835-845. [PMID: 27981613 DOI: 10.1111/1348-0421.12457] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/14/2016] [Accepted: 12/02/2016] [Indexed: 12/20/2022]
Abstract
Dengue virus (DENV) is still a major threat to human health in most tropical and subtropical countries and regions. In the present study, a multi-epitope DNA vaccine that encodes 15 immunogenic and conserved HLA-A*0201-, HLA-A*1101-, HLA-A*2402-restricted CTL epitopes from DENV serotype 1 (DENV-1) was constructed based on the eukaryotic expressing plasmid pcDNATM 3.1/myc-His(-) A. Immunization of HLA-A*0201, HLA-A*1101 and HLA-A*2402 transgenic mice with the recombinant plasmid pcDNATM 3.1/myc-His(-) A-DENV-1-Meg resulted in significantly greater IFN-γ-secreting T-cell responses against most (14/15) CTL epitopes than occurred in mice immunized with the empty plasmid pcDNATM 3.1/myc-His(-) A. Additionally, the epitope-specific T cells directed to some epitopes secreted not only IFN-γ but also IL-6 and/or TNF-α. Finally, the induced epitope-specific T cells also efficiently lysed epitope-pulsed splenocytes and DENV-1-infected splenic monocytes. The present study confirms the immunogenicity of multi-epitope DENV vaccine, suggesting that it may contribute to the development of a universal DENV vaccine.
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Affiliation(s)
- Xin Yu Chen
- Department of Clinical Laboratory, Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Xueyuan West Road, Wenzhou 325000
| | - De Zhou Li
- Department of Liver, The Second Hospital of Ningbo, Ningbo 315010, China
| | - Xiao Zhi Zhong
- Institute of Arboviruses, School of Basic Medical Sciences, Wenzhou Medical University, Chashan, Wenzhou 32500
| | - Bokun Chen
- Institute of Arboviruses, School of Basic Medical Sciences, Wenzhou Medical University, Chashan, Wenzhou 32500
| | - Zhi Liang Duan
- Department of Clinical Laboratory, Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Xueyuan West Road, Wenzhou 325000
| | - Jin Sheng Wen
- Institute of Arboviruses, School of Basic Medical Sciences, Wenzhou Medical University, Chashan, Wenzhou 32500
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22
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Robertson NO, Shah M, Matthews JM. A Quantitative Fluorescence-Based Assay for Assessing LIM Domain-Peptide Interactions. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Neil O. Robertson
- School of Life and Environmental Sciences; The University of Sydney; NSW 2006 Australia
| | - Manan Shah
- School of Life and Environmental Sciences; The University of Sydney; NSW 2006 Australia
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23
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Robertson NO, Shah M, Matthews JM. A Quantitative Fluorescence-Based Assay for Assessing LIM Domain-Peptide Interactions. Angew Chem Int Ed Engl 2016; 55:13236-13239. [DOI: 10.1002/anie.201605964] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Neil O. Robertson
- School of Life and Environmental Sciences; The University of Sydney; NSW 2006 Australia
| | - Manan Shah
- School of Life and Environmental Sciences; The University of Sydney; NSW 2006 Australia
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24
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The promises and challenges of fusion constructs in protein biochemistry and enzymology. Appl Microbiol Biotechnol 2016; 100:8273-81. [PMID: 27541749 DOI: 10.1007/s00253-016-7795-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 08/04/2016] [Accepted: 08/05/2016] [Indexed: 01/05/2023]
Abstract
Fusion constructs are used to improve the properties of or impart novel functionality to proteins for biotechnological applications. The biochemical characteristics of enzymes or functional proteins optimized by fusion include catalytic efficiency, stability, activity, expression, secretion, and solubility. In this review, we summarize the parameters of enzymes or functional proteins that can be modified by fusion constructs. For each parameter, fusion strategies and molecular partners are examined using examples from recent studies. Future prospects in this field are also discussed. This review is expected to increase interest in and advance fusion strategies for optimization of enzymes and other functional proteins.
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25
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Yang Y, Sun W, Guo J, Zhao G, Sun S, Yu H, Guo Y, Li J, Jin X, Du L, Jiang S, Kou Z, Zhou Y. In silico design of a DNA-based HIV-1 multi-epitope vaccine for Chinese populations. Hum Vaccin Immunother 2015; 11:795-805. [PMID: 25839222 DOI: 10.1080/21645515.2015.1012017] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The development of an HIV-1 vaccine that is capable of inducing effective and broadly cross-reactive humoral and cellular immune responses remains a challenging task because of the extensive diversity of HIV-1, the difference of virus subtypes (clades) in different geographical regions, and the polymorphism of human leukocyte antigens (HLA). We performed an in silico design of 3 DNA vaccines, designated pJW4303-MEG1, pJW4303-MEG2 and pJW4303-MEG3, encoding multi-epitopes that are highly conserved within the HIV-1 subtypes most prevalent in China and can be recognized through HLA alleles dominant in China. The pJW4303-MEG1-encoded protein consisted of one Th epitope in Env, and one, 2, and 6 epitopes in Pol, Env, and Gag proteins, respectively, with a GGGS linker sequence between epitopes. The pJW4303-MEG2-encoded protein contained similar epitopes in a different order, but with the same linker as pJW4303-MEG1. The pJW4303-MEG3-encoded protein contained the same epitopes in the same order as that of pJW4303-MEG2, but with a different linker sequence (AAY). To evaluate immunogenicity, mice were immunized intramuscularly with these DNA vaccines. Both pJW4303-MEG1 and pJW4303-MEG2 vaccines induced equally potent humoral and cellular immune responses in the vaccinated mice, while pJW4303-MEG3 did not induce immune responses. These results indicate that both epitope and linker sequences are important in designing effective epitope-based vaccines against HIV-1 and other viruses.
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Affiliation(s)
- Yi Yang
- a State Key Laboratory of Pathogen and Biosecurity ; Beijing Institute of Microbiology and Epidemiology ; Beijing , China
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26
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Kobe B, Ve T, Williams SJ. Fusion-protein-assisted protein crystallization. Acta Crystallogr F Struct Biol Commun 2015; 71:861-9. [PMID: 26144231 PMCID: PMC4498707 DOI: 10.1107/s2053230x15011061] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 06/07/2015] [Indexed: 01/29/2023] Open
Abstract
Fusion proteins can be used directly in protein crystallization to assist crystallization in at least two different ways. In one approach, the `heterologous fusion-protein approach', the fusion partner can provide additional surface area to promote crystal contact formation. In another approach, the `fusion of interacting proteins approach', protein assemblies can be stabilized by covalently linking the interacting partners. The linker connecting the proteins plays different roles in the two applications: in the first approach a rigid linker is required to reduce conformational heterogeneity; in the second, conversely, a flexible linker is required that allows the native interaction between the fused proteins. The two approaches can also be combined. The recent applications of fusion-protein technology in protein crystallization from the work of our own and other laboratories are briefly reviewed.
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Affiliation(s)
- Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Thomas Ve
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Simon J. Williams
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
- School of Biological Sciences, Flinders University, Adelaide, South Australia 5001, Australia
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27
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Baron KD, Al-Zahrani K, Conway J, Labrèche C, Storbeck CJ, Visvader JE, Sabourin LA. Recruitment and activation of SLK at the leading edge of migrating cells requires Src family kinase activity and the LIM-only protein 4. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1683-92. [PMID: 25882817 DOI: 10.1016/j.bbamcr.2015.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 03/20/2015] [Accepted: 04/03/2015] [Indexed: 12/26/2022]
Abstract
The Ste20-like kinase SLK plays a pivotal role in cell migration and focal adhesion turnover and is regulated by the LIM domain-binding proteins Ldb1 and Ldb2. These adapter proteins have been demonstrated to interact with LMO4 in the organization of transcriptional complexes. Therefore, we have assessed the ability of LMO4 to also interact and regulate SLK activity. Our data show that LMO4 can directly bind to SLK and activate its kinase activity in vitro and in vivo. LMO4 can be co-precipitated with SLK following the induction of cell migration by scratch wounding and Cre-mediated deletion of LMO4 in conditional LMO4(fl/fl) fibroblasts inhibits cell migration and SLK activation. Deletion of LMO4 impairs Ldb1 and SLK recruitment to the leading edge of migrating cells. Supporting this, Src/Yes/Fyn-deficient cells (SYF) expressing very low levels of LMO4 do not recruit SLK to the leading edge. Re-expression of wildtype Myc-LMO4 in SYF cells, but not a mutant version, restores SLK localization and kinase activity. Overall, our data suggest that activation of SLK by haptotactic signals requires its recruitment to the leading edge by LMO4 in a Src-dependent manner. Furthermore, this establishes a novel cytosolic role for the transcriptional co-activator LMO4.
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Affiliation(s)
- Kyla D Baron
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Khalid Al-Zahrani
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Jillian Conway
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Cédrik Labrèche
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Christopher J Storbeck
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Jane E Visvader
- Walter and Eliza Hall Institute Biotechnology Centre, Bundoora, Victoria 3086, Australia
| | - Luc A Sabourin
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Ottawa Hospital Research Institute, Cancer Therapeutics, Ottawa, Ontario, Canada.
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28
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Joseph S, Kwan AH, Stokes PH, Mackay JP, Cubeddu L, Matthews JM. The structure of an LIM-only protein 4 (LMO4) and Deformed epidermal autoregulatory factor-1 (DEAF1) complex reveals a common mode of binding to LMO4. PLoS One 2014; 9:e109108. [PMID: 25310299 PMCID: PMC4195752 DOI: 10.1371/journal.pone.0109108] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 08/27/2014] [Indexed: 12/23/2022] Open
Abstract
LIM-domain only protein 4 (LMO4) is a widely expressed protein with important roles in embryonic development and breast cancer. It has been reported to bind many partners, including the transcription factor Deformed epidermal autoregulatory factor-1 (DEAF1), with which LMO4 shares many biological parallels. We used yeast two-hybrid assays to show that DEAF1 binds both LIM domains of LMO4 and that DEAF1 binds the same face on LMO4 as two other LMO4-binding partners, namely LIM domain binding protein 1 (LDB1) and C-terminal binding protein interacting protein (CtIP/RBBP8). Mutagenic screening analysed by the same method, indicates that the key residues in the interaction lie in LMO4LIM2 and the N-terminal half of the LMO4-binding domain in DEAF1. We generated a stable LMO4LIM2-DEAF1 complex and determined the solution structure of that complex. Although the LMO4-binding domain from DEAF1 is intrinsically disordered, it becomes structured on binding. The structure confirms that LDB1, CtIP and DEAF1 all bind to the same face on LMO4. LMO4 appears to form a hub in protein-protein interaction networks, linking numerous pathways within cells. Competitive binding for LMO4 therefore most likely provides a level of regulation between those different pathways.
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Affiliation(s)
- Soumya Joseph
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | - Ann H. Kwan
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | - Philippa H. Stokes
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | - Joel P. Mackay
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | - Liza Cubeddu
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
- School of Science and Health, University of Western Sydney, Campbelltown, NSW Australia
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29
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Salmans ML, Yu Z, Watanabe K, Cam E, Sun P, Smyth P, Dai X, Andersen B. The co-factor of LIM domains (CLIM/LDB/NLI) maintains basal mammary epithelial stem cells and promotes breast tumorigenesis. PLoS Genet 2014; 10:e1004520. [PMID: 25079073 PMCID: PMC4117441 DOI: 10.1371/journal.pgen.1004520] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 06/03/2014] [Indexed: 12/20/2022] Open
Abstract
Mammary gland branching morphogenesis and ductal homeostasis relies on mammary stem cell function for the maintenance of basal and luminal cell compartments. The mechanisms of transcriptional regulation of the basal cell compartment are currently unknown. We explored these mechanisms in the basal cell compartment and identified the Co-factor of LIM domains (CLIM/LDB/NLI) as a transcriptional regulator that maintains these cells. Clims act within the basal cell compartment to promote branching morphogenesis by maintaining the number and proliferative potential of basal mammary epithelial stem cells. Clim2, in a complex with LMO4, supports mammary stem cells by directly targeting the Fgfr2 promoter in basal cells to increase its expression. Strikingly, Clims also coordinate basal-specific transcriptional programs to preserve luminal cell identity. These basal-derived cues inhibit epidermis-like differentiation of the luminal cell compartment and enhance the expression of luminal cell-specific oncogenes ErbB2 and ErbB3. Consistently, basal-expressed Clims promote the initiation and progression of breast cancer in the MMTV-PyMT tumor model, and the Clim-regulated branching morphogenesis gene network is a prognostic indicator of poor breast cancer outcome in humans. Recent advancements in mammary gland biology demonstrate conflicting models in maintenance of basal and luminal cell compartments by either unipotent or bipotent mammary stem cells. However, the molecular mechanisms underlying control of the basal cell compartment, including stem cells, remain poorly understood. Here we explore the currently unknown transcriptional mechanisms of basal stem cell (BSC) maintenance, in addition to addressing the role of the basal cell compartment in preserving luminal cell fate and promoting development of human breast tumors of luminal origin. We discover a novel function for the Co-factor of LIM domains (Clim) transcriptional regulator in promoting mammary gland branching morphogenesis and breast tumorigenesis through maintenance of the basal stem cell population. The transcriptional networks coordinated by Clims in basal mammary epithelial cells also preserve the identity of luminal epithelial cells, demonstrating a crosstalk between these two cellular compartments. Furthermore, we correlate developmental gene expression data with human breast cancer to investigate the role of developmental pathways during the initiation and progression of breast cancer. The gene regulatory networks identified during development, including those specifically coordinated by Clims, correlate with breast cancer patient outcome, suggesting these genes play an important role in the progression of breast cancer.
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MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Carcinogenesis/genetics
- Cell Differentiation/genetics
- DNA-Binding Proteins/genetics
- Epithelial Cells/metabolism
- Epithelial Cells/pathology
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- LIM Domain Proteins/genetics
- Mammary Glands, Human/metabolism
- Mammary Glands, Human/pathology
- Neoplasms, Basal Cell/genetics
- Neoplasms, Basal Cell/metabolism
- Promoter Regions, Genetic
- Protein Structure, Tertiary
- Receptor, ErbB-2/genetics
- Receptor, Fibroblast Growth Factor, Type 2/genetics
- Stem Cells/metabolism
- Stem Cells/pathology
- Transcription Factors/genetics
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Affiliation(s)
- Michael L. Salmans
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California, United States of America
| | - Zhengquan Yu
- State Key Laboratories for AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing, PR China
| | - Kazuhide Watanabe
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Eric Cam
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Peng Sun
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Padhraic Smyth
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California, United States of America
- Department of Computer Science, University of California, Irvine, Irvine, California, United States of America
| | - Xing Dai
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Bogi Andersen
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California, United States of America
- Department of Medicine, University of California, Irvine, Irvine, California, United States of America
- * E-mail:
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30
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Conformational flexibility of the oncogenic protein LMO2 primes the formation of the multi-protein transcription complex. Sci Rep 2014; 4:3643. [PMID: 24407558 PMCID: PMC3887373 DOI: 10.1038/srep03643] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 12/09/2013] [Indexed: 01/07/2023] Open
Abstract
LMO2 was discovered via chromosomal translocations in T-cell leukaemia and shown normally to be essential for haematopoiesis. LMO2 is made up of two LIM only domains (thus it is a LIM-only protein) and forms a bridge in a multi-protein complex. We have studied the mechanism of formation of this complex using a single domain antibody fragment that inhibits LMO2 by sequestering it in a non-functional form. The crystal structure of LMO2 with this antibody fragment has been solved revealing a conformational difference in the positioning and angle between the two LIM domains compared with its normal binding. This contortion occurs by bending at a central helical region of LMO2. This is a unique mechanism for inhibiting an intracellular protein function and the structural contusion implies a model in which newly synthesized, intrinsically disordered LMO2 binds to a partner protein nucleating further interactions and suggests approaches for therapeutic targeting of LMO2.
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31
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LIM-domain-only proteins: multifunctional nuclear transcription coregulators that interacts with diverse proteins. Mol Biol Rep 2013; 41:1067-73. [DOI: 10.1007/s11033-013-2952-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 12/20/2013] [Indexed: 02/07/2023]
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32
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Jones DTW, Northcott PA, Kool M, Pfister SM. The role of chromatin remodeling in medulloblastoma. Brain Pathol 2013; 23:193-9. [PMID: 23432644 DOI: 10.1111/bpa.12019] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 12/29/2012] [Indexed: 12/19/2022] Open
Abstract
The unexpectedly high frequency and universality of alterations to the chromatin machinery is one of the most striking themes emerging from the current deluge of cancer genomics data. Medulloblastoma (MB), a malignant pediatric brain tumor, is no exception to this trend, with a wealth of recent studies indicating multiple alterations at all levels of chromatin processing. MB is typically now regarded as being composed of four major molecular entities (WNT, SHH, Group 3 and Group 4), which vary in their clinical and biological characteristics. Similarities and differences across these subgroups are also reflected in the specific chromatin modifiers that are found to be altered in each group, and each new cancer genome sequence or microarray profile is adding to this important knowledge base. These data are fundamentally changing our understanding of tumor developmental pathways, not just for MB but also for cancer as a whole. They also provide a new class of targets for the development of rational, personalized therapeutic approaches. The mechanisms by which these chromatin remodelers are dysregulated in MB, and the consequences both for future basic research and for translation to the clinic, will be examined here.
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Affiliation(s)
- David T W Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
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33
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Gadd MS, Jacques DA, Nisevic I, Craig VJ, Kwan AH, Guss JM, Matthews JM. A structural basis for the regulation of the LIM-homeodomain protein islet 1 (Isl1) by intra- and intermolecular interactions. J Biol Chem 2013; 288:21924-35. [PMID: 23750000 DOI: 10.1074/jbc.m113.478586] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Islet 1 (Isl1) is a transcription factor of the LIM-homeodomain (LIM-HD) protein family and is essential for many developmental processes. LIM-HD proteins all contain two protein-interacting LIM domains, a DNA-binding homeodomain (HD), and a C-terminal region. In Isl1, the C-terminal region also contains the LIM homeobox 3 (Lhx3)-binding domain (LBD), which interacts with the LIM domains of Lhx3. The LIM domains of Isl1 have been implicated in inhibition of DNA binding potentially through an intramolecular interaction with or close to the HD. Here we investigate the LBD as a candidate intramolecular interaction domain. Competitive yeast-two hybrid experiments indicate that the LIM domains and LBD from Isl1 can interact with apparently low affinity, consistent with no detection of an intermolecular interaction in the same system. Nuclear magnetic resonance studies show that the interaction is specific, whereas substitution of the LBD with peptides of the same amino acid composition but different sequence is not specific. We solved the crystal structure of a similar but higher affinity complex between the LIM domains of Isl1 and the LIM interaction domain from the LIM-HD cofactor protein LIM domain-binding protein 1 (Ldb1) and used these coordinates to generate a homology model of the intramolecular interaction that indicates poorer complementarity for the weak intramolecular interaction. The intramolecular interaction in Isl1 may provide protection against aggregation, minimize unproductive DNA binding, and facilitate cofactor exchange within the cell.
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Affiliation(s)
- Morgan S Gadd
- School of Molecular Bioscience, Building G08, University of Sydney, New South Wales 2006, Australia
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34
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Abstract
LIM-domain proteins are a large family of proteins that are emerging as key molecules in a wide variety of human cancers. In particular, all members of the human LIM-domain-only (LMO) proteins, LMO1-4, which are required for many developmental processes, are implicated in the onset or the progression of several cancers, including T cell leukaemia, breast cancer and neuroblastoma. These small proteins contain two protein-interacting LIM domains but little additional sequence, and they seem to function by nucleating the formation of new transcriptional complexes and/or by disrupting existing transcriptional complexes to modulate gene expression programmes. Through these activities, the LMO proteins have important cellular roles in processes that are relevant to cancer such as self-renewal, cell cycle regulation and metastasis. These functions highlight the therapeutic potential of targeting these proteins in cancer.
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Affiliation(s)
- Jacqueline M Matthews
- School of Molecular Bioscience, The University of Sydney, New South Wales 2006, Australia. jacqui.matthews@ sydney.edu.au
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35
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Stokes PH, Liew CW, Kwan AH, Foo P, Barker HE, Djamirze A, O'Reilly V, Visvader JE, Mackay JP, Matthews JM. Structural basis of the interaction of the breast cancer oncogene LMO4 with the tumour suppressor CtIP/RBBP8. J Mol Biol 2013; 425:1101-10. [PMID: 23353824 DOI: 10.1016/j.jmb.2013.01.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 01/12/2013] [Accepted: 01/15/2013] [Indexed: 12/14/2022]
Abstract
LIM-only protein 4 (LMO4) is strongly linked to the progression of breast cancer. Although the mechanisms underlying this phenomenon are not well understood, a role is emerging for LMO4 in regulation of the cell cycle. We determined the solution structure of LMO4 in complex with CtIP (C-terminal binding protein interacting protein)/RBBP8, a tumour suppressor protein that is involved in cell cycle progression, DNA repair and transcriptional regulation. Our data reveal that CtIP and the essential LMO cofactor LDB1 (LIM-domain binding protein 1) bind to the same face on LMO4 and cannot simultaneously bind to LMO4. We hypothesise that overexpression of LMO4 may disrupt some of the normal tumour suppressor activities of CtIP, thereby contributing to breast cancer progression.
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Affiliation(s)
- P H Stokes
- School of Molecular Bioscience, University of Sydney, NSW 2006, Australia
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36
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Matthews JM, Potts JR. The tandem β-zipper: Modular binding of tandem domains and linear motifs. FEBS Lett 2013; 587:1164-71. [DOI: 10.1016/j.febslet.2013.01.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 01/07/2013] [Accepted: 01/07/2013] [Indexed: 11/17/2022]
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37
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Reddy Chichili VP, Kumar V, Sivaraman J. Linkers in the structural biology of protein-protein interactions. Protein Sci 2013; 22:153-67. [PMID: 23225024 DOI: 10.1002/pro.2206] [Citation(s) in RCA: 233] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 11/08/2012] [Accepted: 11/13/2012] [Indexed: 12/14/2022]
Abstract
Linkers or spacers are short amino acid sequences created in nature to separate multiple domains in a single protein. Most of them are rigid and function to prohibit unwanted interactions between the discrete domains. However, Gly-rich linkers are flexible, connecting various domains in a single protein without interfering with the function of each domain. The advent of recombinant DNA technology made it possible to fuse two interacting partners with the introduction of artificial linkers. Often, independent proteins may not exist as stable or structured proteins until they interact with their binding partner, following which they gain stability and the essential structural elements. Gly-rich linkers have been proven useful for these types of unstable interactions, particularly where the interaction is weak and transient, by creating a covalent link between the proteins to form a stable protein-protein complex. Gly-rich linkers are also employed to form stable covalently linked dimers, and to connect two independent domains that create a ligand-binding site or recognition sequence. The lengths of linkers vary from 2 to 31 amino acids, optimized for each condition so that the linker does not impose any constraints on the conformation or interactions of the linked partners. Various structures of covalently linked protein complexes have been described using X-ray crystallography, nuclear magnetic resonance and cryo-electron microscopy techniques. In this review, we evaluate several structural studies where linkers have been used to improve protein quality, to produce stable protein-protein complexes, and to obtain protein dimers.
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38
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Dastmalchi S, Wilkinson-White L, Kwan AH, Gamsjaeger R, Mackay JP, Matthews JM. Solution structure of a tethered Lmo2(LIM2) /Ldb1(LID) complex. Protein Sci 2012; 21:1768-74. [PMID: 22936624 PMCID: PMC3527713 DOI: 10.1002/pro.2153] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 08/21/2012] [Accepted: 08/24/2012] [Indexed: 11/05/2022]
Abstract
LIM-only protein 2, Lmo2, is a regulatory protein that is essential for hematopoietic development and inappropriate overexpression of Lmo2 in T-cells contributes to T-cell leukemia. It exerts its functions by mediating protein-protein interactions and nucleating multicomponent transcriptional complexes. Lmo2 interacts with LIM domain binding protein 1 (Ldb1) through the tandem LIM domains of Lmo2 and the LIM interaction domain (LID) of Ldb1. Here, we present the solution structure of the LIM2 domain of Lmo2 bound to Ldb1(LID) . The ordered regions of Ldb1 in this complex correspond well with binding hotspots previously defined by mutagenic studies. Comparisons of this Lmo2(LIM2) -Ldb1(LID) structure with previously determined structures of the Lmo2/Ldb1(LID) complexes lead to the conclusion that modular binding of tandem LIM domains in Lmo2 to tandem linear motifs in Ldb1 is accompanied by several disorder-to-order transitions and/or conformational changes in both proteins.
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Affiliation(s)
- Siavoush Dastmalchi
- School of Molecular Bioscience, University of SydneySydney, New South Wales 2006, Australia
- Biotechnology Research Centre and School of Pharmacy, Tabriz University of Medical SciencesTabriz, Iran
| | - Lorna Wilkinson-White
- School of Molecular Bioscience, University of SydneySydney, New South Wales 2006, Australia
| | - Ann H Kwan
- School of Molecular Bioscience, University of SydneySydney, New South Wales 2006, Australia
| | - Roland Gamsjaeger
- School of Molecular Bioscience, University of SydneySydney, New South Wales 2006, Australia
- School of Science and Health, University of Western SydneyPenrith, New South Wales 2751, Australia
| | - Joel P Mackay
- School of Molecular Bioscience, University of SydneySydney, New South Wales 2006, Australia
| | - Jacqueline M Matthews
- School of Molecular Bioscience, University of SydneySydney, New South Wales 2006, Australia
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39
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Gadd MS, Jacques DA, Guss JM, Matthews JM. Crystallization and diffraction of an Isl1-Ldb1 complex. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1398-401. [PMID: 23143258 DOI: 10.1107/s1744309112040031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 09/21/2012] [Indexed: 11/10/2022]
Abstract
A stable intramolecular complex comprising the LIM domains of the LIM-homeodomain protein Isl1 tethered to a peptide region of Ldb1 has been engineered, purified and crystallized. The orthorhombic crystals belonged to space group P222(1), with unit-cell parameters a=57.2, b=56.7, c=179.8 Å, and diffracted to 3.10 Å resolution.
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Affiliation(s)
- Morgan S Gadd
- School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia.
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Zhou X, Sang M, Liu W, Gao W, Xing E, Lü W, Xu Y, Fan X, Jing S, Shan B. LMO4 inhibits p53-mediated proliferative inhibition of breast cancer cells through interacting p53. Life Sci 2012; 91:358-63. [PMID: 22906635 DOI: 10.1016/j.lfs.2012.08.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Revised: 07/14/2012] [Accepted: 08/02/2012] [Indexed: 02/07/2023]
Abstract
AIMS The LIM domain only proteins (LMOs) which consist of four members (LMO1-LMO4) are a family of nuclear transcription coregulators that are characterized by the exclusive presence of two tandem LIM domains and no other functional domains. They regulate gene transcription by functioning as "linker" or "scaffolding" proteins by virtue of their LIM domains and are involved in the formation of multiprotein complexes with several DNA-binding factors and transcriptional regulatory proteins. In the present study, we tried to find the physical interaction between p53 and LMO4, and the effect of LMO4 on p53-mediated proliferative inhibition of breast cancer cells. MAIN METHODS FCM analysis was developed to detect the apoptosis of breast cancer cells after adriamycin (ADR) treatment. RT-PCR and Western blot analysis were performed to detect the expression of LMO4 and p53-related genes and proteins. Immunoprecipitation assay was used to detect the interaction between LMO4 and p53. Colony formation assay was developed to detect the proliferation of breast cancer cells. KEY FINDINGS We found that p53 was induced, but LMO4 was down-regulated in response to ADR. We also found that enforced expression of p53 inhibited the expression of LMO4, suggesting that LMO4 is a direct transcriptional target of p53. Furthermore, LMO4 can interact with p53 and inhibit p53-mediated inhibition of colony formation of breast cancer MDA-MB-453 cells. SIGNIFICANCE The present study showed that LMO4 is a direct target of p53 and inhibits p53-mediated proliferative inhibition of breast cancer cells through interacting p53.
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Affiliation(s)
- Xinliang Zhou
- Research Center, the Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050017, People's Republic of China
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41
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Bhati M, Lee C, Gadd MS, Jeffries CM, Kwan A, Whitten AE, Trewhella J, Mackay JP, Matthews JM. Solution structure of the LIM-homeodomain transcription factor complex Lhx3/Ldb1 and the effects of a pituitary mutation on key Lhx3 interactions. PLoS One 2012; 7:e40719. [PMID: 22848397 PMCID: PMC3405102 DOI: 10.1371/journal.pone.0040719] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 06/12/2012] [Indexed: 01/01/2023] Open
Abstract
Lhx3 is a LIM-homeodomain (LIM-HD) transcription factor that regulates neural cell subtype specification and pituitary development in vertebrates, and mutations in this protein cause combined pituitary hormone deficiency syndrome (CPHDS). The recently published structures of Lhx3 in complex with each of two key protein partners, Isl1 and Ldb1, provide an opportunity to understand the effect of mutations and posttranslational modifications on key protein-protein interactions. Here, we use small-angle X-ray scattering of an Ldb1-Lhx3 complex to confirm that in solution the protein is well represented by our previously determined NMR structure as an ensemble of conformers each comprising two well-defined halves (each made up of LIM domain from Lhx3 and the corresponding binding motif in Ldb1) with some flexibility between the two halves. NMR analysis of an Lhx3 mutant that causes CPHDS, Lhx3(Y114C), shows that the mutation does not alter the zinc-ligation properties of Lhx3, but appears to cause a structural rearrangement of the hydrophobic core of the LIM2 domain of Lhx3 that destabilises the domain and/or reduces the affinity of Lhx3 for both Ldb1 and Isl1. Thus the mutation would affect the formation of Lhx3-containing transcription factor complexes, particularly in the pituitary gland where these complexes are required for the production of multiple pituitary cell types and hormones.
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Affiliation(s)
- Mugdha Bhati
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Christopher Lee
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Morgan S. Gadd
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Cy M. Jeffries
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Ann Kwan
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Andrew E. Whitten
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Jill Trewhella
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Joel P. Mackay
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Jacqueline M. Matthews
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
- * E-mail:
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42
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Cubeddu L, Joseph S, Richard DJ, Matthews JM. Contribution of DEAF1 structural domains to the interaction with the breast cancer oncogene LMO4. PLoS One 2012; 7:e39218. [PMID: 22723967 PMCID: PMC3378519 DOI: 10.1371/journal.pone.0039218] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 05/17/2012] [Indexed: 12/22/2022] Open
Abstract
The proteins LMO4 and DEAF1 contribute to the proliferation of mammary epithelial cells. During breast cancer LMO4 is upregulated, affecting its interaction with other protein partners. This may set cells on a path to tumour formation. LMO4 and DEAF1 interact, but it is unknown how they cooperate to regulate cell proliferation. In this study, we identify a specific LMO4-binding domain in DEAF1. This domain contains an unstructured region that directly contacts LMO4, and a coiled coil that contains the DEAF1 nuclear export signal (NES). The coiled coil region can form tetramers and has the typical properties of a coiled coil domain. Using a simple cell-based assay, we show that LMO4 modulates the activity of the DEAF NES, causing nuclear accumulation of a construct containing the LMO4-interaction region of DEAF1.
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Affiliation(s)
- Liza Cubeddu
- School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales, Australia
- * E-mail: (LC); (JM)
| | - Soumya Joseph
- School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales, Australia
| | - Derek J. Richard
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Queensland, Australia
| | - Jacqueline M. Matthews
- School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales, Australia
- * E-mail: (LC); (JM)
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43
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Liew CW, Kwan AH, Stokes PH, Mackay JP, Matthews JM. ¹H, ¹⁵N and ¹³C assignments of an intramolecular LMO4-LIM1/CtIP complex. BIOMOLECULAR NMR ASSIGNMENTS 2012; 6:31-34. [PMID: 21643835 DOI: 10.1007/s12104-011-9319-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 05/23/2011] [Indexed: 05/30/2023]
Abstract
LMO4 is a broadly expressed LIM-only protein that is involved in neural tube development and implicated in breast cancer. Here we report backbone and side chain NMR assignments for an engineered intramolecular complex of the N-terminal LIM domain from LMO4 tethered to residues 641-685 of C-terminal binding protein interacting protein (CtIP/RBBP8).
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Affiliation(s)
- Chu Wai Liew
- School of Molecular Bioscience, University of Sydney, Building G08, Sydney, NSW 2006, Australia
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44
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Zheng Q, Zhao Y. The diverse biofunctions of LIM domain proteins: determined by subcellular localization and protein-protein interaction. Biol Cell 2012; 99:489-502. [PMID: 17696879 DOI: 10.1042/bc20060126] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The LIM domain is a cysteine- and histidine-rich motif that has been proposed to direct protein-protein interactions. A diverse group of proteins containing LIM domains have been identified, which display various functions including gene regulation and cell fate determination, tumour formation and cytoskeleton organization. LIM domain proteins are distributed in both the nucleus and the cytoplasm, and they exert their functions through interactions with various protein partners.
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Affiliation(s)
- Quanhui Zheng
- Transplantation Biology Research Division, State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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45
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Norris NC, Bingham RJ, Harris G, Speakman A, Jones RPO, Leech A, Turkenburg JP, Potts JR. Structural and functional analysis of the tandem β-zipper interaction of a Streptococcal protein with human fibronectin. J Biol Chem 2011; 286:38311-38320. [PMID: 21840989 PMCID: PMC3207447 DOI: 10.1074/jbc.m111.276592] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 08/01/2011] [Indexed: 11/06/2022] Open
Abstract
Bacterial fibronectin-binding proteins (FnBPs) contain a large intrinsically disordered region (IDR) that mediates adhesion of bacteria to host tissues, and invasion of host cells, through binding to fibronectin (Fn). These FnBP IDRs consist of Fn-binding repeats (FnBRs) that form a highly extended tandem β-zipper interaction on binding to the N-terminal domain of Fn. Several FnBR residues are highly conserved across bacterial species, and here we investigate their contribution to the interaction. Mutation of these residues to alanine in SfbI-5 (a disordered FnBR from the human pathogen Streptococcus pyogenes) reduced binding, but for each residue the change in free energy of binding was <2 kcal/mol. The structure of an SfbI-5 peptide in complex with the second and third F1 modules from Fn confirms that the conserved FnBR residues play equivalent functional roles across bacterial species. Thus, in SfbI-5, the binding energy for the tandem β-zipper interaction with Fn is distributed across the interface rather than concentrated in a small number of "hot spot" residues that are frequently observed in the interactions of folded proteins. We propose that this might be a common feature of the interactions of IDRs and is likely to pose a challenge for the development of small molecule inhibitors of FnBP-mediated adhesion to and invasion of host cells.
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Affiliation(s)
- Nicole C Norris
- Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Richard J Bingham
- Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Gemma Harris
- Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Adrian Speakman
- Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Richard P O Jones
- Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Andrew Leech
- Technology Facility, Department of Biology (Area 15), University of York, York, YO10 5DD, United Kingdom
| | - Johan P Turkenburg
- Department of Chemistry, University of York, York, YO10 5DD, United Kingdom
| | - Jennifer R Potts
- Department of Biology, University of York, York, YO10 5DD, United Kingdom; Department of Chemistry, University of York, York, YO10 5DD, United Kingdom.
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46
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Gadd MS, Bhati M, Jeffries CM, Langley DB, Trewhella J, Guss JM, Matthews JM. Structural basis for partial redundancy in a class of transcription factors, the LIM homeodomain proteins, in neural cell type specification. J Biol Chem 2011; 286:42971-80. [PMID: 22025611 DOI: 10.1074/jbc.m111.248559] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Combinations of LIM homeodomain proteins form a transcriptional "LIM code" to direct the specification of neural cell types. Two paralogous pairs of LIM homeodomain proteins, LIM homeobox protein 3/4 (Lhx3/Lhx4) and Islet-1/2 (Isl1/Isl2), are expressed in developing ventral motor neurons. Lhx3 and Isl1 interact within a well characterized transcriptional complex that triggers motor neuron development, but it was not known whether Lhx4 and Isl2 could participate in equivalent complexes. We have identified an Lhx3-binding domain (LBD) in Isl2 based on sequence homology with the Isl1(LBD) and show that both Isl2(LBD) and Isl1(LBD) can bind each of Lhx3 and Lhx4. X-ray crystal- and small-angle x-ray scattering-derived solution structures of an Lhx4·Isl2 complex exhibit many similarities with that of Lhx3·Isl1; however, structural differences supported by mutagenic studies reveal differences in the mechanisms of binding. Differences in binding have implications for the mode of exchange of protein partners in transcriptional complexes and indicate a divergence in functions of Lhx3/4 and Isl1/2. The formation of weaker Lhx·Isl complexes would likely be masked by the availability of the other Lhx·Isl complexes in postmitotic motor neurons.
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Affiliation(s)
- Morgan S Gadd
- School of Molecular Bioscience, The University of Sydney, New South Wales 2006, Australia
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47
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Hilton JM, Lewis MA, Grati M, Ingham N, Pearson S, Laskowski RA, Adams DJ, Steel KP. Exome sequencing identifies a missense mutation in Isl1 associated with low penetrance otitis media in dearisch mice. Genome Biol 2011; 12:R90. [PMID: 21936904 PMCID: PMC3308053 DOI: 10.1186/gb-2011-12-9-r90] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 08/02/2011] [Accepted: 09/21/2011] [Indexed: 02/06/2023] Open
Abstract
Background Inflammation of the middle ear (otitis media) is very common and can lead to serious complications if not resolved. Genetic studies suggest an inherited component, but few of the genes that contribute to this condition are known. Mouse mutants have contributed significantly to the identification of genes predisposing to otitis media Results The dearisch mouse mutant is an ENU-induced mutant detected by its impaired Preyer reflex (ear flick in response to sound). Auditory brainstem responses revealed raised thresholds from as early as three weeks old. Pedigree analysis suggested a dominant but partially penetrant mode of inheritance. The middle ear of dearisch mutants shows a thickened mucosa and cellular effusion suggesting chronic otitis media with effusion with superimposed acute infection. The inner ear, including the sensory hair cells, appears normal. Due to the low penetrance of the phenotype, normal backcross mapping of the mutation was not possible. Exome sequencing was therefore employed to identify a non-conservative tyrosine to cysteine (Y71C) missense mutation in the Islet1 gene, Isl1Drsh. Isl1 is expressed in the normal middle ear mucosa. The findings suggest the Isl1Drshmutation is likely to predispose carriers to otitis media. Conclusions Dearisch, Isl1Drsh, represents the first point mutation in the mouse Isl1 gene and suggests a previously unrecognized role for this gene. It is also the first recorded exome sequencing of the C3HeB/FeJ background relevant to many ENU-induced mutants. Most importantly, the power of exome resequencing to identify ENU-induced mutations without a mapped gene locus is illustrated.
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48
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Asprer JST, Lee B, Wu CS, Vadakkan T, Dickinson ME, Lu HC, Lee SK. LMO4 functions as a co-activator of neurogenin 2 in the developing cortex. Development 2011; 138:2823-32. [PMID: 21652654 DOI: 10.1242/dev.061879] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The proneural protein neurogenin 2 (NGN2) is a key transcription factor in regulating both neurogenesis and neuronal radial migration in the embryonic cerebral cortex. However, the co-factors that support the action of NGN2 in the cortex remain unclear. Here, we show that the LIM-only protein LMO4 functions as a novel co-factor of NGN2 in the developing cortex. LMO4 and its binding partner nuclear LIM interactor (NLI/LDB1/CLIM2) interact with NGN2 simultaneously, forming a multi-protein transcription complex. This complex is recruited to the E-box containing enhancers of NGN2-target genes, which regulate various aspects of cortical development, and activates NGN2-mediated transcription. Correspondingly, analysis of Lmo4-null embryos shows that the loss of LMO4 leads to impairments of neuronal differentiation in the cortex. In addition, expression of LMO4 facilitates NGN2-mediated radial migration of cortical neurons in the embryonic cortex. Our results indicate that LMO4 promotes the acquisition of cortical neuronal identities by forming a complex with NGN2 and subsequently activating NGN2-dependent gene expression.
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Affiliation(s)
- Joanna S T Asprer
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
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49
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Structural basis of simultaneous recruitment of the transcriptional regulators LMO2 and FOG1/ZFPM1 by the transcription factor GATA1. Proc Natl Acad Sci U S A 2011; 108:14443-8. [PMID: 21844373 DOI: 10.1073/pnas.1105898108] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The control of red blood cell and megakaryocyte development by the regulatory protein GATA1 is a paradigm for transcriptional regulation of gene expression in cell lineage differentiation and maturation. Most GATA1-regulated events require GATA1 to bind FOG1, and essentially all GATA1-activated genes are cooccupied by a TAL1/E2A/LMO2/LDB1 complex; however, it is not known whether FOG1 and TAL1/E2A/LMO2/LDB1 are simultaneously recruited by GATA1. Our structural data reveal that the FOG1-binding domain of GATA1, the N finger, can also directly contact LMO2 and show that, despite the small size (< 50 residues) of the GATA1 N finger, both FOG1 and LMO2 can simultaneously bind this domain. LMO2 in turn can simultaneously contact both GATA1 and the DNA-binding protein TAL1/E2A at bipartite E-box/WGATAR sites. Taken together, our data provide the first structural snapshot of multiprotein complex formation at GATA1-dependent genes and support a model in which FOG1 and TAL1/E2A/LMO2/LDB1 can cooccupy E-box/WGATAR sites to facilitate GATA1-mediated activation of gene activation.
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50
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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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