1
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Kohl B, Zhong X, Herrmann C, Stoll R. Phosphorylation orchestrates the structural ensemble of the intrinsically disordered protein HMGA1a and modulates its DNA binding to the NFκB promoter. Nucleic Acids Res 2020; 47:11906-11920. [PMID: 31340016 PMCID: PMC7145567 DOI: 10.1093/nar/gkz614] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/14/2019] [Accepted: 07/05/2019] [Indexed: 12/27/2022] Open
Abstract
High Mobility Group Protein A1a (HMGA1a) is a highly abundant nuclear protein, which plays a crucial role during embryogenesis, cell differentiation, and neoplasia. Here, we present the first ever NMR-based structural ensemble of full length HMGA1a. Our results show that the protein is not completely random coil but adopts a compact structure consisting of transient long-range contacts, which is regulated by post-translational phosphorylation. The CK2-, cdc2- and cdc2/CK2-phosphorylated forms of HMGA1a each exhibit a different binding affinity towards the PRD2 element of the NFκB promoter. Our study identifies connected regions between phosphorylation sites in the wildtype ensemble that change considerably upon phosphorylation, indicating that these posttranslational modifications sites are part of an electrostatic contact network that alters the structural ensemble by shifting the conformational equilibrium. Moreover, ITC data reveal that the CK2-phosphorylated HMGA1a exhibits a different DNA promoter binding affinity for the PRD2 element. Furthermore, we present the first structural model for AT-hook 1 of HMGA1a that can adopt a transient α-helical structure, which might serve as an additional regulatory mechanism in HMAG1a. Our findings will help to develop new therapeutic strategies against HMGA1a-associated cancers by taking posttranslational modifications into consideration.
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Affiliation(s)
- Bastian Kohl
- Faculty of Chemistry and Biochemistry, Biomolecular NMR Spectroscopy, Ruhr University of Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Xueyin Zhong
- Faculty of Chemistry and Biochemistry, Biomolecular NMR Spectroscopy, Ruhr University of Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Christian Herrmann
- Faculty of Chemistry and Biochemistry, Protein Interactions, Ruhr University of Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Raphael Stoll
- Faculty of Chemistry and Biochemistry, Biomolecular NMR Spectroscopy, Ruhr University of Bochum, Universitätsstraße 150, 44780 Bochum, Germany
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2
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Privalov PL, Crane-Robinson C. Forces maintaining the DNA double helix and its complexes with transcription factors. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 135:30-48. [DOI: 10.1016/j.pbiomolbio.2018.01.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/22/2018] [Indexed: 10/18/2022]
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3
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Dragan AI, Read CM, Crane-Robinson C. Enthalpy-entropy compensation: the role of solvation. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 46:301-308. [PMID: 27796417 PMCID: PMC5384952 DOI: 10.1007/s00249-016-1182-6] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 10/06/2016] [Accepted: 10/17/2016] [Indexed: 11/24/2022]
Abstract
Structural modifications to interacting systems frequently lead to changes in both the enthalpy (heat) and entropy of the process that compensate each other, so that the Gibbs free energy is little changed: a major barrier to the development of lead compounds in drug discovery. The conventional explanation for such enthalpy–entropy compensation (EEC) is that tighter contacts lead to a more negative enthalpy but increased molecular constraints, i.e., a compensating conformational entropy reduction. Changes in solvation can also contribute to EEC but this contribution is infrequently discussed. We review long-established and recent cases of EEC and conclude that the large fluctuations in enthalpy and entropy observed are too great to be a result of only conformational changes and must result, to a considerable degree, from variations in the amounts of water immobilized or released on forming complexes. Two systems exhibiting EEC show a correlation between calorimetric entropies and local mobilities, interpreted to mean conformational control of the binding entropy/free energy. However, a substantial contribution from solvation gives the same effect, as a consequence of a structural link between the amount of bound water and the protein flexibility. Only by assuming substantial changes in solvation—an intrinsically compensatory process—can a more complete understanding of EEC be obtained. Faced with such large, and compensating, changes in the enthalpies and entropies of binding, the best approach to engineering elevated affinities must be through the addition of ionic links, as they generate increased entropy without affecting the enthalpy.
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Affiliation(s)
- Anatoliy I Dragan
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, 64, Volodymyrs'ka St., Kiev, 01601, Ukraine.,Institute of Molecular Biology and Genetics, NASU, 150, Zabolotnogo St., Kiev, 03680, Ukraine
| | - Christopher M Read
- Biophysics Laboratories, School of Biology, University of Portsmouth, Portsmouth, PO1 2DT, UK
| | - Colyn Crane-Robinson
- Biophysics Laboratories, School of Biology, University of Portsmouth, Portsmouth, PO1 2DT, UK.
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4
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Silva APG, Ryan DP, Galanty Y, Low JKK, Vandevenne M, Jackson SP, Mackay JP. The N-terminal Region of Chromodomain Helicase DNA-binding Protein 4 (CHD4) Is Essential for Activity and Contains a High Mobility Group (HMG) Box-like-domain That Can Bind Poly(ADP-ribose). J Biol Chem 2016; 291:924-38. [PMID: 26565020 PMCID: PMC4705410 DOI: 10.1074/jbc.m115.683227] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/09/2015] [Indexed: 01/11/2023] Open
Abstract
Chromodomain Helicase DNA-binding protein 4 (CHD4) is a chromatin-remodeling enzyme that has been reported to regulate DNA-damage responses through its N-terminal region in a poly(ADP-ribose) polymerase-dependent manner. We have identified and determined the structure of a stable domain (CHD4-N) in this N-terminal region. The-fold consists of a four-α-helix bundle with structural similarity to the high mobility group box, a domain that is well known as a DNA binding module. We show that the CHD4-N domain binds with higher affinity to poly(ADP-ribose) than to DNA. We also show that the N-terminal region of CHD4, although not CHD4-N alone, is essential for full nucleosome remodeling activity and is important for localizing CHD4 to sites of DNA damage. Overall, these data build on our understanding of how CHD4-NuRD acts to regulate gene expression and participates in the DNA-damage response.
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Affiliation(s)
- Ana P G Silva
- From the School of Molecular Bioscience, The University of Sydney, New South Wales 2006, Australia,
| | - Daniel P Ryan
- Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, and
| | - Yaron Galanty
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Jason K K Low
- From the School of Molecular Bioscience, The University of Sydney, New South Wales 2006, Australia
| | - Marylene Vandevenne
- From the School of Molecular Bioscience, The University of Sydney, New South Wales 2006, Australia
| | - Stephen P Jackson
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Joel P Mackay
- From the School of Molecular Bioscience, The University of Sydney, New South Wales 2006, Australia,
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5
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Kost N, Kaiser S, Ostwal Y, Riedel D, Stützer A, Nikolov M, Rathke C, Renkawitz-Pohl R, Fischle W. Multimerization of Drosophila sperm protein Mst77F causes a unique condensed chromatin structure. Nucleic Acids Res 2015; 43:3033-45. [PMID: 25735749 PMCID: PMC4381051 DOI: 10.1093/nar/gkv015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/08/2015] [Indexed: 01/09/2023] Open
Abstract
Despite insights on the cellular level, the molecular details of chromatin reorganization in sperm development, which involves replacement of histone proteins by specialized factors to allow ultra most condensation of the genome, are not well understood. Protamines are dispensable for DNA condensation during Drosophila post-meiotic spermatogenesis. Therefore, we analyzed the interaction of Mst77F, another very basic testis-specific protein with chromatin and DNA as well as studied the molecular consequences of such binding. We show that Mst77F on its own causes severe chromatin and DNA aggregation. An intrinsically unstructured domain in the C-terminus of Mst77F binds DNA via electrostatic interaction. This binding results in structural reorganization of the domain, which induces interaction with an N-terminal region of the protein. Via putative cooperative effects Mst77F is induced to multimerize in this state causing DNA aggregation. In agreement, overexpression of Mst77F results in chromatin aggregation in fly sperm. Based on these findings we postulate that Mst77F is crucial for sperm development by giving rise to a unique condensed chromatin structure.
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Affiliation(s)
- Nils Kost
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Sophie Kaiser
- Developmental Biology, FB17, Philipps University, 35037 Marburg, Germany
| | - Yogesh Ostwal
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Dietmar Riedel
- Electron Microscopy Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Alexandra Stützer
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Miroslav Nikolov
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Christina Rathke
- Developmental Biology, FB17, Philipps University, 35037 Marburg, Germany
| | | | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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6
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Stott K, Watson M, Bostock MJ, Mortensen SA, Travers A, Grasser KD, Thomas JO. Structural insights into the mechanism of negative regulation of single-box high mobility group proteins by the acidic tail domain. J Biol Chem 2014; 289:29817-26. [PMID: 25190813 PMCID: PMC4207994 DOI: 10.1074/jbc.m114.591115] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The Drosophila and plant (maize) functional counterparts of the abundant vertebrate chromosomal protein HMGB1 (HMG-D and ZmHMGB1, respectively) differ from HMGB1 in having a single HMG box, as well as basic and acidic flanking regions that vary greatly in length and charge. We show that despite these variations, HMG-D and ZmHMGB1 exist in dynamic assemblies in which the basic HMG boxes and linkers associate with their intrinsically disordered, predominantly acidic, tails in a manner analogous to that observed previously for HMGB1. The DNA-binding surfaces of the boxes and linkers are occluded in “auto-inhibited” forms of the protein, which are in equilibrium with transient, more open structures that are “binding-competent.” This strongly suggests that the mechanism of auto-inhibition may be a general one. HMG-D and ZmHMGB1 differ from HMGB1 in having phosphorylation sites in their tail and linker regions. In both cases, in vitro phosphorylation of serine residues within the acidic tail stabilizes the assembled form, suggesting another level of regulation for interaction with DNA, chromatin, and other proteins that is not possible for the uniformly acidic (hence unphosphorylatable) tail of HMGB1.
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Affiliation(s)
- Katherine Stott
- From the Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom and
| | - Matthew Watson
- From the Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom and
| | - Mark J Bostock
- From the Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom and
| | - Simon A Mortensen
- the Department of Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Andrew Travers
- From the Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom and
| | - Klaus D Grasser
- the Department of Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Jean O Thomas
- From the Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom and
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7
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Hod R, Kohen R, Mandel-Gutfreund Y. Searching for protein signatures using a multilevel alphabet. Proteins 2013; 81:1058-68. [PMID: 23386227 DOI: 10.1002/prot.24261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 01/09/2013] [Accepted: 01/11/2013] [Indexed: 11/07/2022]
Abstract
Short motifs are known to play diverse roles in proteins, such as in mediating the interactions with other molecules, binding to membranes, or conducting a specific biological function. Standard approaches currently employed to detect short motifs in proteins search for enrichment of amino acid motifs considering mostly the sequence information. Here, we presented a new approach to search for common motifs (protein signatures) which share both physicochemical and structural properties, looking simultaneously at different features. Our method takes as an input an amino acid sequence and translates it to a new alphabet that reflects its intrinsic structural and chemical properties. Using the MEME search algorithm, we identified the proteins signatures within subsets of protein which encompass common sequence and structural information. We demonstrated that we can detect enriched structural motifs, such as the amphipathic helix, from large datasets of linear sequences, as well as predicting common structural properties (such as disorder, surface accessibility, or secondary structures) of known functional-motifs. Finally, we applied the method to the yeast protein interactome and identified novel putative interacting motifs. We propose that our approach can be applied for de novo protein function prediction given either sequence or structural information.
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Affiliation(s)
- Ronit Hod
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
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8
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McCauley MJ, Rueter EM, Rouzina I, Maher LJ, Williams MC. Single-molecule kinetics reveal microscopic mechanism by which High-Mobility Group B proteins alter DNA flexibility. Nucleic Acids Res 2012; 41:167-81. [PMID: 23143110 PMCID: PMC3592474 DOI: 10.1093/nar/gks1031] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Eukaryotic High-Mobility Group B (HMGB) proteins alter DNA elasticity while facilitating transcription, replication and DNA repair. We developed a new single-molecule method to probe non-specific DNA interactions for two HMGB homologs: the human HMGB2 box A domain and yeast Nhp6Ap, along with chimeric mutants replacing neutral N-terminal residues of the HMGB2 protein with cationic sequences from Nhp6Ap. Surprisingly, HMGB proteins constrain DNA winding, and this torsional constraint is released over short timescales. These measurements reveal the microscopic dissociation rates of HMGB from DNA. Separate microscopic and macroscopic (or local and non-local) unbinding rates have been previously proposed, but never independently observed. Microscopic dissociation rates for the chimeric mutants (∼10 s−1) are higher than those observed for wild-type proteins (∼0.1–1.0 s−1), reflecting their reduced ability to bend DNA through short-range interactions, despite their increased DNA-binding affinity. Therefore, transient local HMGB–DNA contacts dominate the DNA-bending mechanism used by these important architectural proteins to increase DNA flexibility.
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Affiliation(s)
- Micah J McCauley
- Department of Physics, Northeastern University, Boston, MA 02115, USA
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9
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Malarkey CS, Bestwick M, Kuhlwilm JE, Shadel GS, Churchill MEA. Transcriptional activation by mitochondrial transcription factor A involves preferential distortion of promoter DNA. Nucleic Acids Res 2011; 40:614-24. [PMID: 21948790 PMCID: PMC3258160 DOI: 10.1093/nar/gkr787] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mitochondrial transcription factor A (mtTFA/TFAM) is a nucleus-encoded, high-mobility-group-box (HMG-box) protein that regulates transcription of the mitochondrial genome by specifically recognizing light-strand and heavy-strand promoters (LSP, HSP1). TFAM also binds mitochondrial DNA in a non-sequence specific (NSS) fashion and facilitates its packaging into nucleoid structures. However, the requirement and contribution of DNA-bending for these two different binding modes has not been addressed in detail, which prompted this comparison of binding and bending properties of TFAM on promoter and non-promoter DNA. Promoter DNA increased the stability of TFAM to a greater degree than non-promoter DNA. However, the thermodynamic properties of DNA binding for TFAM with promoter and non-specific (NS) DNA were similar to each other and to other NSS HMG-box proteins. Fluorescence resonance energy transfer assays showed that TFAM bends promoter DNA to a greater degree than NS DNA. In contrast, TFAM lacking the C-terminal tail distorted both promoter and non-promoter DNA to a significantly reduced degree, corresponding with markedly decreased transcriptional activation capacity at LSP and HSP1 in vitro. Thus, the enhanced bending of promoter DNA imparted by the C-terminal tail is a critical component of the ability of TFAM to activate promoter-specific initiation by the core mitochondrial transcription machinery.
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Affiliation(s)
- Christopher S Malarkey
- Department of Pharmacology, University of Colorado Denver, School of Medicine, 12801 E. 17th Ave, Aurora, CO 80045-0511, USA
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10
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Churchill MEA, Klass J, Zoetewey DL. Structural analysis of HMGD-DNA complexes reveals influence of intercalation on sequence selectivity and DNA bending. J Mol Biol 2010; 403:88-102. [PMID: 20800069 DOI: 10.1016/j.jmb.2010.08.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 08/03/2010] [Accepted: 08/16/2010] [Indexed: 10/19/2022]
Abstract
The ubiquitous, eukaryotic, high-mobility group box (HMGB) chromosomal proteins promote many chromatin-mediated cellular activities through their non-sequence-specific binding and bending of DNA. Minor-groove DNA binding by the HMG box results in substantial DNA bending toward the major groove owing to electrostatic interactions, shape complementarity, and DNA intercalation that occurs at two sites. Here, the structures of the complexes formed with DNA by a partially DNA intercalation-deficient mutant of Drosophila melanogaster HMGD have been determined by X-ray crystallography at a resolution of 2.85 Å. The six proteins and 50 bp of DNA in the crystal structure revealed a variety of bound conformations. All of the proteins bound in the minor groove, bridging DNA molecules, presumably because these DNA regions are easily deformed. The loss of the primary site of DNA intercalation decreased overall DNA bending and shape complementarity. However, DNA bending at the secondary site of intercalation was retained and most protein-DNA contacts were preserved. The mode of binding resembles the HMGB1 box A-cisplatin-DNA complex, which also lacks a primary intercalating residue. This study provides new insights into the binding mechanisms used by HMG boxes to recognize varied DNA structures and sequences as well as modulate DNA structure and DNA bending.
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Affiliation(s)
- Mair E A Churchill
- Department of Pharmacology, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA; Molecular Biology Program, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA.
| | - Janet Klass
- Department of Pharmacology, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA
| | - David L Zoetewey
- Molecular Biology Program, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA
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11
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Hill KK, Roemer SC, Jones DNM, Churchill MEA, Edwards DP. A progesterone receptor co-activator (JDP2) mediates activity through interaction with residues in the carboxyl-terminal extension of the DNA binding domain. J Biol Chem 2009; 284:24415-24. [PMID: 19553667 DOI: 10.1074/jbc.m109.003244] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Progesterone receptor (PR) belongs to the nuclear receptor family of ligand-dependent transcription factors and mediates the major biological effects of progesterone. Transcriptional co-activators that are recruited by PR through the carboxyl-terminal ligand binding domain have been studied extensively. Much less is known about co-activators that interact with other regions of receptors. Jun dimerization protein 2 (JDP2) is a PR co-activator that enhances the transcriptional activity of the amino-terminal domain by increasing the alpha-helical content and stability of the intrinsically disordered amino-terminal domain. To gain insights into the mechanism of JDP2 co-activation of PR, the structural basis of JDP2-PR interaction was analyzed using NMR. The smallest regions of each protein needed for efficient protein interaction were used for NMR and included the basic region plus leucine zipper (bZIP) domain of JDP2 and the core zinc modules of the PR DNA binding domain plus the intrinsically disordered carboxyl-terminal extension (CTE) of the DNA binding domain. Chemical shift changes in PR upon titration with JDP2 revealed that most of the residues involved in binding of JDP2 reside within the CTE. The importance of the CTE for binding JDP2 was confirmed by peptide competition and mutational analyses. Point mutations within CTE sites identified by NMR and a CTE domain swapping experiment also confirmed the functional importance of JDP2 interaction with the CTE for enhancement of PR transcriptional activity. These studies provide insights into the role and functional importance of the CTE for co-activator interactions.
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Affiliation(s)
- Krista K Hill
- Molecular Biology Program, School of Medicine, University of Colorado Denver, Aurora, Colorado 80045, USA
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12
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Briquet S, Boschet C, Gissot M, Tissandié E, Sevilla E, Franetich JF, Thiery I, Hamid Z, Bourgouin C, Vaquero C. High-mobility-group box nuclear factors of Plasmodium falciparum. EUKARYOTIC CELL 2006; 5:672-82. [PMID: 16607015 PMCID: PMC1459676 DOI: 10.1128/ec.5.4.672-682.2006] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In eukaryotes, the high-mobility-group (HMG) nuclear factors are highly conserved throughout evolution and are divided into three families, including HGMB, characterized by an HMG box domain. Some HMGB factors are DNA structure specific and preferentially interact with distorted DNA sequences, trigger DNA bending, and hence facilitate the binding of nucleoprotein complexes that in turn activate or repress transcription. In Plasmodium falciparum, two HMGB factors were predicted: PfHMGB1 and PfHMGB2. They are small proteins, under 100 amino acids long, encompassing a characteristic HMG box domain closely related to box B of metazoan factors, which comprises two HMG box domains, A and B, in tandem. Computational analyses supported the conclusion that the Plasmodium proteins were genuine architectural HMGB factors, and in vitro analyses performed with both recombinant proteins established that they were able to interact with distorted DNA structures and bend linear DNA with different affinities. These proteins were detected in both asexual- and gametocyte-stage cells in Western blotting experiments and mainly in the parasite nuclei. PfHMGB1 is preferentially expressed in asexual erythrocytic stages and PfHMGB2 in gametocytes, in good correlation with transcript levels of expression. Finally, immunofluorescence studies revealed differential subcellular localizations: both factors were observed in the nucleus of asexual- and sexual-stage cells, and PfHMGB2 was also detected in the cytoplasm of gametocytes. In conclusion, in light of differences in their levels of expression, subcellular localizations, and capacities for binding and bending DNA, these factors are likely to play nonredundant roles in transcriptional regulation of Plasmodium development in erythrocytes.
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Affiliation(s)
- Sylvie Briquet
- INSERM, U511, Université Pierre et Marie Curie, Paris VI, Centre Hospitalo-Universitaire de la Pitié-Salpêtrière, Paris, France, Biologie et Génétique du Paludisme, CEPIA (Centre de Production et d'Infection des Anophèles), Institut Pasteur, Paris, France
- Corresponding author. Mailing address: INSERM, U511, Université Pierre et Marie Curie, Paris VI, Centre Hospitalo-Universitaire de la Pitié-Salpêtrière, 91 boulevard de l'Hôpital, 75013 Paris, France. Phone: 33 (0) 1 40 77 81 14. Fax: 33 (0) 1 45 83 88 58. E-mail for Sylvie Briquet: . E-mail for Catherine Vaquero:
| | - Charlotte Boschet
- INSERM, U511, Université Pierre et Marie Curie, Paris VI, Centre Hospitalo-Universitaire de la Pitié-Salpêtrière, Paris, France, Biologie et Génétique du Paludisme, CEPIA (Centre de Production et d'Infection des Anophèles), Institut Pasteur, Paris, France
| | - Mathieu Gissot
- INSERM, U511, Université Pierre et Marie Curie, Paris VI, Centre Hospitalo-Universitaire de la Pitié-Salpêtrière, Paris, France, Biologie et Génétique du Paludisme, CEPIA (Centre de Production et d'Infection des Anophèles), Institut Pasteur, Paris, France
| | - Emilie Tissandié
- INSERM, U511, Université Pierre et Marie Curie, Paris VI, Centre Hospitalo-Universitaire de la Pitié-Salpêtrière, Paris, France, Biologie et Génétique du Paludisme, CEPIA (Centre de Production et d'Infection des Anophèles), Institut Pasteur, Paris, France
| | - Elisa Sevilla
- INSERM, U511, Université Pierre et Marie Curie, Paris VI, Centre Hospitalo-Universitaire de la Pitié-Salpêtrière, Paris, France, Biologie et Génétique du Paludisme, CEPIA (Centre de Production et d'Infection des Anophèles), Institut Pasteur, Paris, France
| | - Jean-François Franetich
- INSERM, U511, Université Pierre et Marie Curie, Paris VI, Centre Hospitalo-Universitaire de la Pitié-Salpêtrière, Paris, France, Biologie et Génétique du Paludisme, CEPIA (Centre de Production et d'Infection des Anophèles), Institut Pasteur, Paris, France
| | - Isabelle Thiery
- INSERM, U511, Université Pierre et Marie Curie, Paris VI, Centre Hospitalo-Universitaire de la Pitié-Salpêtrière, Paris, France, Biologie et Génétique du Paludisme, CEPIA (Centre de Production et d'Infection des Anophèles), Institut Pasteur, Paris, France
| | - Zuhal Hamid
- INSERM, U511, Université Pierre et Marie Curie, Paris VI, Centre Hospitalo-Universitaire de la Pitié-Salpêtrière, Paris, France, Biologie et Génétique du Paludisme, CEPIA (Centre de Production et d'Infection des Anophèles), Institut Pasteur, Paris, France
| | - Catherine Bourgouin
- INSERM, U511, Université Pierre et Marie Curie, Paris VI, Centre Hospitalo-Universitaire de la Pitié-Salpêtrière, Paris, France, Biologie et Génétique du Paludisme, CEPIA (Centre de Production et d'Infection des Anophèles), Institut Pasteur, Paris, France
| | - Catherine Vaquero
- INSERM, U511, Université Pierre et Marie Curie, Paris VI, Centre Hospitalo-Universitaire de la Pitié-Salpêtrière, Paris, France, Biologie et Génétique du Paludisme, CEPIA (Centre de Production et d'Infection des Anophèles), Institut Pasteur, Paris, France
- Corresponding author. Mailing address: INSERM, U511, Université Pierre et Marie Curie, Paris VI, Centre Hospitalo-Universitaire de la Pitié-Salpêtrière, 91 boulevard de l'Hôpital, 75013 Paris, France. Phone: 33 (0) 1 40 77 81 14. Fax: 33 (0) 1 45 83 88 58. E-mail for Sylvie Briquet: . E-mail for Catherine Vaquero:
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13
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Crane-Robinson C, Dragan AI, Privalov PL. The extended arms of DNA-binding domains: a tale of tails. Trends Biochem Sci 2006; 31:547-52. [PMID: 16920361 DOI: 10.1016/j.tibs.2006.08.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2006] [Revised: 07/17/2006] [Accepted: 08/03/2006] [Indexed: 10/24/2022]
Abstract
DNA-binding domains (DBDs) frequently have N- or C-terminal tails, rich in lysine and/or arginine and disordered in free solution, that bind the DNA separately from and in the opposite groove to the folded domain. Is their role simply to increase affinity for DNA or do they have a role in specificity, that is, sequence recognition? One approach to answering this question is to analyze the contribution of such tails to the overall energetics of binding. It turns out that, despite similarities of amino acid sequence, three distinct categories of DBD extension exist: (i) those that are purely electrostatic and lack specificity, (ii) those that are largely non-electrostatic with a high contribution to specificity and (iii) those of mixed character that show sequence preference. Because in all cases the tails also increase the affinity for target DNA, they represent a crucial component of the machinery for selective gene activation or repression.
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Dragan AI, Read CM, Makeyeva EN, Milgotina EI, Churchill MEA, Crane-Robinson C, Privalov PL. DNA Binding and Bending by HMG Boxes: Energetic Determinants of Specificity. J Mol Biol 2004; 343:371-93. [PMID: 15451667 DOI: 10.1016/j.jmb.2004.08.035] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2004] [Revised: 06/23/2004] [Accepted: 08/06/2004] [Indexed: 11/26/2022]
Abstract
To clarify the physical basis of DNA binding specificity, the thermodynamic properties and DNA binding and bending abilities of the DNA binding domains (DBDs) of sequence-specific (SS) and non-sequence-specific (NSS) HMG box proteins were studied with various DNA recognition sequences using micro-calorimetric and optical methods. Temperature-induced unfolding of the free DBDs showed that their structure does not represent a single cooperative unit but is subdivided into two (in the case of NSS DBDs) or three (in the case of SS DBDs) sub-domains, which differ in stability. Both types of HMG box, most particularly SS, are partially unfolded even at room temperature but association with DNA results in stabilization and cooperation of all the sub-domains. Binding and bending measurements using fluorescence spectroscopy over a range of ionic strengths, combined with calorimetric data, allowed separation of the electrostatic and non-electrostatic components of the Gibbs energies of DNA binding, yielding their enthalpic and entropic terms and an estimate of their contributions to DNA binding and bending. In all cases electrostatic interactions dominate non-electrostatic in the association of a DBD with DNA. The main difference between SS and NSS complexes is that SS are formed with an enthalpy close to zero and a negative heat capacity effect, while NSS are formed with a very positive enthalpy and a positive heat capacity effect. This indicates that formation of SS HMG box-DNA complexes is specified by extensive van der Waals contacts between apolar groups, i.e. a more tightly packed interface forms than in NSS complexes. The other principal difference is that DNA bending by the NSS DBDs is driven almost entirely by the electrostatic component of the binding energy, while DNA bending by SS DBDs is driven mainly by the non-electrostatic component. The basic extensions of both categories of HMG box play a similar role in DNA binding and bending, making solely electrostatic interactions with the DNA.
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Affiliation(s)
- Anatoly I Dragan
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
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Santangelo TJ, Roberts JW. Formation of long DNA templates containing site-specific alkane-disulfide DNA interstrand cross-links for use in transcription reactions. Methods Enzymol 2004; 371:120-32. [PMID: 14712695 DOI: 10.1016/s0076-6879(03)71008-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Thomas J Santangelo
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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16
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Chromosomal HMG-box proteins. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/s0167-7306(03)39005-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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17
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Dragan AI, Klass J, Read C, Churchill MEA, Crane-Robinson C, Privalov PL. DNA binding of a non-sequence-specific HMG-D protein is entropy driven with a substantial non-electrostatic contribution. J Mol Biol 2003; 331:795-813. [PMID: 12909011 DOI: 10.1016/s0022-2836(03)00785-x] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The thermal properties of two forms of the Drosophila melanogaster HMG-D protein, with and without its highly basic 26 residue C-terminal tail (D100 and D74) and the thermodynamics of their non-sequence-specific interaction with linear DNA duplexes were studied using scanning and titration microcalorimetry, spectropolarimetry, fluorescence anisotropy and FRET techniques at different temperatures and salt concentrations. It was shown that the C-terminal tail of D100 is unfolded at all temperatures, whilst the state of the globular part depends on temperature in a rather complex way, being completely folded only at temperatures close to 0 degrees C and unfolding with significant heat absorption at temperatures below those of the gross denaturational changes. The association constant and thus Gibbs energy of binding for D100 is much greater than for D74 but the enthalpies of their association are similar and are large and positive, i.e. DNA binding is a completely entropy-driven process. The positive entropy of association is due to release of counterions and dehydration upon forming the protein/DNA complex. Ionic strength variation showed that electrostatic interactions play an important but not exclusive role in the DNA binding of the globular part of this non-sequence-specific protein, whilst binding of the positively charged C-terminal tail of D100 is almost completely electrostatic in origin. This interaction with the negative charges of the DNA phosphate groups significantly enhances the DNA bending. An important feature of the non-sequence-specific association of these HMG boxes with DNA is that the binding enthalpy is significantly more positive than for the sequence-specific association of the HMG box from Sox-5, despite the fact that these proteins bend the DNA duplex to a similar extent. This difference shows that the enthalpy of dehydration of apolar groups at the HMG-D/DNA interface is not fully compensated by the energy of van der Waals interactions between these groups, i.e. the packing density at the interface must be lower than for the sequence-specific Sox-5 HMG box.
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Affiliation(s)
- Anatoly I Dragan
- Department of Biology, Johns Hopkins University, Mudd Hall, 3400 N Charles Street, Baltimore, MD 21218-2685, USA
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Klass J, Murphy FV, Fouts S, Serenil M, Changela A, Siple J, Churchill MEA. The role of intercalating residues in chromosomal high-mobility-group protein DNA binding, bending and specificity. Nucleic Acids Res 2003; 31:2852-64. [PMID: 12771212 PMCID: PMC156723 DOI: 10.1093/nar/gkg389] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Ubiquitous high-mobility-group (HMGB) chromosomal proteins bind DNA in a non-sequence- specific fashion to promote chromatin function and gene regulation. Minor groove DNA binding of the HMG domain induces substantial DNA bending toward the major groove, and several interfacial residues contribute by DNA intercalation. The role of the intercalating residues in DNA binding, bending and specificity was systematically examined for a series of mutant Drosophila HMGB (HMG-D) proteins. The primary intercalating residue of HMG-D, Met13, is required both for high-affinity DNA binding and normal DNA bending. Leu9 and Tyr12 directly interact with Met13 and are required for HMG domain stability in addition to linear DNA binding and bending, which is an important function for these residues. In contrast, DNA binding and bending is retained in truncations of intercalating residues Val32 and Thr33 to alanine, but DNA bending is decreased for the glycine substitutions. Furthermore, substitution of the intercalating residues with those predicted to be involved in the specificity of the HMG domain transcription factors results in increased DNA affinity and decreased DNA bending without increased specificity. These studies reveal the importance of residues that buttress intercalating residues and suggest that features of the HMG domain other than a few base-specific hydrogen bonds distinguish the sequence-specific and non-sequence-specific HMG domain functions.
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Affiliation(s)
- Janet Klass
- Department of Pharmacology, The University of Colorado Health Sciences Center, 4200 East Ninth Avenue, Denver, CO 80262, USA
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Webb M, Payet D, Lee KB, Travers AA, Thomas JO. Structural requirements for cooperative binding of HMG1 to DNA minicircles. J Mol Biol 2001; 309:79-88. [PMID: 11491303 DOI: 10.1006/jmbi.2001.4667] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
DNA minicircles, where the length of DNA is below the persistence length, are highly effective, preferred, ligands for HMG-box proteins. The proteins bind to them "structure-specifically" with affinities in the nanomolar range, presumably to an exposed widened minor groove. To understand better the basis of this preference, we have studied the binding of HMG1 (which has two tandem HMG boxes linked by a basic extension to a long acidic tail) and Drosophila HMG-D (one HMG box linked by a basic region to a short and less acidic tail), and their HMG-box domains, to 88 bp and 75 bp DNA minicircles. In some cases we see cooperative binding of two molecules to the circles. The requirements for strong cooperativity are two HMG boxes and the basic extension; the latter also appears to stabilize and constrain the complex, preventing binding of further protein molecules. HMG-D, with a single HMG box, does not bind cooperatively. In the case of HMG1, the acidic tail is not required for cooperativity and does not affect binding significantly, in contrast to a much greater effect with linear DNA, or even four-way junctions (another distorted DNA substrate). Such effects could be relevant in the hierarchy of binding of HMG-box proteins to DNA distortions in vivo, where both single-box and two-box proteins might co-exist, with or without basic extensions and acidic tails.
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Affiliation(s)
- M Webb
- Cambridge Centre for Molecular Recognition, Department of Biochemistry, University of Cambridge, UK
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Abstract
The HMG-box proteins, one of the three classes of high mobility group (HMG) chromosomal proteins, bend DNA and bind preferentially to distorted DNA structures. The proteins appear to act primarily as architectural facilitators in the assembly of nucleoprotein complexes; for example, in effecting recombination and in the initiation of transcription. HMG-box proteins might be targeted to particular DNA sites in chromatin by either protein-protein interactions or recognition of specific DNA structures.
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Affiliation(s)
- J O Thomas
- Cambridge Centre for Molecular Recognition, University of Cambridge, 80 Tennis Court Road, Cambridge, UK CB2 1GA.
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21
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Abstract
An NMR model is presented for the structure of HMG-D, one of the Drosophila counterparts of mammalian HMG1/2 proteins, bound to a particular distorted DNA structure, a dA(2) DNA bulge. The complex is in fast to intermediate exchange on the NMR chemical shift time scale and suffers substantial linebroadening for the majority of interfacial resonances. This essentially precludes determination of a high-resolution structure for the interface based on NMR data alone. However, by introducing a small number of additional constraints based on chemical shift and linewidth footprinting combined with analogies to known structures, an ensemble of model structures was generated using a computational strategy equivalent to that for a conventional NMR structure determination. We find that the base pair adjacent to the dA(2) bulge is not formed and that the protein recognizes this feature in forming the complex; intermolecular NOE enhancements are observed from the sidechain of Thr 33 to all four nucleotides of the DNA sequence step adjacent to the bulge. Our results form the first experimental demonstration that when binding to deformed DNA, non-sequence-specific HMG proteins recognize the junction between duplex and nonduplex DNA. Similarities and differences of the present structural model relative to other HMG-DNA complex structures are discussed.
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Affiliation(s)
- R Cerdan
- M.R.C. Laboratory of Molecular Biology, Cambridge CB2 2QH, UK
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