1
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von Ehr J, Oberstrass L, Yazgan E, Schnaubelt LI, Blümel N, McNicoll F, Weigand JE, Zarnack K, Müller-McNicoll M, Korn SM, Schlundt A. Arid5a uses disordered extensions of its core ARID domain for distinct DNA- and RNA-recognition and gene regulation. J Biol Chem 2024; 300:107457. [PMID: 38866324 PMCID: PMC11262183 DOI: 10.1016/j.jbc.2024.107457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/23/2024] [Accepted: 06/01/2024] [Indexed: 06/14/2024] Open
Abstract
AT-rich interacting domain (ARID)-containing proteins, Arids, are a heterogeneous DNA-binding protein family involved in transcription regulation and chromatin processing. For the member Arid5a, no exact DNA-binding preference has been experimentally defined so far. Additionally, the protein binds to mRNA motifs for transcript stabilization, supposedly through the DNA-binding ARID domain. To date, however, no unbiased RNA motif definition and clear dissection of nucleic acid-binding through the ARID domain have been undertaken. Using NMR-centered biochemistry, we here define the Arid5a DNA preference. Further, high-throughput in vitro binding reveals a consensus RNA-binding motif engaged by the core ARID domain. Finally, transcriptome-wide binding (iCLIP2) reveals that Arid5a has a weak preference for (A)U-rich regions in pre-mRNA transcripts of factors related to RNA processing. We find that the intrinsically disordered regions flanking the ARID domain modulate the specificity and affinity of DNA binding, while they appear crucial for RNA interactions. Ultimately, our data suggest that Arid5a uses its extended ARID domain for bifunctional gene regulation and that the involvement of IDR extensions is a more general feature of Arids in interacting with different nucleic acids at the chromatin-mRNA interface.
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Affiliation(s)
- Julian von Ehr
- Institute for Molecular Biosciences and Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Frankfurt, Germany; IMPRS on Cellular Biophysics, Frankfurt, Germany
| | - Lasse Oberstrass
- University of Marburg, Department of Pharmacy, Institute of Pharmaceutical Chemistry, Marburg, Germany
| | - Ege Yazgan
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Lara Ina Schnaubelt
- Institute for Molecular Biosciences and Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Frankfurt, Germany
| | - Nicole Blümel
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Francois McNicoll
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Julia E Weigand
- University of Marburg, Department of Pharmacy, Institute of Pharmaceutical Chemistry, Marburg, Germany
| | - Kathi Zarnack
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Michaela Müller-McNicoll
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany; Max-Planck Institute for Biophysics, Frankfurt, Germany
| | - Sophie Marianne Korn
- Institute for Molecular Biosciences and Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Frankfurt, Germany; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA.
| | - Andreas Schlundt
- Institute for Molecular Biosciences and Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Frankfurt, Germany; University of Greifswald, Institute of Biochemistry, Greifswald, Germany.
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2
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Guo CC, Xu HE, Ma X. ARID3a from the ARID family: structure, role in autoimmune diseases and drug discovery. Acta Pharmacol Sin 2023; 44:2139-2150. [PMID: 37488425 PMCID: PMC10618457 DOI: 10.1038/s41401-023-01134-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/09/2023] [Indexed: 07/26/2023] Open
Abstract
The AT-rich interaction domain (ARID) family of DNA-binding proteins is a group of transcription factors and chromatin regulators with a highly conserved ARID domain that recognizes specific AT-rich DNA sequences. Dysfunction of ARID family members has been implicated in various human diseases including cancers and intellectual disability. Among them, ARID3a has gained increasing attention due to its potential involvement in autoimmunity. In this article we provide an overview of the ARID family, focusing on the structure and biological functions of ARID3a. It explores the role of ARID3a in autoreactive B cells and its contribution to autoimmune diseases such as systemic lupus erythematosus and primary biliary cholangitis. Furthermore, we also discuss the potential for drug discovery targeting ARID3a and present a plan for future research in this field.
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Affiliation(s)
- Cheng-Cen Guo
- Department of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, 200001, China.
| | - H Eric Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Xiong Ma
- Department of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, 200001, China.
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3
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Yu H, Yang H, Haridas S, Hayes RD, Lynch H, Andersen S, Newman M, Li G, Martínez-Soto D, Milo-Cochavi S, Hazal Ayhan D, Zhang Y, Grigoriev IV, Ma LJ. Conservation and Expansion of Transcriptional Factor Repertoire in the Fusarium oxysporum Species Complex. J Fungi (Basel) 2023; 9:359. [PMID: 36983527 PMCID: PMC10056406 DOI: 10.3390/jof9030359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
The Fusarium oxysporum species complex (FOSC) includes both plant and human pathogens that cause devastating plant vascular wilt diseases and threaten public health. Each F. oxysporum genome comprises core chromosomes (CCs) for housekeeping functions and accessory chromosomes (ACs) that contribute to host-specific adaptation. This study inspects global transcription factor profiles (TFomes) and their potential roles in coordinating CC and AC functions to accomplish host-specific interactions. Remarkably, we found a clear positive correlation between the sizes of TFomes and the proteomes of an organism. With the acquisition of ACs, the FOSC TFomes were larger than the other fungal genomes included in this study. Among a total of 48 classified TF families, 14 families involved in transcription/translation regulations and cell cycle controls were highly conserved. Among the 30 FOSC expanded families, Zn2-C6 and Znf_C2H2 were most significantly expanded to 671 and 167 genes per family including well-characterized homologs of Ftf1 (Zn2-C6) and PacC (Znf_C2H2) that are involved in host-specific interactions. Manual curation of characterized TFs increased the TFome repertoires by 3% including a disordered protein Ren1. RNA-Seq revealed a steady pattern of expression for conserved TF families and specific activation for AC TFs. Functional characterization of these TFs could enhance our understanding of transcriptional regulation involved in FOSC cross-kingdom interactions, disentangle species-specific adaptation, and identify targets to combat diverse diseases caused by this group of fungal pathogens.
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Affiliation(s)
- Houlin Yu
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - He Yang
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Sajeet Haridas
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, University of California Berkeley, Berkeley, CA 94720, USA
| | - Richard D. Hayes
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, University of California Berkeley, Berkeley, CA 94720, USA
| | - Hunter Lynch
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Sawyer Andersen
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Madison Newman
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Gengtan Li
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Domingo Martínez-Soto
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Shira Milo-Cochavi
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Dilay Hazal Ayhan
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Yong Zhang
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Igor V. Grigoriev
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94598, USA
| | - Li-Jun Ma
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
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4
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Cell context-dependent CFI-1/ARID3 functions control neuronal terminal differentiation. Cell Rep 2023; 42:112220. [PMID: 36897776 PMCID: PMC10124151 DOI: 10.1016/j.celrep.2023.112220] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 12/21/2022] [Accepted: 02/20/2023] [Indexed: 03/11/2023] Open
Abstract
AT-rich interaction domain 3 (ARID3) transcription factors are expressed in the nervous system, but their mechanisms of action are largely unknown. Here, we provide, in vivo, a genome-wide binding map for CFI-1, the sole C. elegans ARID3 ortholog. We identify 6,396 protein-coding genes as putative direct targets of CFI-1, most of which encode neuronal terminal differentiation markers. In head sensory neurons, CFI-1 directly activates multiple terminal differentiation genes, thereby acting as a terminal selector. In motor neurons, however, CFI-1 acts as a direct repressor, continuously antagonizing three transcriptional activators. By focusing on the glr-4/GRIK4 glutamate receptor locus, we identify proximal CFI-1 binding sites and histone methyltransferase activity as necessary for glr-4 repression. Rescue assays reveal functional redundancy between core and extended DNA-binding ARID domains and a strict requirement for REKLES, the ARID3 oligomerization domain. Altogether, this study uncovers cell-context-dependent mechanisms through which a single ARID3 protein controls the terminal differentiation of distinct neuron types.
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5
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Yu H, Yang H, Haridas S, Hayes RD, Lynch H, Andersen S, Li G, Mart Nez-Soto D, Milo-Cochavi S, Hazal Ayhan D, Zhang Y, Grigoriev IV, Ma LJ. Conservation and Expansion of Transcriptional Factor Repertoire in the Fusarium oxysporum Species Complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.09.527873. [PMID: 36798233 PMCID: PMC9934661 DOI: 10.1101/2023.02.09.527873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The Fusarium oxysporum species complex (FOSC) includes both plant and human pathogens that cause devastating plant vascular wilt diseases and threaten public health. Each F. oxysporum genome comprises core chromosomes (CCs) for housekeeping functions and accessory chromosomes (ACs) that contribute to host-specific adaptation. This study inspected global transcription factor profiles (TFomes) and their potential roles in coordinating CCs and ACs functions to accomplish host-specific pathogenicity. Remarkably, we found a clear positive correlation between the sizes of TFome and proteome of an organism, and FOSC TFomes are larger due to the acquisition of ACs. Among a total of 48 classified TF families, 14 families involved in transcription/translation regulations and cell cycle controls are highly conserved. Among 30 FOSC expanded families, Zn2-C6 and Znf_C2H2 are most significantly expanded to 671 and 167 genes per family, including well-characterized homologs of Ftf1 (Zn2-C6) and PacC (Znf_C2H2) involved in host-specific interactions. Manual curation of characterized TFs increased the TFome repertoires by 3%, including a disordered protein Ren1. Expression profiles revealed a steady expression of conserved TF families and specific activation of AC TFs. Functional characterization of these TFs could enhance our understanding of transcriptional regulation involved in FOSC cross-kingdom interactions, disentangle species-specific adaptation, and identify targets to combat diverse diseases caused by this group of fungal pathogens.
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6
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Deák G, Cook AG. Missense Variants Reveal Functional Insights Into the Human ARID Family of Gene Regulators. J Mol Biol 2022; 434:167529. [PMID: 35257783 PMCID: PMC9077328 DOI: 10.1016/j.jmb.2022.167529] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/10/2022] [Accepted: 03/01/2022] [Indexed: 11/16/2022]
Abstract
Missense variants are alterations to protein coding sequences that result in amino acid substitutions. They can be deleterious if the amino acid is required for maintaining structure or/and function, but are likely to be tolerated at other sites. Consequently, missense variation within a healthy population can mirror the effects of negative selection on protein structure and function, such that functional sites on proteins are often depleted of missense variants. Advances in high-throughput sequencing have dramatically increased the sample size of available human variation data, allowing for population-wide analysis of selective pressures. In this study, we developed a convenient set of tools, called 1D-to-3D, for visualizing the positions of missense variants on protein sequences and structures. We used these tools to characterize human homologues of the ARID family of gene regulators. ARID family members are implicated in multiple cancer types, developmental disorders, and immunological diseases but current understanding of their mechanistic roles is incomplete. Combined with phylogenetic and structural analyses, our approach allowed us to characterise sites important for protein-protein interactions, histone modification recognition, and DNA binding by the ARID proteins. We find that comparing missense depletion patterns among paralogs can reveal sub-functionalization at the level of domains. We propose that visualizing missense variants and their depletion on structures can serve as a valuable tool for complementing evolutionary and experimental findings.
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Affiliation(s)
- Gauri Deák
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, United Kingdom. https://twitter.com/GauriDeak
| | - Atlanta G Cook
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, United Kingdom.
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7
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Giri M, Gupta P, Maulik A, Gracias M, Singh M. Structure and DNA binding analysis of AT-rich interaction domain present in human BAF-B specific subunit BAF250b. Protein Sci 2022; 31:e4294. [PMID: 35481652 PMCID: PMC8994505 DOI: 10.1002/pro.4294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 02/21/2022] [Accepted: 02/28/2022] [Indexed: 11/06/2022]
Abstract
BAF250b and its paralog BAF250a are the DNA-binding central hub proteins present in BAF-B and BAF-A classes of SWI/SNF chromatin-remodeling complexes. BAF250b contains an AT-rich interaction domain (ARID) and C-terminal BAF250_C domain, and it is found mutated in several cancers. ARID is a conserved helix-turn-helix motif-containing DNA-binding domain present in several eukaryotic proteins. The ARID of BAF250b has been proposed to play roles in recruiting SWI/SNF to the target gene promoters for their activation. BAF250b ARID structures had been deposited in the protein data bank by a structural genomics consortium. However, it is not well-studied for its DNA-binding and solution dynamic properties. Here, we report complete backbone NMR resonance assignments of human BAF250b ARID. NMR chemical shifts and the backbone dynamics showed that the solution structure of the protein matched the reported crystal structures. The structure and chemical shift indexing revealed the presence of a short β-sheet in the DNA-binding region of BAF250b ARID that was absent in the structure of its paralog BAF250a ARID. NMR chemical shift perturbations identified DNA-binding residues and revealed the DNA-binding interface on BAF250b ARID. NMR data-driven HADDOCK models of BAF250b ARID - DNA complexes revealed its plausible mode of DNA-binding. Isothermal titration calorimetry experiments showed that BAF250b ARID interacts with DNA sequences with moderate affinities like BAF250a ARID. However, distinct thermodynamic signatures were observed for binding of BAF250a ARID and BAF250b ARID to AT-rich DNA sequence, suggesting that subtle sequence and structural differences in these two proteins influence their DNA-binding.
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Affiliation(s)
- Malyasree Giri
- Molecular Biophysics UnitIndian Institute of ScienceBengaluruIndia
| | - Parul Gupta
- Molecular Biophysics UnitIndian Institute of ScienceBengaluruIndia
| | - Aditi Maulik
- Molecular Biophysics UnitIndian Institute of ScienceBengaluruIndia
| | - Magaly Gracias
- Molecular Biophysics UnitIndian Institute of ScienceBengaluruIndia
| | - Mahavir Singh
- Molecular Biophysics UnitIndian Institute of ScienceBengaluruIndia
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8
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Owen BM, Davidovich C. DNA binding by polycomb-group proteins: searching for the link to CpG islands. Nucleic Acids Res 2022; 50:4813-4839. [PMID: 35489059 PMCID: PMC9122586 DOI: 10.1093/nar/gkac290] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/25/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Polycomb group proteins predominantly exist in polycomb repressive complexes (PRCs) that cooperate to maintain the repressed state of thousands of cell-type-specific genes. Targeting PRCs to the correct sites in chromatin is essential for their function. However, the mechanisms by which PRCs are recruited to their target genes in mammals are multifactorial and complex. Here we review DNA binding by polycomb group proteins. There is strong evidence that the DNA-binding subunits of PRCs and their DNA-binding activities are required for chromatin binding and CpG targeting in cells. In vitro, CpG-specific binding was observed for truncated proteins externally to the context of their PRCs. Yet, the mere DNA sequence cannot fully explain the subset of CpG islands that are targeted by PRCs in any given cell type. At this time we find very little structural and biophysical evidence to support a model where sequence-specific DNA-binding activity is required or sufficient for the targeting of CpG-dinucleotide sequences by polycomb group proteins while they are within the context of their respective PRCs, either PRC1 or PRC2. We discuss the current knowledge and open questions on how the DNA-binding activities of polycomb group proteins facilitate the targeting of PRCs to chromatin.
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Affiliation(s)
- Brady M Owen
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Chen Davidovich
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia.,EMBL-Australia, Clayton, VIC, Australia
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9
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Korn SM, Schlundt A. Structures and nucleic acid-binding preferences of the eukaryotic ARID domain. Biol Chem 2022; 403:731-747. [PMID: 35119801 DOI: 10.1515/hsz-2021-0404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/17/2022] [Indexed: 12/28/2022]
Abstract
The DNA-binding AT-rich interactive domain (ARID) exists in a wide range of proteins throughout eukaryotic kingdoms. ARID domain-containing proteins are involved in manifold biological processes, such as transcriptional regulation, cell cycle control and chromatin remodeling. Their individual domain composition allows for a sub-classification within higher mammals. ARID is categorized as binder of double-stranded AT-rich DNA, while recent work has suggested ARIDs as capable of binding other DNA motifs and also recognizing RNA. Despite a broad variability on the primary sequence level, ARIDs show a highly conserved fold, which consists of six α-helices and two loop regions. Interestingly, this minimal core domain is often found extended by helices at the N- and/or C-terminus with potential roles in target specificity and, subsequently function. While high-resolution structural information from various types of ARIDs has accumulated over two decades now, there is limited access to ARID-DNA complex structures. We thus find ourselves left at the beginning of understanding ARID domain target specificities and the role of accompanying domains. Here, we systematically summarize ARID domain conservation and compare the various types with a focus on their structural differences and DNA-binding preferences, including the context of multiple other motifs within ARID domain containing proteins.
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Affiliation(s)
- Sophie Marianne Korn
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Andreas Schlundt
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
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10
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Structural Insight into Chromatin Recognition by Multiple Domains of the Tumor Suppressor RBBP1. J Mol Biol 2021; 433:167224. [PMID: 34506790 DOI: 10.1016/j.jmb.2021.167224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/22/2021] [Accepted: 08/27/2021] [Indexed: 01/04/2023]
Abstract
Retinoblastoma-binding protein 1 (RBBP1) is involved in gene regulation, epigenetic regulation, and disease processes. RBBP1 contains five domains with DNA-binding or histone-binding activities, but how RBBP1 specifically recognizes chromatin is still unknown. An AT-rich interaction domain (ARID) in RBBP1 was proposed to be the key region for DNA-binding and gene suppression. Here, we first determined the solution structure of a tandem PWWP-ARID domain mutant of RBBP1 after deletion of a long flexible acidic loop L12 in the ARID domain. NMR titration results indicated that the ARID domain interacts with DNA with no GC- or AT-rich preference. Surprisingly, we found that the loop L12 binds to the DNA-binding region of the ARID domain as a DNA mimic and inhibits DNA binding. The loop L12 can also bind weakly to the Tudor and chromobarrel domains of RBBP1, but binds more strongly to the DNA-binding region of the histone H2A-H2B heterodimer. Furthermore, both the loop L12 and DNA can enhance the binding of the chromobarrel domain to H3K4me3 and H4K20me3. Based on these results, we propose a model of chromatin recognition by RBBP1, which highlights the unexpected multiple key roles of the disordered acidic loop L12 in the specific binding of RBBP1 to chromatin.
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11
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Arabidopsis RPD3-like histone deacetylases form multiple complexes involved in stress response. J Genet Genomics 2021; 48:369-383. [PMID: 34144927 DOI: 10.1016/j.jgg.2021.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/31/2021] [Accepted: 04/15/2021] [Indexed: 12/13/2022]
Abstract
The Arabidopsis thaliana RPD3-type histone deacetylases have been known to form conserved SIN3-type histone deacetylase complexes, but whether they form other types of complexes is unknown. Here, we perform affinity purification followed by mass spectrometry and demonstrate that the Arabidopsis RPD3-type histone deacetylases HDA6 and HDA19 interact with several previously uncharacterized proteins, thereby forming three types of plant-specific histone deacetylase complexes, which we named SANT, ESANT, and ARID. RNA-seq indicates that the newly identified components function together with HDA6 and HDA19 and coregulate the expression of a number of genes. HDA6 and HDA19 were previously thought to repress gene transcription by histone deacetylation. We find that the histone deacetylase complexes can repress gene expression via both histone deacetylation-dependent and -independent mechanisms. In the mutants of histone deacetylase complexes, the expression of a number of stress-induced genes is up-regulated, and several mutants of the histone deacetylase complexes show severe retardation in growth. Considering that growth retardation is thought to be a trade-off for an increase in stress tolerance, we infer that the histone deacetylase complexes identified in this study prevent overexpression of stress-induced genes and thereby ensure normal growth of plants under nonstress conditions.
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12
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Salewski I, Gladbach YS, Kuntoff S, Irmscher N, Hahn O, Junghanss C, Maletzki C. In vivo vaccination with cell line-derived whole tumor lysates: neoantigen quality, not quantity matters. J Transl Med 2020; 18:402. [PMID: 33087163 PMCID: PMC7579816 DOI: 10.1186/s12967-020-02570-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Cancer vaccines provide a complex source of neoantigens. Still, increasing evidence reveals that the neoantigen quality rather than the quantity is predictive for treatment outcome. METHODS Using the preclinical Mlh1-/- tumor model, we performed a side-by side comparison of two autologous cell-line derived tumor lysates (namely 328 and A7450 T1 M1) harboring different tumor mutational burden (TMB; i.e. ultra-high: 328; moderate-high: A7450 T1 M1). Mice received repetitive prophylactic or therapeutic applications of the vaccine. Tumor incidence, immune responses and tumor microenvironment was examined. RESULTS Both tumor cell lysates delayed tumor formation in the prophylactic setting, with the A7450 T1 M1 lysate being more effective in decelerating tumor growth than the 328 lysate (median overall survival: 37 vs. 25 weeks). Comparable results were achieved in therapeutic setting and could be traced back to antigen-driven immune stimulation. Reactive T cells isolated from A7450 T1 M1-treated mice recognized autologous Mlh1-/- tumor cells in IFNγ ELISpot, but likewise YAC-1 cells, indicative for stimulation of both arms of the immune system. By deciphering local effects, vaccines shaped the tumor microenvironment differently. While A7450 T1 M1 prophylactically vaccinated tumors harbored low numbers of myeloid-derived suppressor cells (MDSC) and elevated CD8-T cell infiltrates, vaccination with the 328 lysate evoked MDSC infiltration. Similar effects were seen in the therapeutic setting with stable disease induction only upon A7450 T1 M1 vaccination. Untangling individual response profiles revealed strong infiltration with LAG3+ and PD-L1+ immune cells when treatments failed, but almost complete exclusion of checkpoint-expressing lymphocytes in long-term survivors. CONCLUSIONS By applying two tumor cell lysates we demonstrate that neoantigen quality outranks quantity. This should be considered prior to designing cancer vaccine-based combination approaches.
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Affiliation(s)
- Inken Salewski
- Department of Medicine, Clinic III-Hematology, Oncology, Palliative Care, Rostock University Medical Center, Ernst-Heydemann-Str. 6, 18057, Rostock, Germany
| | - Yvonne Saara Gladbach
- Institute for Biostatistics and Informatics in Medicine and Ageing Research (IBIMA), Rostock University Medical Center, University of Rostock, 18057, Rostock, Germany.,Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany.,Division of Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Steffen Kuntoff
- Department of Medicine, Clinic III-Hematology, Oncology, Palliative Care, Rostock University Medical Center, Ernst-Heydemann-Str. 6, 18057, Rostock, Germany
| | - Nina Irmscher
- Department of Medicine, Clinic III-Hematology, Oncology, Palliative Care, Rostock University Medical Center, Ernst-Heydemann-Str. 6, 18057, Rostock, Germany
| | - Olga Hahn
- Department of Cell Biology, Rostock University Medical Center, 18057, Rostock, Germany
| | - Christian Junghanss
- Department of Medicine, Clinic III-Hematology, Oncology, Palliative Care, Rostock University Medical Center, Ernst-Heydemann-Str. 6, 18057, Rostock, Germany
| | - Claudia Maletzki
- Department of Medicine, Clinic III-Hematology, Oncology, Palliative Care, Rostock University Medical Center, Ernst-Heydemann-Str. 6, 18057, Rostock, Germany.
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13
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Tan LM, Liu R, Gu BW, Zhang CJ, Luo J, Guo J, Wang Y, Chen L, Du X, Li S, Shao CR, Su YN, Cai XW, Lin RN, Li L, Chen S, Du J, He XJ. Dual Recognition of H3K4me3 and DNA by the ISWI Component ARID5 Regulates the Floral Transition in Arabidopsis. THE PLANT CELL 2020; 32:2178-2195. [PMID: 32358072 PMCID: PMC7346560 DOI: 10.1105/tpc.19.00944] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 04/09/2020] [Accepted: 04/27/2020] [Indexed: 05/07/2023]
Abstract
Chromatin remodeling and histone modifications are important for development and floral transition in plants. However, it is largely unknown whether and how these two epigenetic regulators coordinately regulate the important biological processes. Here, we identified three types of Imitation Switch (ISWI) chromatin-remodeling complexes in Arabidopsis (Arabidopsis thaliana). We found that AT-RICH INTERACTING DOMAIN5 (ARID5), a subunit of a plant-specific ISWI complex, can regulate development and floral transition. The ARID-PHD dual domain cassette of ARID5 recognizes both the H3K4me3 histone mark and AT-rich DNA. We determined the ternary complex structure of the ARID5 ARID-PHD cassette with an H3K4me3 peptide and an AT-containing DNA. The H3K4me3 peptide is combinatorially recognized by the PHD and ARID domains, while the DNA is specifically recognized by the ARID domain. Both PHD and ARID domains are necessary for the association of ARID5 with chromatin. The results suggest that the dual recognition of AT-rich DNA and H3K4me3 by the ARID5 ARID-PHD cassette may facilitate the association of the ISWI complex with specific chromatin regions to regulate development and floral transition.
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Affiliation(s)
- Lian-Mei Tan
- National Institute of Biological Sciences, Beijing 102206, China
| | - Rui Liu
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Bo-Wen Gu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Cui-Jun Zhang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Jinyan Luo
- National Key Laboratory of Plant Molecular Genetics and Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Jing Guo
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yuhua Wang
- National Key Laboratory of Plant Molecular Genetics and Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Lixian Chen
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- National Key Laboratory of Plant Molecular Genetics and Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuan Du
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Sisi Li
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Chang-Rong Shao
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yin-Na Su
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xue-Wei Cai
- National Institute of Biological Sciences, Beijing 102206, China
| | - Rong-Nan Lin
- National Institute of Biological Sciences, Beijing 102206, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing 102206, China
| | - She Chen
- National Institute of Biological Sciences, Beijing 102206, China
| | - Jiamu Du
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
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14
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Giri M, Maulik A, Singh M. Signatures of Specific DNA Binding by the AT-Rich Interaction Domain of BAF250a. Biochemistry 2019; 59:100-113. [PMID: 31825600 DOI: 10.1021/acs.biochem.9b00852] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The AT-rich interaction domain (ARID) containing BAF250a is a subunit of the BAF-A class of SWI/SNF chromatin remodeling complexes. The ARID belongs to a family of conserved DNA binding domains found in several eukaryotic proteins; however, its exact contribution to BAF250a function and the mechanism of its DNA binding are not well understood. Here we have probed the interaction of the BAF250a ARID with three different double-stranded DNA (dsDNA) sequences to understand its DNA binding properties. A comprehensive biophysical and thermodynamic study using nuclear magnetic resonance (NMR) spectroscopy and isothermal titration calorimetry revealed the complex nature of BAF250a ARID-DNA interactions. The thermodynamic signatures of the BAF250a ARID with 12 A-T bp dsDNA (AT-12) are distinct from those of 12 G-C bp dsDNA (GC-12) or 12 bp Dickerson dodecamer DNA (DD-12) sequences. We observed that the binding of the BAF250a ARID with AT-12 DNA is enthalpically driven in a tested temperature range of 5-25 °C. BAF250a ARID/AT-12 DNA interaction exhibited a larger negative calorimetric specific heat change (ΔCp) compared to that of BAF250a ARID/GC-12 DNA or BAF250a ARID/DD-12 DNA interactions. In the presence of salt (NaCl), ARID/AT-12 DNA binding was less perturbed than ARID/GC-12 DNA or ARID/DD-12 DNA binding. Overall, these results show that BAF250a ARID/AT-12 DNA interaction has signatures of "specific" binding. Furthermore, using NMR chemical shift perturbation experiments, we have identified DNA binding residues on the BAF250a ARID and generated a data-driven HADDOCK model of the ARID/DNA complex that was further supported by mutating key lysine residues that were found to be important for DNA binding.
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Affiliation(s)
- Malyasree Giri
- Molecular Biophysics Unit , Indian Institute of Science , Bengaluru 560012 , India
| | - Aditi Maulik
- Molecular Biophysics Unit , Indian Institute of Science , Bengaluru 560012 , India
| | - Mahavir Singh
- Molecular Biophysics Unit , Indian Institute of Science , Bengaluru 560012 , India.,NMR Research Centre , Indian Institute of Science , Bengaluru 560012 , India
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15
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Maulik A, Giri M, Singh M. Molecular determinants of complex formation between
DNA
and the
AT
‐rich interaction domain of
BAF
250a. FEBS Lett 2019; 593:2716-2729. [DOI: 10.1002/1873-3468.13540] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 07/08/2019] [Accepted: 07/15/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Aditi Maulik
- Molecular Biophysics Unit Indian Institute of Science Bengaluru India
| | - Malyasree Giri
- Molecular Biophysics Unit Indian Institute of Science Bengaluru India
| | - Mahavir Singh
- Molecular Biophysics Unit Indian Institute of Science Bengaluru India
- NMR Research Centre Indian Institute of Science Bengaluru India
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16
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Gong W, Yao X, Liang Q, Tong Y, Perrett S, Feng Y. Resonance assignments for the tandem PWWP-ARID domains of human RBBP1. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:177-181. [PMID: 30666492 DOI: 10.1007/s12104-019-09873-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 01/16/2019] [Indexed: 06/09/2023]
Abstract
Retinoblastoma-binding protein 1 (RBBP1), also known as AT-rich interaction domain 4A (ARID4A), is a tumour suppressor involved in the regulation of the epigenetic programming in leukemia and Prader-Willi/Angelman syndromes. The ARID domain of RBBP1 binds to DNA non-specifically and has gene suppression activity. However, no structural data has been obtained for the human RBBP1 ARID domain so far. Here we report the near-complete 1H, 13C, 15N backbone and side-chain NMR assignment of a 27 kDa tandem PWWP-ARID domain construct that spans residues 171-414 with the removal of a short disordered region between the two domains. The predicted secondary structure based on the assigned chemical shifts is consistent with the structures of the isolated PWWP domain of human RBBP1 previously solved and the homologous ARID domains of other proteins.
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Affiliation(s)
- Weibin Gong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xingzhe Yao
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of the Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Qihui Liang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of the Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Yufeng Tong
- Department of Chemistry & Biochemistry, University of Windsor, Windsor, ON, N9B 3P4, Canada
| | - Sarah Perrett
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of the Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, China.
| | - Yingang Feng
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
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17
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Singh A, Paul MS, Dutta D, Mutsuddi M, Mukherjee A. Regulation of notch signaling by a chromatin modeling protein Hat-trick. Development 2019; 146:dev.170837. [DOI: 10.1242/dev.170837] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 05/16/2019] [Indexed: 01/08/2023]
Abstract
Notch signaling plays pleiotropic role in astounding variety of cellular processes including cell fate determination, differentiation, proliferation and apoptosis. The increasingly complex regulatory mechanisms of Notch signaling account for the multitude of functions exhibited by Notch during development. We identified Hat-trick (Htk), a DNA binding protein, as an interacting partner of Notch-ICD in a yeast two-hybrid screen and their physical interaction was further validated by co-immunoprecipitation experiments. htk genetically interacts with Notch pathway components in trans-heterozygous combinations. Loss of htk function in htk mutant somatic clones showed down-regulation of Notch targets, whereas over-expression of htk caused ectopic expression of Notch target, without affecting the level of Notch protein. Immunocytochemical analysis has demonstrated that Htk co-localizes with over-expressed Notch-ICD in the same nuclear compartment. We have shown here that Htk cooperates with Notch-ICD and Suppressor of Hairless to form activation complex and binds to the regulatory sequences of Notch downstream targets, Enhancer of Split complex genes to direct their expression. Taken together, our results suggest a novel mode of regulation of Notch signaling by a chromatin modeling protein Htk.
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Affiliation(s)
- Ankita Singh
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi-221005, Uttar Pradesh, India
| | - Maimuna S. Paul
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi-221005, Uttar Pradesh, India
| | - Debdeep Dutta
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi-221005, Uttar Pradesh, India
| | - Mousumi Mutsuddi
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi-221005, Uttar Pradesh, India
| | - Ashim Mukherjee
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi-221005, Uttar Pradesh, India
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18
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Roy A, Dutta A, Roy D, Ganguly P, Ghosh R, Kar RK, Bhunia A, Mukhopadhyay J, Chaudhuri S. Deciphering the role of the AT-rich interaction domain and the HMG-box domain of ARID-HMG proteins of Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2016; 92:371-88. [PMID: 27503561 DOI: 10.1007/s11103-016-0519-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 07/28/2016] [Indexed: 05/22/2023]
Abstract
ARID-HMG DNA-binding proteins represent a novel group of HMG-box containing protein family where the AT-rich interaction domain (ARID) is fused with the HMG-box domain in a single polypeptide chain. ARID-HMG proteins are highly plant specific with homologs found both in flowering plants as well as in moss such as Physcomitrella. The expression of these proteins is ubiquitous in plant tissues and primarily localises in the cell nucleus. HMGB proteins are involved in several nuclear processes, but the role of ARID-HMG proteins in plants remains poorly explored. Here, we performed DNA-protein interaction studies with Arabidopsis ARID-HMG protein HMGB11 (At1g55650) to understand the functionality of this protein and its individual domains. DNA binding assays revealed that AtHMGB11 can bind double-stranded DNA with a weaker affinity (Kd = 475 ± 17.9 nM) compared to Arabidopsis HMGB1 protein (Kd = 39.8 ± 2.68 nM). AtHMGB11 also prefers AT-rich DNA as a substrate and shows structural bias for supercoiled DNA. Molecular docking of the DNA-AtHMGB11 complex indicated that the protein interacts with the DNA major groove, mainly through its ARID domain and the junction region connecting the ARID and the HMG-box domain. Also, predicted by the docking model, mutation of Lys(85) from the ARID domain and Arg(199) & Lys(202) from the junction region affects the DNA binding affinity of AtHMGB11. In addition, AtHMGB11 and its truncated form containing the HMG-box domain can not only promote DNA mini-circle formation but are also capable of inducing negative supercoils into relaxed plasmid DNA suggesting the involvement of this protein in several nuclear events. Overall, the study signifies that both the ARID and the HMG-box domain contribute to the optimal functioning of ARID-HMG protein in vivo.
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Affiliation(s)
- Adrita Roy
- Division of Plant Biology, Bose Institute, Kolkata, 700054, India
| | - Arkajyoti Dutta
- Department of Chemistry, Bose Institute, Kolkata, 700054, India
| | - Dipan Roy
- Division of Plant Biology, Bose Institute, Kolkata, 700054, India
| | - Payel Ganguly
- Division of Plant Biology, Bose Institute, Kolkata, 700054, India
| | - Ritesh Ghosh
- School of Biotechnology, Yeungnam University, Gyeongsan, 712-749, South Korea
| | - Rajiv K Kar
- Department of Biophysics, Bose Institute, Kolkata, 700054, India
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, Kolkata, 700054, India
| | | | - Shubho Chaudhuri
- Division of Plant Biology, Bose Institute, Kolkata, 700054, India.
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19
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An inhibitor of KDM5 demethylases reduces survival of drug-tolerant cancer cells. Nat Chem Biol 2016; 12:531-8. [PMID: 27214401 DOI: 10.1038/nchembio.2085] [Citation(s) in RCA: 232] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 04/06/2016] [Indexed: 01/03/2023]
Abstract
The KDM5 family of histone demethylases catalyzes the demethylation of histone H3 on lysine 4 (H3K4) and is required for the survival of drug-tolerant persister cancer cells (DTPs). Here we report the discovery and characterization of the specific KDM5 inhibitor CPI-455. The crystal structure of KDM5A revealed the mechanism of inhibition of CPI-455 as well as the topological arrangements of protein domains that influence substrate binding. CPI-455 mediated KDM5 inhibition, elevated global levels of H3K4 trimethylation (H3K4me3) and decreased the number of DTPs in multiple cancer cell line models treated with standard chemotherapy or targeted agents. These findings show that pretreatment of cancer cells with a KDM5-specific inhibitor results in the ablation of a subpopulation of cancer cells that can serve as the founders for therapeutic relapse.
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20
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Mutations in the KDM5C ARID Domain and Their Plausible Association with Syndromic Claes-Jensen-Type Disease. Int J Mol Sci 2015; 16:27270-87. [PMID: 26580603 PMCID: PMC4661880 DOI: 10.3390/ijms161126022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/01/2015] [Accepted: 11/04/2015] [Indexed: 11/30/2022] Open
Abstract
Mutations in KDM5C gene are linked to X-linked mental retardation, the syndromic Claes-Jensen-type disease. This study focuses on non-synonymous mutations in the KDM5C ARID domain and evaluates the effects of two disease-associated missense mutations (A77T and D87G) and three not-yet-classified missense mutations (R108W, N142S, and R179H). We predict the ARID domain’s folding and binding free energy changes due to mutations, and also study the effects of mutations on protein dynamics. Our computational results indicate that A77T and D87G mutants have minimal effect on the KDM5C ARID domain stability and DNA binding. In parallel, the change in the free energy unfolding caused by the mutants A77T and D87G were experimentally measured by urea-induced unfolding experiments and were shown to be similar to the in silico predictions. The evolutionary conservation analysis shows that the disease-associated mutations are located in a highly-conserved part of the ARID structure (N-terminal domain), indicating their importance for the KDM5C function. N-terminal residues’ high conservation suggests that either the ARID domain utilizes the N-terminal to interact with other KDM5C domains or the N-terminal is involved in some yet unknown function. The analysis indicates that, among the non-classified mutations, R108W is possibly a disease-associated mutation, while N142S and R179H are probably harmless.
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21
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Sun Q, Zhu T, Wang CY, Ma D. Binding of human SWI1 ARID domain to DNA without sequence specificity: A molecular dynamics study. ACTA ACUST UNITED AC 2015. [PMID: 26223912 DOI: 10.1007/s11596-015-1455-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
SWI1 is a member of a new class of tumor DNA-binding proteins named as the AT-rich interaction domain family (ARID), and considered to bind with AT base pairs specifically. Genomic and functional data support ARID1A as a tumor suppressor because ARID1A/BAF250a (SWI1) subunit of the SWI/SNF chromatin-remodeling complex has emerged as recurrently mutated in a broad array of tumor types. But the crystal structure of SWI1 has not been solved as yet. Using docking and molecular dynamics, we predicted the DNA interaction pattern of human SWI1 ARID and made comparisons with the other two representative ARID family members, human Mrf-2 ARID and Drosophila Dri ARID. Dynamic results revealed that the N-terminal and loop L1 of SWI1 ARID bound with the DNA major groove, while the loop L2 and helix H6 bound with the minor groove. Moreover, it was found that SWI1 ARID bound with DNA apparently in a sequence-nonspecific manner. It was concluded that SWI1 ARID can form stable complex with sequence-nonspecific DNA segment comparing to Mrf-2 ARID/DNA and Dri ARID/DNA sequence-specific complexes.
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Affiliation(s)
- Qian Sun
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Tao Zhu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Chang-Yu Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Ding Ma
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
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22
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Fork C, Gu L, Hitzel J, Josipovic I, Hu J, SzeKa Wong M, Ponomareva Y, Albert M, Schmitz SU, Uchida S, Fleming I, Helin K, Steinhilber D, Leisegang MS, Brandes RP. Epigenetic Regulation of Angiogenesis by JARID1B-Induced Repression of HOXA5. Arterioscler Thromb Vasc Biol 2015; 35:1645-52. [PMID: 26023081 DOI: 10.1161/atvbaha.115.305561] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/17/2015] [Indexed: 12/31/2022]
Abstract
OBJECTIVE Altering endothelial biology through epigenetic modifiers is an attractive novel concept, which is, however, just in its beginnings. We therefore set out to identify chromatin modifiers important for endothelial gene expression and contributing to angiogenesis. APPROACH AND RESULTS To identify chromatin modifying enzymes in endothelial cells, histone demethylases were screened by microarray and polymerase chain reaction. The histone 3 lysine 4 demethylase JARID1B was identified as a highly expressed enzyme at the mRNA and protein levels. Knockdown of JARID1B by shRNA in human umbilical vein endothelial cells attenuated cell migration, angiogenic sprouting, and tube formation. Similarly, pharmacological inhibition and overexpression of a catalytic inactive JARID1B mutant reduced the angiogenic capacity of human umbilical vein endothelial cells. To identify the in vivo relevance of JARID1B in the vascular system, Jarid1b knockout mice were studied. As global knockout results in increased mortality and developmental defects, tamoxifen-inducible and endothelial-specific knockout mice were generated. Acute knockout of Jarid1b attenuated retinal angiogenesis and endothelial sprout outgrowth from aortic segments. To identify the underlying mechanism, a microarray experiment was performed, which led to the identification of the antiangiogenic transcription factor HOXA5 to be suppressed by JARID1B. Importantly, downregulation or inhibition of JARID1B, but not of JARID1A and JARID1C, induced HOXA5 expression in human umbilical vein endothelial cells. Consistently, chromatin immunoprecipitation revealed that JARID1B occupies and reduces the histone 3 lysine 4 methylation levels at the HOXA5 promoter, demonstrating a direct function of JARID1B in endothelial HOXA5 gene regulation. CONCLUSIONS JARID1B, by suppressing HOXA5, maintains the endothelial angiogenic capacity in a demethylase-dependent manner.
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Affiliation(s)
- Christian Fork
- From the Institute for Cardiovascular Physiology, Medical Faculty (C.F., L.G., J.H., I.J., M.S.W., M.S.L., R.P.B.), Institutes of Vascular Signalling (J.H., I.F.) and Cardiovascular Regeneration (Y.P., S.U.), Centre for Molecular Medicine, and Institute of Pharmaceutical Chemistry/ZAFES (D.S.), Goethe-University Frankfurt, Frankfurt am Main, Germany; Biotech Research and Innovation Centre (BRIC) (M.A., S.U.S., K.H.), Centre for Epigenetics (M.A., S.U.S., K.H.), University of Copenhagen, Copenhagen, Denmark; and German Center for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany (C.F., L.G., J.H., I.J., M.S.W., Y.P., S.U., I.F., M.S.L., R.P.B.).
| | - Lunda Gu
- From the Institute for Cardiovascular Physiology, Medical Faculty (C.F., L.G., J.H., I.J., M.S.W., M.S.L., R.P.B.), Institutes of Vascular Signalling (J.H., I.F.) and Cardiovascular Regeneration (Y.P., S.U.), Centre for Molecular Medicine, and Institute of Pharmaceutical Chemistry/ZAFES (D.S.), Goethe-University Frankfurt, Frankfurt am Main, Germany; Biotech Research and Innovation Centre (BRIC) (M.A., S.U.S., K.H.), Centre for Epigenetics (M.A., S.U.S., K.H.), University of Copenhagen, Copenhagen, Denmark; and German Center for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany (C.F., L.G., J.H., I.J., M.S.W., Y.P., S.U., I.F., M.S.L., R.P.B.)
| | - Juliane Hitzel
- From the Institute for Cardiovascular Physiology, Medical Faculty (C.F., L.G., J.H., I.J., M.S.W., M.S.L., R.P.B.), Institutes of Vascular Signalling (J.H., I.F.) and Cardiovascular Regeneration (Y.P., S.U.), Centre for Molecular Medicine, and Institute of Pharmaceutical Chemistry/ZAFES (D.S.), Goethe-University Frankfurt, Frankfurt am Main, Germany; Biotech Research and Innovation Centre (BRIC) (M.A., S.U.S., K.H.), Centre for Epigenetics (M.A., S.U.S., K.H.), University of Copenhagen, Copenhagen, Denmark; and German Center for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany (C.F., L.G., J.H., I.J., M.S.W., Y.P., S.U., I.F., M.S.L., R.P.B.)
| | - Ivana Josipovic
- From the Institute for Cardiovascular Physiology, Medical Faculty (C.F., L.G., J.H., I.J., M.S.W., M.S.L., R.P.B.), Institutes of Vascular Signalling (J.H., I.F.) and Cardiovascular Regeneration (Y.P., S.U.), Centre for Molecular Medicine, and Institute of Pharmaceutical Chemistry/ZAFES (D.S.), Goethe-University Frankfurt, Frankfurt am Main, Germany; Biotech Research and Innovation Centre (BRIC) (M.A., S.U.S., K.H.), Centre for Epigenetics (M.A., S.U.S., K.H.), University of Copenhagen, Copenhagen, Denmark; and German Center for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany (C.F., L.G., J.H., I.J., M.S.W., Y.P., S.U., I.F., M.S.L., R.P.B.)
| | - Jiong Hu
- From the Institute for Cardiovascular Physiology, Medical Faculty (C.F., L.G., J.H., I.J., M.S.W., M.S.L., R.P.B.), Institutes of Vascular Signalling (J.H., I.F.) and Cardiovascular Regeneration (Y.P., S.U.), Centre for Molecular Medicine, and Institute of Pharmaceutical Chemistry/ZAFES (D.S.), Goethe-University Frankfurt, Frankfurt am Main, Germany; Biotech Research and Innovation Centre (BRIC) (M.A., S.U.S., K.H.), Centre for Epigenetics (M.A., S.U.S., K.H.), University of Copenhagen, Copenhagen, Denmark; and German Center for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany (C.F., L.G., J.H., I.J., M.S.W., Y.P., S.U., I.F., M.S.L., R.P.B.)
| | - Michael SzeKa Wong
- From the Institute for Cardiovascular Physiology, Medical Faculty (C.F., L.G., J.H., I.J., M.S.W., M.S.L., R.P.B.), Institutes of Vascular Signalling (J.H., I.F.) and Cardiovascular Regeneration (Y.P., S.U.), Centre for Molecular Medicine, and Institute of Pharmaceutical Chemistry/ZAFES (D.S.), Goethe-University Frankfurt, Frankfurt am Main, Germany; Biotech Research and Innovation Centre (BRIC) (M.A., S.U.S., K.H.), Centre for Epigenetics (M.A., S.U.S., K.H.), University of Copenhagen, Copenhagen, Denmark; and German Center for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany (C.F., L.G., J.H., I.J., M.S.W., Y.P., S.U., I.F., M.S.L., R.P.B.)
| | - Yuliya Ponomareva
- From the Institute for Cardiovascular Physiology, Medical Faculty (C.F., L.G., J.H., I.J., M.S.W., M.S.L., R.P.B.), Institutes of Vascular Signalling (J.H., I.F.) and Cardiovascular Regeneration (Y.P., S.U.), Centre for Molecular Medicine, and Institute of Pharmaceutical Chemistry/ZAFES (D.S.), Goethe-University Frankfurt, Frankfurt am Main, Germany; Biotech Research and Innovation Centre (BRIC) (M.A., S.U.S., K.H.), Centre for Epigenetics (M.A., S.U.S., K.H.), University of Copenhagen, Copenhagen, Denmark; and German Center for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany (C.F., L.G., J.H., I.J., M.S.W., Y.P., S.U., I.F., M.S.L., R.P.B.)
| | - Mareike Albert
- From the Institute for Cardiovascular Physiology, Medical Faculty (C.F., L.G., J.H., I.J., M.S.W., M.S.L., R.P.B.), Institutes of Vascular Signalling (J.H., I.F.) and Cardiovascular Regeneration (Y.P., S.U.), Centre for Molecular Medicine, and Institute of Pharmaceutical Chemistry/ZAFES (D.S.), Goethe-University Frankfurt, Frankfurt am Main, Germany; Biotech Research and Innovation Centre (BRIC) (M.A., S.U.S., K.H.), Centre for Epigenetics (M.A., S.U.S., K.H.), University of Copenhagen, Copenhagen, Denmark; and German Center for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany (C.F., L.G., J.H., I.J., M.S.W., Y.P., S.U., I.F., M.S.L., R.P.B.)
| | - Sandra U Schmitz
- From the Institute for Cardiovascular Physiology, Medical Faculty (C.F., L.G., J.H., I.J., M.S.W., M.S.L., R.P.B.), Institutes of Vascular Signalling (J.H., I.F.) and Cardiovascular Regeneration (Y.P., S.U.), Centre for Molecular Medicine, and Institute of Pharmaceutical Chemistry/ZAFES (D.S.), Goethe-University Frankfurt, Frankfurt am Main, Germany; Biotech Research and Innovation Centre (BRIC) (M.A., S.U.S., K.H.), Centre for Epigenetics (M.A., S.U.S., K.H.), University of Copenhagen, Copenhagen, Denmark; and German Center for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany (C.F., L.G., J.H., I.J., M.S.W., Y.P., S.U., I.F., M.S.L., R.P.B.)
| | - Shizuka Uchida
- From the Institute for Cardiovascular Physiology, Medical Faculty (C.F., L.G., J.H., I.J., M.S.W., M.S.L., R.P.B.), Institutes of Vascular Signalling (J.H., I.F.) and Cardiovascular Regeneration (Y.P., S.U.), Centre for Molecular Medicine, and Institute of Pharmaceutical Chemistry/ZAFES (D.S.), Goethe-University Frankfurt, Frankfurt am Main, Germany; Biotech Research and Innovation Centre (BRIC) (M.A., S.U.S., K.H.), Centre for Epigenetics (M.A., S.U.S., K.H.), University of Copenhagen, Copenhagen, Denmark; and German Center for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany (C.F., L.G., J.H., I.J., M.S.W., Y.P., S.U., I.F., M.S.L., R.P.B.)
| | - Ingrid Fleming
- From the Institute for Cardiovascular Physiology, Medical Faculty (C.F., L.G., J.H., I.J., M.S.W., M.S.L., R.P.B.), Institutes of Vascular Signalling (J.H., I.F.) and Cardiovascular Regeneration (Y.P., S.U.), Centre for Molecular Medicine, and Institute of Pharmaceutical Chemistry/ZAFES (D.S.), Goethe-University Frankfurt, Frankfurt am Main, Germany; Biotech Research and Innovation Centre (BRIC) (M.A., S.U.S., K.H.), Centre for Epigenetics (M.A., S.U.S., K.H.), University of Copenhagen, Copenhagen, Denmark; and German Center for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany (C.F., L.G., J.H., I.J., M.S.W., Y.P., S.U., I.F., M.S.L., R.P.B.)
| | - Kristian Helin
- From the Institute for Cardiovascular Physiology, Medical Faculty (C.F., L.G., J.H., I.J., M.S.W., M.S.L., R.P.B.), Institutes of Vascular Signalling (J.H., I.F.) and Cardiovascular Regeneration (Y.P., S.U.), Centre for Molecular Medicine, and Institute of Pharmaceutical Chemistry/ZAFES (D.S.), Goethe-University Frankfurt, Frankfurt am Main, Germany; Biotech Research and Innovation Centre (BRIC) (M.A., S.U.S., K.H.), Centre for Epigenetics (M.A., S.U.S., K.H.), University of Copenhagen, Copenhagen, Denmark; and German Center for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany (C.F., L.G., J.H., I.J., M.S.W., Y.P., S.U., I.F., M.S.L., R.P.B.)
| | - Dieter Steinhilber
- From the Institute for Cardiovascular Physiology, Medical Faculty (C.F., L.G., J.H., I.J., M.S.W., M.S.L., R.P.B.), Institutes of Vascular Signalling (J.H., I.F.) and Cardiovascular Regeneration (Y.P., S.U.), Centre for Molecular Medicine, and Institute of Pharmaceutical Chemistry/ZAFES (D.S.), Goethe-University Frankfurt, Frankfurt am Main, Germany; Biotech Research and Innovation Centre (BRIC) (M.A., S.U.S., K.H.), Centre for Epigenetics (M.A., S.U.S., K.H.), University of Copenhagen, Copenhagen, Denmark; and German Center for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany (C.F., L.G., J.H., I.J., M.S.W., Y.P., S.U., I.F., M.S.L., R.P.B.)
| | - Matthias S Leisegang
- From the Institute for Cardiovascular Physiology, Medical Faculty (C.F., L.G., J.H., I.J., M.S.W., M.S.L., R.P.B.), Institutes of Vascular Signalling (J.H., I.F.) and Cardiovascular Regeneration (Y.P., S.U.), Centre for Molecular Medicine, and Institute of Pharmaceutical Chemistry/ZAFES (D.S.), Goethe-University Frankfurt, Frankfurt am Main, Germany; Biotech Research and Innovation Centre (BRIC) (M.A., S.U.S., K.H.), Centre for Epigenetics (M.A., S.U.S., K.H.), University of Copenhagen, Copenhagen, Denmark; and German Center for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany (C.F., L.G., J.H., I.J., M.S.W., Y.P., S.U., I.F., M.S.L., R.P.B.)
| | - Ralf P Brandes
- From the Institute for Cardiovascular Physiology, Medical Faculty (C.F., L.G., J.H., I.J., M.S.W., M.S.L., R.P.B.), Institutes of Vascular Signalling (J.H., I.F.) and Cardiovascular Regeneration (Y.P., S.U.), Centre for Molecular Medicine, and Institute of Pharmaceutical Chemistry/ZAFES (D.S.), Goethe-University Frankfurt, Frankfurt am Main, Germany; Biotech Research and Innovation Centre (BRIC) (M.A., S.U.S., K.H.), Centre for Epigenetics (M.A., S.U.S., K.H.), University of Copenhagen, Copenhagen, Denmark; and German Center for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany (C.F., L.G., J.H., I.J., M.S.W., Y.P., S.U., I.F., M.S.L., R.P.B.)
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Communication routes in ARID domains between distal residues in helix 5 and the DNA-binding loops. PLoS Comput Biol 2014; 10:e1003744. [PMID: 25187961 PMCID: PMC4154638 DOI: 10.1371/journal.pcbi.1003744] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Accepted: 06/12/2014] [Indexed: 11/19/2022] Open
Abstract
ARID is a DNA-binding domain involved in several transcriptional regulatory processes, including cell-cycle regulation and embryonic development. ARID domains are also targets of the Human Cancer Protein Interaction Network. Little is known about the molecular mechanisms related to conformational changes in the family of ARID domains. Thus, we have examined their structural dynamics to enrich the knowledge on this important family of regulatory proteins. In particular, we used an approach that integrates atomistic simulations and methods inspired by graph theory. To relate these properties to protein function we studied both the free and DNA-bound forms. The interaction with DNA not only stabilizes the conformations of the DNA-binding loops, but also strengthens pre-existing paths in the native ARID ensemble for long-range communication to those loops. Residues in helix 5 are identified as critical mediators for intramolecular communication to the DNA-binding regions. In particular, we identified a distal tyrosine that plays a key role in long-range communication to the DNA-binding loops and that is experimentally known to impair DNA-binding. Mutations at this tyrosine and in other residues of helix 5 are also demonstrated, by our approach, to affect the paths of communication to the DNA-binding loops and alter their native dynamics. Overall, our results are in agreement with a scenario in which ARID domains exist as an ensemble of substates, which are shifted by external perturbation, such as the interaction with DNA. Conformational changes at the DNA-binding loops are transmitted long-range by intramolecular paths, which have their heart in helix 5.
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Abstract
Every known SWI/SNF chromatin-remodeling complex incorporates an ARID DNA binding domain-containing subunit. Despite being a ubiquitous component of the complex, physiological roles for this domain remain undefined. Here, we show that disruption of ARID1a-DNA binding in mice results in embryonic lethality, with mutant embryos manifesting prominent defects in the heart and extraembryonic vasculature. The DNA binding-defective mutant ARID1a subunit is stably expressed and capable of assembling into a SWI/SNF complex with core catalytic properties, but nucleosome substrate binding and promoter occupancy by ARID1a-containing SWI/SNF complexes (BAF-A) are impaired. Depletion of ARID domain-dependent, BAF-A associations at THROMBOSPONDIN 1 (THBS1) led to the concomitant upregulation of this SWI/SNF target gene. Using a THBS1 promoter-reporter gene, we further show that BAF-A directly regulates THBS1 promoter activity in an ARID domain-dependent manner. Our data not only demonstrate that ARID1a-DNA interactions are physiologically relevant in higher eukaryotes but also indicate that these interactions facilitate SWI/SNF binding to target sites in vivo. These findings support the model wherein cooperative interactions among intrinsic subunit-chromatin interaction domains and sequence-specific transcription factors drive SWI/SNF recruitment.
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25
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Antosch M, Mortensen SA, Grasser KD. Plant proteins containing high mobility group box DNA-binding domains modulate different nuclear processes. PLANT PHYSIOLOGY 2012; 159:875-83. [PMID: 22585776 PMCID: PMC3387713 DOI: 10.1104/pp.112.198283] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
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26
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Wang T, Zhang J, Zhang X, Tu X. Solution structure of SWI1 AT-rich interaction domain from Saccharomyces cerevisiae and its nonspecific binding to DNA. Proteins 2012; 80:1911-7. [PMID: 22488857 DOI: 10.1002/prot.24091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 03/23/2012] [Accepted: 03/30/2012] [Indexed: 11/05/2022]
Abstract
SWI1 is a subunit of the SWI/SNF complex involved in chromatin remodeling. It contains an AT-rich interaction domain (ARID) which has the potential DNA binding activity. In this study, we determined the solution structure of the SWI1 ARID domain from Saccharomyces cerevisiae by nuclear magnetic resonance spectroscopy. Yeast SWI1 ARID domain is composed of seven alpha helices, six of which are conserved among the ARID family. In addition, the DNA-binding activity of the SWI1 ARID domain was confirmed by chemical shift perturbation assay. Similar to its human homolog, the yeast SWI1 ARID domain binds DNA nonspecifically.
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Affiliation(s)
- Tao Wang
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
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27
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Sam MD, Clubb RT. Preparation and optimization of protein-DNA complexes suitable for detailed NMR studies. Methods Mol Biol 2012; 831:219-32. [PMID: 22167677 PMCID: PMC3590071 DOI: 10.1007/978-1-61779-480-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
This chapter describes the methods to form and optimize samples of protein-DNA complexes that are suitable for detailed structure and dynamics studies by NMR spectroscopy.
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Affiliation(s)
- My D Sam
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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28
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Characterization of a new ARID family transcription factor (Brightlike/ARID3C) that co-activates Bright/ARID3A-mediated immunoglobulin gene transcription. Mol Immunol 2011; 49:260-72. [PMID: 21955986 DOI: 10.1016/j.molimm.2011.08.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 08/27/2011] [Indexed: 11/21/2022]
Abstract
Two members, Bright/ARID3A and Bdp/ARID3B, of the ARID (AT-Rich Interaction Domain) transcription family are distinguished by their ability to specifically bind to DNA and to self-associate via a second domain, REKLES. Bright and Bdp positively regulate immunoglobulin heavy chain gene (IgH) transcription by binding to AT-rich motifs within Matrix Associating Regions (MARs) residing within a subset of V(H) promoters and the Eμ intronic enhancer. In addition, REKLES provides Bright nuclear export function, and a small pool of Bright is directed to plasma membrane sub-domains/lipid rafts where it associates with and modulates signaling of the B cell antigen receptor (BCR). Here, we characterize a third, highly conserved, physically condensed ARID3 locus, Brightlike/ARID3C. Brightlike encodes two alternatively spliced, SUMO-I-modified isoforms that include or exclude (Δ6) the REKLES-encoding exon 6. Brightlike transcripts and proteins are expressed preferentially within B lineage lymphocytes and coordinate with highest Bright expression in activated follicular B cells. Brightlike, but not BrightlikeΔ6, undergoes nuclear-cytoplasmic shuttling with a fraction localizing within lipid rafts following BCR stimulation. Brightlike, but not BrightlikeΔ6, associates with Bright in solution, at common DNA binding sites in vitro, and is enriched at Bright binding sites in chromatin. Although possessing little transactivation capacity of its own, Brightlike significantly co-activates Bright-dependent IgH transcription with maximal activity mediated by the unsumoylated form. In sum, this report introduces Brightlike as an additional functional member of the family of ARID proteins, which should be considered in regulatory circuits, previously ascribed to be mediated by Bright.
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29
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Weirauch MT, Hughes TR. A catalogue of eukaryotic transcription factor types, their evolutionary origin, and species distribution. Subcell Biochem 2011; 52:25-73. [PMID: 21557078 DOI: 10.1007/978-90-481-9069-0_3] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Transcription factors (TFs) play key roles in the regulation of gene expression by binding in a sequence-specific manner to genomic DNA. In eukaryotes, DNA binding is achieved by a wide range of structural forms and motifs. TFs are typically classified by their DNA-binding domain (DBD) type. In this chapter, we catalogue and survey 91 different TF DBD types in metazoa, plants, fungi, and protists. We briefly discuss well-characterized TF families representing the major DBD superclasses. We also examine the species distributions and inferred evolutionary histories of the various families, and the potential roles played by TF family expansion and dimerization.
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Affiliation(s)
- Matthew T Weirauch
- Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada,
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30
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Liu G, Huang YJ, Xiao R, Wang D, Acton TB, Montelione GT. Solution NMR structure of the ARID domain of human AT-rich interactive domain-containing protein 3A: a human cancer protein interaction network target. Proteins 2010; 78:2170-5. [PMID: 20455271 DOI: 10.1002/prot.22718] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Gaohua Liu
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA.
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31
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Wang YT, Pan YJ, Cho CC, Lin BC, Su LH, Huang YC, Sun CH. A novel pax-like protein involved in transcriptional activation of cyst wall protein genes in Giardia lamblia. J Biol Chem 2010; 285:32213-26. [PMID: 20699219 DOI: 10.1074/jbc.m110.156620] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Giardia lamblia differentiates into infectious cysts to survive outside of the host. It is of interest to identify factors involved in up-regulation of cyst wall proteins (CWPs) during this differentiation. Pax proteins are important regulators of development and cell differentiation in Drosophila and vertebrates. No member of this gene family has been reported to date in yeast, plants, or protozoan parasites. We have identified a pax-like gene (pax1) encoding a putative paired domain in the G. lamblia genome. Epitope-tagged Pax1 localized to nuclei during both vegetative growth and encystation. Recombinant Pax1 specifically bound to the AT-rich initiator elements of the encystation-induced cwp1 to -3 and myb2 genes. Interestingly, overexpression of Pax1 increased cwp1 to -3 and myb2 gene expression and cyst formation. Deletion of the C-terminal paired domain or mutation of the basic amino acids of the paired domain resulted in a decrease of the transactivation function of Pax1. Our results indicate that the Pax family has been conserved during evolution, and Pax1 could up-regulate the key encystation-induced genes to regulate differentiation of the protozoan eukaryote, G. lamblia.
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Affiliation(s)
- Yi-Ting Wang
- Department of Parasitology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
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32
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Yao W, Peng Y, Lin D. The flexible loop L1 of the H3K4 demethylase JARID1B ARID domain has a crucial role in DNA-binding activity. Biochem Biophys Res Commun 2010; 396:323-8. [PMID: 20403335 DOI: 10.1016/j.bbrc.2010.04.091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Accepted: 04/14/2010] [Indexed: 10/19/2022]
Abstract
JARID1B, a member of the JmjC demethylase family, has a crucial role in H3K4me3 demethylation. The ARID domain is a potential DNA-binding domain of JARID1B. Previous studies indicate that a GC-rich DNA motif is the specific target of the ARID domain. However, the details of the interaction between the ARID domain and duplex DNA require further study. Here, we utilized NMR spectroscopy to assign the backbone amino acids and mapped the DNA-binding sites of the human JARID1B ARID domain. Perturbations to (1)H-(15)N correlation spectra revealed that the flexible loop L1 of ARID was the main DNA-binding interface. EMSA and intrinsic fluorescence experiments demonstrated that mutations on loop L1 strongly reduced the DNA-binding activity of JARID1B ARID. Furthermore, transfection of mutant forms resulted in a distinct loss of intrinsic H3K4 demethylase activity, implying that the flexible loop L1 made a major contribution to sustaining the DNA-binding ability of JARID1B ARID domain.
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Affiliation(s)
- Wenming Yao
- Key Laboratory of Optical and Magnetic Resonance Spectroscopy, East China Normal University, Shanghai 200062, China
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33
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Suree N, Liew CK, Villareal VA, Thieu W, Fadeev EA, Clemens JJ, Jung ME, Clubb RT. The structure of the Staphylococcus aureus sortase-substrate complex reveals how the universally conserved LPXTG sorting signal is recognized. J Biol Chem 2009; 284:24465-77. [PMID: 19592495 PMCID: PMC2782039 DOI: 10.1074/jbc.m109.022624] [Citation(s) in RCA: 148] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Revised: 06/16/2009] [Indexed: 02/01/2023] Open
Abstract
In Gram-positive bacteria, sortase enzymes assemble surface proteins and pili in the cell wall envelope. Sortases catalyze a transpeptidation reaction that joins a highly conserved LPXTG sorting signal within their polypeptide substrate to the cell wall or to other pilin subunits. The molecular basis of transpeptidation and sorting signal recognition are not well understood, because the intermediates of catalysis are short lived. We have overcome this problem by synthesizing an analog of the LPXTG signal whose stable covalent complex with the enzyme mimics a key thioacyl catalytic intermediate. Here we report the solution structure and dynamics of its covalent complex with the Staphylococcus aureus SrtA sortase. In marked contrast to a previously reported crystal structure, we show that SrtA adaptively recognizes the LPXTG sorting signal by closing and immobilizing an active site loop. We have also used chemical shift mapping experiments to localize the binding site for the triglycine portion of lipid II, the second substrate to which surface proteins are attached. We propose a unified model of the transpeptidation reaction that explains the functions of key active site residues. Since the sortase-catalyzed anchoring reaction is required for the virulence of a number of bacterial pathogens, the results presented here may facilitate the development of new anti-infective agents.
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Affiliation(s)
- Nuttee Suree
- From the Department of Chemistry and Biochemistry and
- the UCLA-Department of Energy Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095-1570
| | - Chu Kong Liew
- From the Department of Chemistry and Biochemistry and
| | - Valerie A. Villareal
- From the Department of Chemistry and Biochemistry and
- the UCLA-Department of Energy Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095-1570
| | - William Thieu
- From the Department of Chemistry and Biochemistry and
- the UCLA-Department of Energy Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095-1570
| | - Evgeny A. Fadeev
- From the Department of Chemistry and Biochemistry and
- the UCLA-Department of Energy Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095-1570
| | | | | | - Robert T. Clubb
- From the Department of Chemistry and Biochemistry and
- the UCLA-Department of Energy Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095-1570
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34
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Kusunoki H, Takeuchi T, Kohno T. Solution structure of the AT-rich interaction domain of Jumonji/JARID2. Proteins 2009; 76:1023-8. [DOI: 10.1002/prot.22449] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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35
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Fadeev EA, Sam MD, Clubb RT. NMR structure of the amino-terminal domain of the lambda integrase protein in complex with DNA: immobilization of a flexible tail facilitates beta-sheet recognition of the major groove. J Mol Biol 2009; 388:682-90. [PMID: 19324050 DOI: 10.1016/j.jmb.2009.03.041] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2009] [Revised: 03/12/2009] [Accepted: 03/13/2009] [Indexed: 10/21/2022]
Abstract
The integrase protein (Int) from bacteriophage lambda is the archetypal member of the tyrosine recombinase family, a large group of enzymes that rearrange DNA in all domains of life. Int catalyzes the insertion and excision of the viral genome into and out of the Escherichia coli chromosome. Recombination transpires within higher-order nucleoprotein complexes that form when its amino-terminal domain binds to arm-type DNA sequences that are located distal to the site of strand exchange. Arm-site binding by Int is essential for catalysis, as it promotes Int-mediated bridge structures that stabilize the recombination machinery. We have elucidated how Int is able to sequence specifically recognize the arm-type site sequence by determining the solution structure of its amino-terminal domain (Int(N), residues Met1 to Leu64) in complex with its P'2 DNA binding site. Previous studies have shown that Int(N) adopts a rare monomeric DNA binding fold that consists of a three-stranded antiparallel beta-sheet that is packed against a carboxy-terminal alpha helix. A low-resolution crystal structure of the full-length protein also revealed that the sheet is inserted into the major groove of the arm-type site. The solution structure presented here reveals how Int(N) specifically recognizes the arm-type site sequence. A novel feature of the new solution structure is the use of an 11-residue tail that is located at the amino terminus. DNA binding induces the folding of a 3(10) helix in the tail that projects the amino terminus of the protein deep into the minor groove for stabilizing DNA contacts. This finding reveals the structural basis for the observation that the "unstructured" amino terminus is required for recombination.
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Affiliation(s)
- Evgeny A Fadeev
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1570, USA
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36
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Hansen FT, Madsen CK, Nordland AM, Grasser M, Merkle T, Grasser KD. A Novel Family of Plant DNA-Binding Proteins Containing both HMG-Box and AT-Rich Interaction Domains. Biochemistry 2008; 47:13207-14. [DOI: 10.1021/bi801772k] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Frederik T. Hansen
- Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark, and Genome Research, Faculty of Biology, University of Bielefeld, Universitätsstrasse 25, D-33594 Bielefeld, Germany
| | - Claus K. Madsen
- Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark, and Genome Research, Faculty of Biology, University of Bielefeld, Universitätsstrasse 25, D-33594 Bielefeld, Germany
| | - Anne Mette Nordland
- Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark, and Genome Research, Faculty of Biology, University of Bielefeld, Universitätsstrasse 25, D-33594 Bielefeld, Germany
| | - Marion Grasser
- Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark, and Genome Research, Faculty of Biology, University of Bielefeld, Universitätsstrasse 25, D-33594 Bielefeld, Germany
| | - Thomas Merkle
- Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark, and Genome Research, Faculty of Biology, University of Bielefeld, Universitätsstrasse 25, D-33594 Bielefeld, Germany
| | - Klaus D. Grasser
- Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark, and Genome Research, Faculty of Biology, University of Bielefeld, Universitätsstrasse 25, D-33594 Bielefeld, Germany
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Zhu H, Chen T, Zhu M, Fang Q, Kang H, Hong Z, Zhang Z. A novel ARID DNA-binding protein interacts with SymRK and is expressed during early nodule development in Lotus japonicus. PLANT PHYSIOLOGY 2008; 148:337-47. [PMID: 18633121 PMCID: PMC2528112 DOI: 10.1104/pp.108.119164] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2008] [Accepted: 06/13/2008] [Indexed: 05/18/2023]
Abstract
During the establishment of symbiosis in legume roots, the rhizobial Nod factor signal is perceived by the host cells via receptor-like kinases, including SymRK. The NODULE INCEPTION (NIN) gene in Lotus japonicus is required for rhizobial entry into root cells and for nodule organogenesis. We describe here a novel DNA-binding protein from L. japonicus, referred to as SIP1, because it was identified as a SymRK-interacting protein. SIP1 contains a conserved AT-rich interaction domain (ARID) and represents a unique member of the ARID-containing proteins in plants. The C terminus of SIP1 was found to be responsible for its interaction with the kinase domain of SymRK and for homodimerization in the absence of DNA. SIP1 specifically binds to the promoter of LjNIN but not to that of LjCBP1 (a calcium-binding protein gene), both of which are known to be inducible by Nod factors. SIP1 recognizes two of the three AT-rich domains present in the NIN gene promoter. Deletion of one of the AT-rich domains at the NIN promoter diminishes the binding of SIP1 to the NIN promoter. The protein is localized to the nuclei when expressed as a red fluorescence fusion protein in the onion (Allium cepa) epidermal cells. The SIP1 gene is expressed constitutively in the uninfected roots, and its expression levels are elevated after infection by Mesorhizobium loti. It is proposed that SIP1 may be required for the expression of NIN and involved in the initial communications between the rhizobia and the host root cells.
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Affiliation(s)
- Hui Zhu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
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38
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Koehler C, Bishop S, Dowler EF, Schmieder P, Diehl A, Oschkinat H, Ball LJ. Backbone and sidechain 1H, 13C and 15N resonance assignments of the Bright/ARID domain from the human JARID1C (SMCX) protein. BIOMOLECULAR NMR ASSIGNMENTS 2008; 2:9-11. [PMID: 19636912 DOI: 10.1007/s12104-007-9071-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Accepted: 11/24/2007] [Indexed: 05/28/2023]
Abstract
We have assigned 1H, 13C and 15N resonances of the Bright/ARID DNA-binding domain from the human JARID1C protein, a newly discovered histone demethylase belonging to the JmjC domain-containing protein family.
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Affiliation(s)
- Christian Koehler
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
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39
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The ARID domain of the H3K4 demethylase RBP2 binds to a DNA CCGCCC motif. Nat Struct Mol Biol 2008; 15:419-21. [PMID: 18270511 DOI: 10.1038/nsmb.1400] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2007] [Accepted: 02/06/2008] [Indexed: 11/08/2022]
Abstract
The histone H3 lysine 4 demethylase RBP2 contains a DNA binding domain, the AT-rich interaction domain (ARID). We solved the structure of ARID by NMR, identified its DNA binding motif (CCGCCC) and characterized the binding contacts. Immunofluorescence and luciferase assays indicated that ARID is required for RBP2 demethylase activity in cells and that DNA recognition is essential to regulate transcription.
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40
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Doucleff M, Pelton JG, Lee PS, Nixon BT, Wemmer DE. Structural basis of DNA recognition by the alternative sigma-factor, sigma54. J Mol Biol 2007; 369:1070-8. [PMID: 17481658 PMCID: PMC2680387 DOI: 10.1016/j.jmb.2007.04.019] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2007] [Revised: 03/31/2007] [Accepted: 04/03/2007] [Indexed: 11/15/2022]
Abstract
The sigma subunit of bacterial RNA polymerase (RNAP) regulates gene expression by directing RNAP to specific promoters. Unlike sigma(70)-type proteins, the alternative sigma factor, sigma(54), requires interaction with an ATPase to open DNA. We present the solution structure of the C-terminal domain of sigma(54) bound to the -24 promoter element, in which the conserved RpoN box motif inserts into the major groove of the DNA. This structure elucidates the basis for sequence specific recognition of the -24 element, orients sigma(54) on the promoter, and suggests how the C-terminal domain of sigma(54) interacts with RNAP.
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Affiliation(s)
- Michaeleen Doucleff
- Physical Biosciences Division, Lawrence Berkeley National Laboratory and the Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Jeffrey G. Pelton
- Physical Biosciences Division, Lawrence Berkeley National Laboratory and the Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Peter S. Lee
- Physical Biosciences Division, Lawrence Berkeley National Laboratory and the Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - B. Tracy Nixon
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - David E. Wemmer
- Physical Biosciences Division, Lawrence Berkeley National Laboratory and the Department of Chemistry, University of California, Berkeley, California 94720, USA
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41
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Cai S, Zhu L, Zhang Z, Chen Y. Determination of the three-dimensional structure of the Mrf2-DNA complex using paramagnetic spin labeling. Biochemistry 2007; 46:4943-50. [PMID: 17407261 PMCID: PMC2527749 DOI: 10.1021/bi061738h] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding the mechanism of protein-DNA interactions at the molecular level is one of the main focuses in structural and molecular biological investigations. At present, NMR spectroscopy is the only approach that can provide atomic details of protein-DNA recognition in solution. However, determining the structures of protein-DNA complexes using NMR spectroscopy has been dependent on the observation of intermolecular nuclear Overhauser effects (NOE) and their assignments, which are difficult to obtain in many cases. In this study, we have shown that intermolecular distance constraints derived from a single spin-label in combination with docking calculations have defined many specific contacts of the complex between the AT-rich interaction domain (ARID) of Mrf2 and its target DNA. Mrf2 contacts DNA mainly using the two flexible loops, L1 and L2. While the L1 loop contacts the phosphate backbone, L2 and several residues in the adjacent helices interact with AT base pairs in the major groove of DNA. Despite the structural diversity in the ARID family of DNA-binding proteins, Mrf2 maintains contacts with DNA similar to those observed in the homologous Dri-DNA complex.
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Affiliation(s)
- Sheng Cai
- Division of Immunology, Beckman Research Institute of City of Hope, 1500 Duarte Road, Duarte, CA
| | - Lingyang Zhu
- Division of Immunology, Beckman Research Institute of City of Hope, 1500 Duarte Road, Duarte, CA
| | - Ziming Zhang
- Division of Immunology, Beckman Research Institute of City of Hope, 1500 Duarte Road, Duarte, CA
| | - Yuan Chen
- Division of Immunology, Beckman Research Institute of City of Hope, 1500 Duarte Road, Duarte, CA
- *To whom correspondence should be addressed. E-mail: . Fax: 626-301-8186. Phone: 626-930-5408
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42
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Kim D, Probst L, Das C, Tucker PW. REKLES is an ARID3-restricted multifunctional domain. J Biol Chem 2007; 282:15768-77. [PMID: 17400556 DOI: 10.1074/jbc.m700397200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Bright/Dril1/ARID3a is a B cell-specific, matrix association (or attachment) region-binding transcriptional regulator of immunoglobulin heavy chain genes and of E2F1-dependent cell cycle progression. Bright contains a central DNA binding domain termed ARID (AT-rich interacting domain) and a C-terminal region termed REKLES (for a conserved amino acid motif). The ARID domain has been identified in seven highly conserved families of metazoan proteins (ARID1-5 and JARID1-2), whereas REKLES is found only in the ARID3 subfamily (composed of Bright/ARID3a, Bdp/ARID3b, and Bright-like/ARID3c). REKLES consists of two subdomains: a modestly conserved N-terminal REKLESalpha and a highly conserved (among ARID3 orthologous proteins) C-terminal REKLESbeta. Previously we showed that Bright undergoes nucleocytoplasmic shuttling and that REKLESalpha and -beta were required, respectively, for nuclear import and Crm1-dependent nuclear export. Here we show that Bright further requires REKLESbeta for self-association or paralogue association and for nuclear matrix targeting. REK-LES promotes and regulates the extent of Bright multimerization, which occurs in the absence or presence of target DNA and is necessary for specific DNA binding. REKLESbeta-mediated interaction of Bright with Bdp, which localizes strictly to the nucleus, traps Bright within the nucleus via neutralization of its nuclear export activity. These results identify REKLES as a multifunctional domain that has co-evolved with and regulates functional properties of the ARID3 DNA binding domain.
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Affiliation(s)
- Dongkyoon Kim
- Section of Molecular Genetics and Microbiology and Institute of Cell and Molecular Biology, University of Texas, Austin, Texas 78712-0162, USA
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43
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Wang CH, Su LH, Sun CH. A novel ARID/Bright-like protein involved in transcriptional activation of cyst wall protein 1 gene in Giardia lamblia. J Biol Chem 2007; 282:8905-14. [PMID: 17244608 DOI: 10.1074/jbc.m611170200] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The capability of protozoan parasite Giardia lamblia to encyst is critical for survival outside the host and its transmission. AT-rich interaction domain (ARID) or Bright homologs constitute a large family of transcription factors in higher eukaryotes that regulate cell proliferation, development, and differentiation. We asked whether Giardia has ARID-like genes and whether they influence gene expression during Giardia encystation. Blast searches of the Giardia genome data base identified two genes with putative ARID/Bright domains (gARID1 and 2). Epitope-tagged gARID1 was found to localize to nuclei. Recombinant gARID1 specifically bound to the encystation-induced cyst wall protein (cwp) gene promoters. Mutation analysis revealed that AT-rich initiators were required for binding of gARID1 to the cwp promoters. gARID1 contains several key residues for DNA binding, and its binding sequences are similar to those of the known ARID family proteins. The gARID1 binding sequences were positive cis-acting elements of the cwp1 promoter during both vegetative growth and encystation. We also found that gARID1 transactivated the cwp1 promoter through its binding sequences in vivo. Our results suggest that the ARID family has been conserved during evolution and that gARID1 is an important transactivator in regulation of the Giardia cwp1 gene, which is key to Giardia differentiation into cysts.
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Affiliation(s)
- Chih-Hung Wang
- Department of Parasitology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
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44
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Amore G, Davidson EH. cis-Regulatory control of cyclophilin, a member of the ETS-DRI skeletogenic gene battery in the sea urchin embryo. Dev Biol 2006; 293:555-64. [PMID: 16574094 DOI: 10.1016/j.ydbio.2006.02.024] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2005] [Revised: 02/03/2006] [Accepted: 02/16/2006] [Indexed: 11/30/2022]
Abstract
The Strongylocentrotus purpuratus cyclophilin1 gene (Sp-cyp1) is expressed exclusively in skeletogenic mesenchyme cells of the embryo, beginning in the micromere lineage of the early blastula stage and continuing after gastrulation during the syncytial deposition of the skeleton. This gene encodes a protein which is a member of the peptidyl-prolyl cis-trans isomerase (PPIase) family. Sp-cyp1 is among the differentiation genes activated in the skeletogenic territory as a terminal function of the endomesodermal gene regulatory network. Network perturbation analysis had predicted the skeletogenic regulators Ets1 and Deadringer (Dri) to be its driver inputs. Here, we show that a 218-bp cis-regulatory DNA fragment recapitulates skeletogenic Sp-cyp1 expression; that elimination of either Ets1 or Dri inputs severely depresses the activity of expression constructs containing this DNA fragment; and that Ets1 and Dri target sites within the 218 bp fragment are required for normal expression. This indicates that the predicted inputs are direct. Other studies indicate that the same inputs are evidently necessary for expression of several other skeletogenic differentiation genes, and these genes probably constitute a skeletogenic gene battery, defined by its Ets plus Dri regulatory inputs.
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Affiliation(s)
- Gabriele Amore
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
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45
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Takebe A, Era T, Okada M, Martin Jakt L, Kuroda Y, Nishikawa SI. Microarray analysis of PDGFR alpha+ populations in ES cell differentiation culture identifies genes involved in differentiation of mesoderm and mesenchyme including ARID3b that is essential for development of embryonic mesenchymal cells. Dev Biol 2006; 293:25-37. [PMID: 16530748 DOI: 10.1016/j.ydbio.2005.12.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2005] [Revised: 11/18/2005] [Accepted: 12/06/2005] [Indexed: 12/24/2022]
Abstract
An inherent difficulty in using DNA microarray technology on the early mouse embryo is its relatively small size. In this study, we investigated whether use of ES cell differentiation culture, which has no theoretical limit in the number of cells that can be generated, can improve this situation. Seven distinct ES-cell-derived populations were analyzed by DNA microarray and examined for genes whose distribution patterns are similar to those of PDGFRalpha, a gene implicated in differentiation of mesoderm/mesenchymal lineages. Using software developed in our laboratory, we formed a group of 30 genes which showed the highest similarity to PDGFRalpha, 18 of these genes were shown to be involved in development of either mesodermal, mesenchymal or neural crest cells. This list also contains several genes whose role in embryogenesis has not yet been fully identified. One such molecule is mARID3b. The mARID3b expression is found in the paraxial mesoderm and cranial mesenchyme. mARID3b-null mouse showed early embryonic lethality, and most phenotypes of this mutant appear to develop from a failure to generate a sufficient number of cranial mesenchymal cells. These results demonstrate the potential use of ES cell differentiation culture in identifying novel genes playing an indispensable role in embryogenesis.
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Affiliation(s)
- Atsushi Takebe
- Laboratory for Stem Cell Biology, RIKEN Center for Development Biology, 2-2-3 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
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46
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McLaughlin WA, Kulp DW, de la Cruz J, Lu XJ, Lawson CL, Berman HM. A structure-based method for identifying DNA-binding proteins and their sites of DNA-interaction. ACTA ACUST UNITED AC 2005; 5:255-65. [PMID: 15704013 DOI: 10.1007/s10969-005-4902-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2004] [Accepted: 11/17/2004] [Indexed: 01/11/2023]
Abstract
A classification model of a DNA-binding protein chain was created based on identification of alpha helices within the chain likely to bind to DNA. Using the model, all chains in the Protein Data Bank were classified. For many of the chains classified with high confidence, previous documentation for DNA-binding was found, yet no sequence homology to the structures used to train the model was detected. The result indicates that the chain model can be used to supplement sequence based methods for annotating the function of DNA-binding. Four new candidates for DNA-binding were found, including two structures solved through structural genomics efforts. For each of the candidate structures, possible sites of DNA-binding are indicated by listing the residue ranges of alpha helices likely to interact with DNA.
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Affiliation(s)
- William A McLaughlin
- Department of Chemistry and Chemical Biology, Rutgers-The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA
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47
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Iwahara J, Peterson RD, Clubb RT. Compensating increases in protein backbone flexibility occur when the Dead ringer AT-rich interaction domain (ARID) binds DNA: a nitrogen-15 relaxation study. Protein Sci 2005; 14:1140-50. [PMID: 15802641 PMCID: PMC2253272 DOI: 10.1110/ps.041154405] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
AT-rich interaction domains (ARIDs) are found in a large number of eukaryotic transcription factors that regulate cell proliferation, differentiation, and development. Previously we elucidated how ARIDs recognize DNA by determining the solution structure of the Drosophila melanogaster Dead ringer protein in both its DNA-free and -bound states. In order to quantitatively determine how ARIDs alter their mobility to recognize DNA, we have measured the relaxation parameters of the backbone nitrogen-15 nuclei of Dead ringer in its free and bound forms, and interpreted these data using the model-free approach. We show that Dead ringer undergoes significant changes in its mobility upon binding, with residues in the loop connecting helices H5 and H6 becoming immobilized in the major groove and contacts to the minor groove slowing down the motion of residues at the C terminus. A DNA-induced rotation and displacement of the N-terminal subdomain of the protein increases the mobility of helix H1 located distal to the DNA interface and may partially negate the entropic cost of immobilizing interfacial residues. Elevated motions on the micro- to millisecond timescale in the N-terminal domain prior to DNA binding appear to foreshadow the DNA-induced conformation change.
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Affiliation(s)
- Junji Iwahara
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 405 Hilgard Avenue, Los Angeles, CA 90095-1570, USA
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48
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Abstract
The ARID (A–T Rich Interaction Domain) is a helix–turn–helix motif-based DNA-binding domain, conserved in all eukaryotes and diagnostic of a family that includes 15 distinct human proteins with important roles in development, tissue-specific gene expression and proliferation control. The 15 human ARID family proteins can be divided into seven subfamilies based on the degree of sequence identity between individual members. Most ARID family members have not been characterized with respect to their DNA-binding behavior, but it is already apparent that not all ARIDs conform to the pattern of binding AT-rich sequences. To understand better the divergent characteristics of the ARID proteins, we undertook a survey of DNA-binding properties across the entire ARID family. The results indicate that the majority of ARID subfamilies (i.e. five out of seven) bind DNA without obvious sequence preference. DNA-binding affinity also varies somewhat between subfamilies. Site-specific mutagenesis does not support suggestions made from structure analysis that specific amino acids in Loop 2 or Helix 5 are the main determinants of sequence specificity. Most probably, this is determined by multiple interacting differences across the entire ARID structure.
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Affiliation(s)
| | | | - Elizabeth Moran
- To whom correspondence should be addressed. Tel: +215 707 7313; Fax: +215 707 6989;
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49
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Abstract
Structure determination of protein?RNA complexes in solution provides unique insights into factors that are involved in protein/RNA recognition. Here, we review the methodology used in our laboratory to overcome the challenges of protein?RNA structure determination by nuclear magnetic resonance (NMR). We use as two examples complexes recently solved in our laboratory, the nucleolin RBD12/b2NRE and Rnt1p dsRBD/snR47h complexes. Topics covered are protein and RNA preparation, complex formation, identification of the protein/RNA interface, protein and RNA resonance assignment, intermolecular NOE assignment, and structure calculation and analysis.
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Affiliation(s)
- Haihong Wu
- Department of Chemistry and Biochemistry, University of California, Los Angeles 90095, USA
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50
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Ditch LM, Shirangi T, Pitman JL, Latham KL, Finley KD, Edeen PT, Taylor BJ, McKeown M. Drosophila retained/dead ringer is necessary for neuronal pathfinding, female receptivity and repression of fruitless independent male courtship behaviors. Development 2004; 132:155-64. [PMID: 15576402 PMCID: PMC1950442 DOI: 10.1242/dev.01568] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Mutations in the Drosophila retained/dead ringer (retn) gene lead to female behavioral defects and alter a limited set of neurons in the CNS. retn is implicated as a major repressor of male courtship behavior in the absence of the fruitless (fru) male protein. retn females show fru-independent male-like courtship of males and females, and are highly resistant to courtship by males. Males mutant for retn court with normal parameters, although feminization of retn cells in males induces bisexuality. Alternatively spliced RNAs appear in the larval and pupal CNS, but none shows sex specificity. Post-embryonically, retn RNAs are expressed in a limited set of neurons in the CNS and eyes. Neural defects of retn mutant cells include mushroom body beta-lobe fusion and pathfinding errors by photoreceptor and subesophageal neurons. We posit that some of these retn-expressing cells function to repress a male behavioral pathway activated by fruM.
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Affiliation(s)
- Lynn M. Ditch
- Molecular Biology, Cell Biology, and Biochemistry Department, Brown University, Providence, RI 02912, USA
- Molecular Biology and Virology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Troy Shirangi
- Molecular Biology, Cell Biology, and Biochemistry Department, Brown University, Providence, RI 02912, USA
| | - Jeffrey L. Pitman
- Molecular Biology, Cell Biology, and Biochemistry Department, Brown University, Providence, RI 02912, USA
- Molecular Biology and Virology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Kristin L. Latham
- Department of Zoology, Oregon State University, Corvallis, OR 97331, USA
| | - Kim D. Finley
- Molecular Biology and Virology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Philip T. Edeen
- Molecular Biology and Virology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Barbara J. Taylor
- Department of Zoology, Oregon State University, Corvallis, OR 97331, USA
| | - Michael McKeown
- Molecular Biology, Cell Biology, and Biochemistry Department, Brown University, Providence, RI 02912, USA
- Molecular Biology and Virology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Author for correspondence (e-mail: )
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