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Malik A, Jayarathna DK, Fisher M, Barbhuiya TK, Gandhi NS, Batra J. Dynamics and recognition of homeodomain containing protein-DNA complex of IRX4. Proteins 2024; 92:282-301. [PMID: 37861198 DOI: 10.1002/prot.26604] [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: 01/15/2022] [Revised: 09/15/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023]
Abstract
Iroquois Homeobox 4 (IRX4) belongs to a family of homeobox TFs having roles in embryogenesis, cell specification, and organ development. Recently, large scale genome-wide association studies and epigenetic studies have highlighted the role of IRX4 and its associated variants in prostate cancer. No studies have investigated and characterized the structural aspect of the IRX4 homeodomain and its potential to bind to DNA. The current study uses sequence analysis, homology modeling, and molecular dynamics simulations to explore IRX4 homeodomain-DNA recognition mechanisms and the role of somatic mutations affecting these interactions. Using publicly available databases, gene expression of IRX4 was found in different tissues, including prostate, heart, skin, vagina, and the protein expression was found in cancer cell lines (HCT166, HEK293), B cells, ascitic fluid, and brain. Sequence conservation of the homeodomain shed light on the importance of N- and C-terminal residues involved in DNA binding. The specificity of IRX4 homodimer bound to consensus human DNA sequence was confirmed by molecular dynamics simulations, representing the role of conserved amino acids including R145, A194, N195, S190, R198, and R199 in binding to DNA. Additional N-terminal residues like T144 and G143 were also found to have specific interactions highlighting the importance of N-terminus of the homeodomain in DNA recognition. Additionally, the effects of somatic mutations, including the conserved Arginine (R145, R198, and R199) residues on DNA binding elucidated the importance of these residues in stabilizing the protein-DNA complex. Secondary structure and hydrogen bonding analysis showed the roles of specific residues (R145, T191, A194, N195, R198, and R199) in maintaining the homogeneity of the structure and its interaction with DNA. The differences in relative binding free energies of all the mutants shed light on the structural modularity of this protein and the dynamics behind protein-DNA interaction. We also have predicted that the C-terminal sequence of the IRX4 homeodomain could act as a potential cell-penetrating peptide, emphasizing the role these small peptides could play in targeting homeobox TFs.
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Affiliation(s)
- Adil Malik
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Dulari K Jayarathna
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
- School of Chemistry and Physics, Faculty of Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Mark Fisher
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Tabassum Khair Barbhuiya
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
- School of Chemistry and Physics, Faculty of Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Neha S Gandhi
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
- School of Chemistry and Physics, Faculty of Science, Queensland University of Technology, Brisbane, Queensland, Australia
- Department of Computer Science and Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Udupi, Karnataka, India
| | - Jyotsna Batra
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Queensland, Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
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2
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Malbranke C, Rostain W, Depardieu F, Cocco S, Monasson R, Bikard D. Computational design of novel Cas9 PAM-interacting domains using evolution-based modelling and structural quality assessment. PLoS Comput Biol 2023; 19:e1011621. [PMID: 37976326 PMCID: PMC10729993 DOI: 10.1371/journal.pcbi.1011621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 12/19/2023] [Accepted: 10/19/2023] [Indexed: 11/19/2023] Open
Abstract
We present here an approach to protein design that combines (i) scarce functional information such as experimental data (ii) evolutionary information learned from a natural sequence variants and (iii) physics-grounded modeling. Using a Restricted Boltzmann Machine (RBM), we learn a sequence model of a protein family. We use semi-supervision to leverage available functional information during the RBM training. We then propose a strategy to explore the protein representation space that can be informed by external models such as an empirical force-field method (FoldX). Our approach is applied to a domain of the Cas9 protein responsible for recognition of a short DNA motif. We experimentally assess the functionality of 71 variants generated to explore a range of RBM and FoldX energies. Sequences with as many as 50 differences (20% of the protein domain) to the wild-type retained functionality. Overall, 21/71 sequences designed with our method were functional. Interestingly, 6/71 sequences showed an improved activity in comparison with the original wild-type protein sequence. These results demonstrate the interest in further exploring the synergies between machine-learning of protein sequence representations and physics grounded modeling strategies informed by structural information.
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Affiliation(s)
- Cyril Malbranke
- Laboratory of Physics of the Ecole Normale Superieure, PSL Research, CNRS UMR 8023, Sorbonne Université, Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Synthetic Biology, Paris, France
| | - William Rostain
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Synthetic Biology, Paris, France
| | - Florence Depardieu
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Synthetic Biology, Paris, France
| | - Simona Cocco
- Laboratory of Physics of the Ecole Normale Superieure, PSL Research, CNRS UMR 8023, Sorbonne Université, Paris, France
| | - Rémi Monasson
- Laboratory of Physics of the Ecole Normale Superieure, PSL Research, CNRS UMR 8023, Sorbonne Université, Paris, France
| | - David Bikard
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Synthetic Biology, Paris, France
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3
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Bera S, Shi K, Aihara H, Grandgenett DP, Pandey KK. Molecular determinants for Rous sarcoma virus intasome assemblies involved in retroviral integration. J Biol Chem 2023; 299:104730. [PMID: 37084813 PMCID: PMC10209032 DOI: 10.1016/j.jbc.2023.104730] [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: 03/02/2023] [Revised: 04/13/2023] [Accepted: 04/16/2023] [Indexed: 04/23/2023] Open
Abstract
Integration of retroviral DNA into the host genome involves the formation of integrase (IN)-DNA complexes termed intasomes. Further characterization of these complexes is needed to understand their assembly process. Here, we report the single-particle cryo-EM structure of the Rous sarcoma virus (RSV) strand transfer complex (STC) intasome produced with IN and a preassembled viral/target DNA substrate at 3.36 Å resolution. The conserved intasome core region consisting of IN subunits contributing active sites interacting with viral/target DNA has a resolution of 3 Å. Our structure demonstrated the flexibility of the distal IN subunits relative to the IN subunits in the conserved intasome core, similar to results previously shown with the RSV octameric cleaved synaptic complex intasome produced with IN and viral DNA only. An extensive analysis of higher resolution STC structure helped in the identification of nucleoprotein interactions important for intasome assembly. Using structure-function studies, we determined the mechanisms of several IN-DNA interactions critical for assembly of both RSV intasomes. We determined the role of IN residues R244, Y246, and S124 in cleaved synaptic complex and STC intasome assemblies and their catalytic activities, demonstrating differential effects. Taken together, these studies advance our understanding of different RSV intasome structures and molecular determinants involved in their assembly.
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Affiliation(s)
- Sibes Bera
- Department of Molecular Microbiology and Immunology, School of Medicine, Saint Louis University, St Louis, Missouri, USA
| | - Ke Shi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Duane P Grandgenett
- Department of Molecular Microbiology and Immunology, School of Medicine, Saint Louis University, St Louis, Missouri, USA
| | - Krishan K Pandey
- Department of Molecular Microbiology and Immunology, School of Medicine, Saint Louis University, St Louis, Missouri, USA.
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4
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Duckworth AT, Ducos PL, McMillan SD, Satyshur KA, Blumenthal KH, Deorio HR, Larson JA, Sandler SJ, Grant T, Keck JL. Replication fork binding triggers structural changes in the PriA helicase that govern DNA replication restart in E. coli. Nat Commun 2023; 14:2725. [PMID: 37169801 PMCID: PMC10175261 DOI: 10.1038/s41467-023-38144-x] [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: 01/06/2023] [Accepted: 04/18/2023] [Indexed: 05/13/2023] Open
Abstract
Bacterial replisomes often dissociate from replication forks before chromosomal replication is complete. To avoid the lethal consequences of such situations, bacteria have evolved replication restart pathways that reload replisomes onto prematurely terminated replication forks. To understand how the primary replication restart pathway in E. coli (PriA-PriB) selectively acts on replication forks, we determined the cryogenic-electron microscopy structure of a PriA/PriB/replication fork complex. Replication fork specificity arises from extensive PriA interactions with each arm of the branched DNA. These interactions reshape the PriA protein to create a pore encircling single-stranded lagging-strand DNA while also exposing a surface of PriA onto which PriB docks. Together with supporting biochemical and genetic studies, the structure reveals a switch-like mechanism for replication restart initiation in which restructuring of PriA directly couples replication fork recognition to PriA/PriB complex formation to ensure robust and high-fidelity replication re-initiation.
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Affiliation(s)
- Alexander T Duckworth
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Peter L Ducos
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI, 53715, USA
| | - Sarah D McMillan
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Kenneth A Satyshur
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Katelien H Blumenthal
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Haley R Deorio
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Joseph A Larson
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Steven J Sandler
- Department of Microbiology, University of Massachusetts at Amherst, Amherst, MA, 01003, USA.
| | - Timothy Grant
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI, 53715, USA.
| | - James L Keck
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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5
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Khatoon H, Raza RZ, Saleem S, Batool F, Arshad S, Abrar M, Ali S, Hussain I, Shubin NH, Abbasi AA. Evolutionary relevance of single nucleotide variants within the forebrain exclusive human accelerated enhancer regions. BMC Mol Cell Biol 2023; 24:13. [PMID: 36991330 PMCID: PMC10053400 DOI: 10.1186/s12860-023-00474-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
Abstract
Background
Human accelerated regions (HARs) are short conserved genomic sequences that have acquired significantly more nucleotide substitutions than expected in the human lineage after divergence from chimpanzees. The fast evolution of HARs may reflect their roles in the origin of human-specific traits. A recent study has reported positively-selected single nucleotide variants (SNVs) within brain-exclusive human accelerated enhancers (BE-HAEs) hs1210 (forebrain), hs563 (hindbrain) and hs304 (midbrain/forebrain). By including data from archaic hominins, these SNVs were shown to be Homo sapiens-specific, residing within transcriptional factors binding sites (TFBSs) for SOX2 (hs1210), RUNX1/3 (hs563), and FOS/JUND (hs304). Although these findings suggest that the predicted modifications in TFBSs may have some role in present-day brain structure, work is required to verify the extent to which these changes translate into functional variation.
Results
To start to fill this gap, we investigate the SOX2 SNV, with both forebrain expression and strong signal of positive selection in humans. We demonstrate that the HMG box of SOX2 binds in vitro with Homo sapiens-specific derived A-allele and ancestral T-allele carrying DNA sites in BE-HAE hs1210. Molecular docking and simulation analysis indicated highly favourable binding of HMG box with derived A-allele containing DNA site when compared to site carrying ancestral T-allele.
Conclusion
These results suggest that adoptive changes in TF affinity within BE-HAE hs1210 and other HAR enhancers in the evolutionary history of Homo sapiens might.
have brought about changes in gene expression patterns and have functional consequences on forebrain formation and evolution.
Methods
The present study employ electrophoretic mobility shift assays (EMSA) and molecular docking and molecular dynamics simulations approaches.
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6
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Smiley AT, Tompkins KJ, Pawlak MR, Krueger AJ, Evans RL, Shi K, Aihara H, Gordon WR. Watson-Crick Base-Pairing Requirements for ssDNA Recognition and Processing in Replication-Initiating HUH Endonucleases. mBio 2023; 14:e0258722. [PMID: 36541758 PMCID: PMC9973303 DOI: 10.1128/mbio.02587-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Replication-initiating HUH endonucleases (Reps) are sequence-specific nucleases that cleave and rejoin single-stranded DNA (ssDNA) during rolling-circle replication. These functions are mediated by covalent linkage of the Rep to its substrate post cleavage. Here, we describe the structures of the endonuclease domain from the Muscovy duck circovirus Rep in complex with its cognate ssDNA 10-mer with and without manganese in the active site. Structural and functional analyses demonstrate that divalent cations play both catalytic and structural roles in Reps by polarizing and positioning their substrate. Further structural comparisons highlight the importance of an intramolecular substrate Watson-Crick (WC) base pairing between the -4 and +1 positions. Subsequent kinetic and functional analyses demonstrate a functional dependency on WC base pairing between these positions regardless of the pair's identity (i.e., A·T, T·A, G·C, or C·G), highlighting a structural specificity for substrate interaction. Finally, considering how well WC swaps were tolerated in vitro, we sought to determine to what extent the canonical -4T·+1A pairing is conserved in circular Rep-encoding single-stranded DNA viruses and found evidence of noncanonical pairings in a minority of these genomes. Altogether, our data suggest that substrate intramolecular WC base pairing is a universal requirement for separation and reunion of ssDNA in Reps. IMPORTANCE Circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses are a ubiquitous group of viruses that infect organisms across all domains of life. These viruses negatively impact both agriculture and human health. All members of this viral family employ a multifunctional nuclease (Rep) to initiate replication. Reps are structurally similar throughout this family, making them targets of interest for viral inhibition strategies. Here, we investigate the functional dependencies of the Rep protein from Muscovy duck circovirus for ssDNA interaction. We demonstrate that this Rep requires an intramolecular Watson-Crick base pairing for origin of replication (Ori) recognition and interaction. We show that noncognate base pair swaps are well tolerated, highlighting a local structural specificity over sequence specificity. Bioinformatic analysis found that the vast majority of CRESS-DNA Oris form base pairs in conserved positions, suggesting this pairing is a universal requirement for replication initiation in the CRESS-DNA virus family.
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Affiliation(s)
- Adam T. Smiley
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Kassidy J. Tompkins
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Matthew R. Pawlak
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - August J. Krueger
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Robert L. Evans
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Wendy R. Gordon
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
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7
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Abstract
Despite the negative charge of the DNA backbone, acidic residues (Asp/Glu) commonly participate in the base readout, with a strong preference for cytosine. In fact, in the solved DNA/protein structures, cytosine is recognized almost exclusively by Asp/Glu through a direct hydrogen bond, while at the same time, adenine, regardless of its amino group, shows no propensity for Asp/Glu. Here, we analyzed the contribution of Asp/Glu to sequence-specific DNA binding using classical and ab initio simulations of selected transcription factors and found that it is governed by a fine balance between the repulsion from backbone phosphates and attractive interactions with cytosine. Specifically, Asp/Glu lower the affinity for noncytosine sites and thus act as negative selectors preventing off-target binding. At cytosine-containing sites, the favorable contribution does not merely rely on the formation of a single H-bond but usually requires the presence of positive potential generated by multiple cytosines, consistently with the observed excess of cytosine in the target sites. Finally, we show that the preference of Asp/Glu for cytosine over adenine is a result of the repulsion from the adenine imidazole ring and a tendency of purine-purine dinucleotides to adopt the BII conformation.
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8
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Jain P, Sudandiradoss C. Andrographolide-based potential anti-inflammatory transcription inhibitors against nuclear factor NF-kappa-B p50 subunit (NF-κB p50): an integrated molecular and quantum mechanical approach. 3 Biotech 2023; 13:15. [PMID: 36540414 PMCID: PMC9759609 DOI: 10.1007/s13205-022-03431-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
The unregulated activation of nuclear factor-κB (NF-κB) is a critical event in the progression of various inflammatory diseases such as ulcerative colitis, asthma, rheumatoid arthritis, bacterial induced gastritis, etc. Hence, blocking the transcriptional activity of NF-κB is a promising strategy towards the development of an anti-inflammatory agent. In this study, an integrated molecular and quantum mechanical approach was carried out to find a new potent andrographolide (AGP)-based analog that can inhibit DNA binding to NF-κB p50 and manifest anti-inflammatory activity. Our approach includes multiple sequence alignment, virtual screening, molecular docking (protein-ligand and protein-DNA), in silico site-directed mutagenesis, ADMET prediction, DFT (HOMO, LUMO, HLG, and EPM energy) analysis, MD simulation, and MM/GBSA rescoring. The virtual screening analysis of 237 AGP analogs yielded the five lead compounds based on the binding affinity. Further, molecular interactive docking and ADMET prediction of hit analogs revealed that Ana2 ((3Z,4S)-3-[2-[(4aR,6aS,7R,10aS,10bR)-3,3,6a,10b-tetramethyl-8-methylidene-1,4a,5,6,7,9,10,10a-octahydronaphtho[2,1-d][1,3]dioxin-7-yl]ethylidene]-4-hydroxyoxolan-2-one) is the most potent moiety as it displays the strongest binding affinity and better molecular/pharmacokinetic features. Moreover, DFT, MD simulation, and MM/GBSA studies corroborated the docking results and demonstrated better chemical and dynamic stability with the least binding free energy (- 29.99 kcal/mol) for the Ana2. Site-directed mutagenesis investigation (Cys62Ala) establishes the importance of the Cys62 amino acid residue towards the binding interaction and stability of Ana2 with NF-κB p50. Overall, the identified NF-κB p50 inhibitor opens up a new research horizon towards the development of plant-based anti-inflammatory drugs to combat progressive inflammatory diseases. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03431-9.
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Affiliation(s)
- Priyanka Jain
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
| | - C Sudandiradoss
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
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9
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Pal A, Chakrabarti P, Dey S. ProDFace: A web-tool for the dissection of protein-DNA interfaces. Front Mol Biosci 2022; 9:978310. [PMID: 36148013 PMCID: PMC9486321 DOI: 10.3389/fmolb.2022.978310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 08/09/2022] [Indexed: 11/30/2022] Open
Abstract
Protein-DNA interactions play a crucial role in gene expression and regulation. Identifying the DNA binding surface of proteins has long been a challenge–in comparison to protein-protein interactions, limited progress has been made in the development of efficient DNA binding site prediction and protein-DNA docking methods. Here we present ProDFace, a web tool that characterizes the binding region of a protein-DNA complex based on amino acid propensity, hydrogen bond (HB) donor capacity (number of solvent accessible HB donor groups), sequence conservation at the interface core and rim region, and geometry. The program takes as input the structure of a protein-DNA complex in PDB (Protein Data Bank) format, and outputs various physicochemical and geometric parameters of the interface, as well as conservation of the interface residues in the protein component. Values are provided for the whole interface, and after dissecting it into core and rim regions. Details of water mediated HBs between protein and DNA, potential HB donor groups present at the binding surface of protein, and conserved interface residues are also provided as downloadable text files. These parameters can be useful in evaluating and validating protein-DNA docking solutions, structures derived from simulation as well as solutions from the available prediction tools, and facilitate the development of more efficient prediction methods. The web-tool is freely available at structbioinfo.iitj.ac.in/resources/bioinfo/pd_interface.
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Affiliation(s)
- Arumay Pal
- School of Bioengineering, Vellore Institute of Technology, Bhopal, India
| | | | - Sucharita Dey
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Karwar, India
- *Correspondence: Sucharita Dey,
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10
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Jóźwik IK, Li W, Zhang DW, Wong D, Grawenhoff J, Ballandras-Colas A, Aiyer S, Cherepanov P, Engelman A, Lyumkis D. B-to-A transition in target DNA during retroviral integration. Nucleic Acids Res 2022; 50:8898-8918. [PMID: 35947647 PMCID: PMC9410886 DOI: 10.1093/nar/gkac644] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/06/2022] [Accepted: 07/19/2022] [Indexed: 01/21/2023] Open
Abstract
Integration into host target DNA (tDNA), a hallmark of retroviral replication, is mediated by the intasome, a multimer of integrase (IN) assembled on viral DNA (vDNA) ends. To ascertain aspects of tDNA recognition during integration, we have solved the 3.5 Å resolution cryo-EM structure of the mouse mammary tumor virus (MMTV) strand transfer complex (STC) intasome. The tDNA adopts an A-like conformation in the region encompassing the sites of vDNA joining, which exposes the sugar-phosphate backbone for IN-mediated strand transfer. Examination of existing retroviral STC structures revealed conservation of A-form tDNA in the analogous regions of these complexes. Furthermore, analyses of sequence preferences in genomic integration sites selectively targeted by six different retroviruses highlighted consistent propensity for A-philic sequences at the sites of vDNA joining. Our structure additionally revealed several novel MMTV IN-DNA interactions, as well as contacts seen in prior STC structures, including conserved Pro125 and Tyr149 residues interacting with tDNA. In infected cells, Pro125 substitutions impacted the global pattern of MMTV integration without significantly altering local base sequence preferences at vDNA insertion sites. Collectively, these data advance our understanding of retroviral intasome structure and function, as well as factors that influence patterns of vDNA integration in genomic DNA.
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Affiliation(s)
- Ilona K Jóźwik
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Wen Li
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Center, Boston, MA 02215, USA,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Da-Wei Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Center, Boston, MA 02215, USA,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA,Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Doris Wong
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Center, Boston, MA 02215, USA
| | - Julia Grawenhoff
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Center, Boston, MA 02215, USA
| | | | - Sriram Aiyer
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, UK,Department of Infectious Disease, St-Mary's Campus, Imperial College London, London W2 1PG, UK
| | - Alan N Engelman
- Correspondence may also be addressed to Alan N. Engelman. Tel: +1 617 632 4361; Fax: +1 617 632 4338;
| | - Dmitry Lyumkis
- To whom correspondence should be addressed. Tel: +1 858 453 4100 (Ext 1155);
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11
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Huber EM, Hortschansky P, Scheven MT, Misslinger M, Haas H, Brakhage AA, Groll M. Structural insights into cooperative DNA recognition by the CCAAT-binding complex and its bZIP transcription factor HapX. Structure 2022; 30:934-946.e4. [PMID: 35472306 DOI: 10.1016/j.str.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/21/2022] [Accepted: 03/31/2022] [Indexed: 11/25/2022]
Abstract
The heterotrimeric CCAAT-binding complex (CBC) is a fundamental eukaryotic transcription factor recognizing the CCAAT box. In certain fungi, like Aspergilli, the CBC cooperates with the basic leucine zipper HapX to control iron metabolism. HapX functionally depends on the CBC, and the stable interaction of both requires DNA. To study this cooperative effect, X-ray structures of the CBC-HapX-DNA complex were determined. Downstream of the CCAAT box, occupied by the CBC, a HapX dimer binds to the major groove. The leash-like N terminus of the distal HapX subunit contacts the CBC, and via a flexible polyproline type II helix mediates minor groove interactions that stimulate sequence promiscuity. In vitro and in vivo mutagenesis suggest that the structural and functional plasticity of HapX results from local asymmetry and its ability to target major and minor grooves simultaneously. The latter feature may also apply to related transcription factors such as yeast Hap4 and distinct Yap family members.
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Affiliation(s)
- Eva M Huber
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748 Garching, Germany
| | - Peter Hortschansky
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (Leibniz-HKI), Adolf-Reichwein-Straße 23, 07745 Jena, Germany
| | - Mareike T Scheven
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (Leibniz-HKI), Adolf-Reichwein-Straße 23, 07745 Jena, Germany
| | - Matthias Misslinger
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Hubertus Haas
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (Leibniz-HKI), Adolf-Reichwein-Straße 23, 07745 Jena, Germany; Institute for Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743 Jena, Germany.
| | - Michael Groll
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748 Garching, Germany.
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12
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Developing Community Resources for Nucleic Acid Structures. Life (Basel) 2022; 12:life12040540. [PMID: 35455031 PMCID: PMC9031032 DOI: 10.3390/life12040540] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 01/14/2023] Open
Abstract
In this review, we describe the creation of the Nucleic Acid Database (NDB) at Rutgers University and how it became a testbed for the current infrastructure of the RCSB Protein Data Bank. We describe some of the special features of the NDB and how it has been used to enable research. Plans for the next phase as the Nucleic Acid Knowledgebase (NAKB) are summarized.
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13
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Prediction of effector proteins and their implications in pathogenicity of phytopathogenic filamentous fungi: A review. Int J Biol Macromol 2022; 206:188-202. [PMID: 35227707 DOI: 10.1016/j.ijbiomac.2022.02.133] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/11/2022] [Accepted: 02/22/2022] [Indexed: 12/14/2022]
Abstract
Plant pathogenic fungi encode and secrete effector proteins to promote pathogenesis. In recent years, the important role of effector proteins in fungi and plant host interactions has become increasingly prominent. In this review, the functional characterization and molecular mechanisms by which fungal effector proteins modulate biological processes and suppress the defense of plant hosts are discussed, with an emphasis on cell localization during fungal infection. This paper also provides a comprehensive review of bioinformatic and experimental methods that are currently available for the identification of fungal effector proteins. We additionally summarize the secretion pathways and the methods for verifying the presence effector proteins in plant host cells. For future research, comparative genomic studies of different pathogens with varying life cycles will allow comprehensive and systematic identification of effector proteins. Additionally, functional analysis of effector protein interactions with a wider range of hosts (especially non-model crops) will provide more detailed repertoires of fungal effectors. Identifying effector proteins and verifying their functions will improve our understanding of their role in causing disease and in turn guide future strategies for combatting fungal infections.
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14
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Shan Z, Ghadirian N, Lyumkis D, Horton NC. Pre-Transition State and Apo Structures of the Filament-Forming Enzyme SgrAI Elucidate Mechanisms of Activation and Substrate Specificity. J Biol Chem 2022; 298:101760. [PMID: 35202658 PMCID: PMC8960973 DOI: 10.1016/j.jbc.2022.101760] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 12/01/2022] Open
Abstract
Enzyme filamentation is a widespread phenomenon that mediates enzyme regulation and function. For the filament-forming sequence-specific DNA endonuclease SgrAI, the process of filamentation both accelerates its DNA cleavage activity and expands its DNA sequence specificity, thus allowing for many additional DNA sequences to be rapidly cleaved. Both outcomes—the acceleration of DNA cleavage and the expansion of sequence specificity—are proposed to regulate critical processes in bacterial innate immunity. However, the mechanistic bases underlying these events remain unclear. Herein, we describe two new structures of the SgrAI enzyme that shed light on its catalytic function. First, we present the cryo-EM structure of filamentous SgrAI bound to intact primary site DNA and Ca2+ resolved to ∼2.5 Å within the catalytic center, which represents the trapped enzyme–DNA complex prior to the DNA cleavage reaction. This structure reveals important conformational changes that contribute to the catalytic mechanism and the binding of a second divalent cation in the enzyme active site, which is expected to contribute to increased DNA cleavage activity of SgrAI in the filamentous state. Second, we present an X-ray crystal structure of DNA-free (apo) SgrAI resolved to 2.0 Å resolution, which reveals a disordered loop involved in DNA recognition. Collectively, these multiple new observations clarify the mechanism of expansion of DNA sequence specificity of SgrAI, including the indirect readout of sequence-dependent DNA structure, changes in protein–DNA interactions, and the disorder-to-order transition of a crucial DNA recognition element.
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Affiliation(s)
- Zelin Shan
- Laboratory of Genetics, The Salk Institute of Biological Sciences, La Jolla, CA, USA 92037
| | - Niloofar Ghadirian
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA 85721
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute of Biological Sciences, La Jolla, CA, USA 92037; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA 92037.
| | - N C Horton
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA 85721.
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15
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Miller I, Totrov M, Korotchkina L, Kazyulkin DN, Gudkov AV, Korolev S. Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease. Nucleic Acids Res 2021; 49:11350-11366. [PMID: 34554261 PMCID: PMC8565326 DOI: 10.1093/nar/gkab826] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 11/12/2022] Open
Abstract
Long interspersed nuclear element-1 (L1) is an autonomous non-LTR retrotransposon comprising ∼20% of the human genome. L1 self-propagation causes genomic instability and is strongly associated with aging, cancer and other diseases. The endonuclease domain of L1’s ORFp2 protein (L1-EN) initiates de novo L1 integration by nicking the consensus sequence 5′-TTTTT/AA-3′. In contrast, related nucleases including structurally conserved apurinic/apyrimidinic endonuclease 1 (APE1) are non-sequence specific. To investigate mechanisms underlying sequence recognition and catalysis by L1-EN, we solved crystal structures of L1-EN complexed with DNA substrates. This showed that conformational properties of the preferred sequence drive L1-EN’s sequence-specificity and catalysis. Unlike APE1, L1-EN does not bend the DNA helix, but rather causes ‘compression’ near the cleavage site. This provides multiple advantages for L1-EN’s role in retrotransposition including facilitating use of the nicked poly-T DNA strand as a primer for reverse transcription. We also observed two alternative conformations of the scissile bond phosphate, which allowed us to model distinct conformations for a nucleophilic attack and a transition state that are likely applicable to the entire family of nucleases. This work adds to our mechanistic understanding of L1-EN and related nucleases and should facilitate development of L1-EN inhibitors as potential anticancer and antiaging therapeutics.
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Affiliation(s)
- Ian Miller
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | | | | | | | - Andrei V Gudkov
- Genome Protection, Inc., Buffalo, NY 14203, USA.,Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Sergey Korolev
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
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16
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Liu X, Weikum ER, Tilo D, Vinson C, Ortlund EA. Structural basis for glucocorticoid receptor recognition of both unmodified and methylated binding sites, precursors of a modern recognition element. Nucleic Acids Res 2021; 49:8923-8933. [PMID: 34289059 PMCID: PMC8421226 DOI: 10.1093/nar/gkab605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/24/2021] [Accepted: 07/20/2021] [Indexed: 11/20/2022] Open
Abstract
The most common form of DNA methylation involves the addition of a methyl group to a cytosine base in the context of a cytosine–phosphate–guanine (CpG) dinucleotide. Genomes from more primitive organisms are more abundant in CpG sites that, through the process of methylation, deamination and subsequent mutation to thymine–phosphate–guanine (TpG) sites, can produce new transcription factor binding sites. Here, we examined the evolutionary history of the over 36 000 glucocorticoid receptor (GR) consensus binding motifs in the human genome and identified a subset of them in regulatory regions that arose via a deamination and subsequent mutation event. GR can bind to both unmodified and methylated pre-GR binding sequences (GBSs) that contain a CpG site. Our structural analyses show that CpG methylation in a pre-GBS generates a favorable interaction with Arg447 mimicking that made with a TpG in a GBS. This methyl-specific recognition arose 420 million years ago and was conserved during the evolution of GR and likely helps fix the methylation on the relevant cytosines. Our study provides the first genetic, biochemical and structural evidence of high-affinity binding for the likely evolutionary precursor of extant TpG-containing GBS.
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Affiliation(s)
- Xu Liu
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Emily R Weikum
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Desiree Tilo
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Charles Vinson
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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17
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Wan T, Horová M, Beltran DG, Li S, Wong HX, Zhang LM. Structural insights into the functional divergence of WhiB-like proteins in Mycobacterium tuberculosis. Mol Cell 2021; 81:2887-2900.e5. [PMID: 34171298 DOI: 10.1016/j.molcel.2021.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/12/2021] [Accepted: 05/31/2021] [Indexed: 12/12/2022]
Abstract
WhiB7 represents a distinct subclass of transcription factors in the WhiB-Like (Wbl) family, a unique group of iron-sulfur (4Fe-4S] cluster-containing proteins exclusive to the phylum of Actinobacteria. In Mycobacterium tuberculosis (Mtb), WhiB7 interacts with domain 4 of the primary sigma factor (σA4) in the RNA polymerase holoenzyme and activates genes involved in multiple drug resistance and redox homeostasis. Here, we report crystal structures of the WhiB7:σA4 complex alone and bound to its target promoter DNA at 1.55-Å and 2.6-Å resolution, respectively. These structures show how WhiB7 regulates gene expression by interacting with both σA4 and the AT-rich sequence upstream of the -35 promoter DNA via its C-terminal DNA-binding motif, the AT-hook. By combining comparative structural analysis of the two high-resolution σA4-bound Wbl structures with molecular and biochemical approaches, we identify the structural basis of the functional divergence between the two distinct subclasses of Wbl proteins in Mtb.
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Affiliation(s)
- Tao Wan
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Magdaléna Horová
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Daisy Guiza Beltran
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Shanren Li
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Huey-Xian Wong
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Li-Mei Zhang
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
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18
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Lin M, Malik FK, Guo JT. A comparative study of protein-ssDNA interactions. NAR Genom Bioinform 2021; 3:lqab006. [PMID: 33655206 PMCID: PMC7902235 DOI: 10.1093/nargab/lqab006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/24/2020] [Accepted: 01/26/2021] [Indexed: 12/18/2022] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) play crucial roles in DNA replication, recombination and repair, and serve as key players in the maintenance of genomic stability. While a number of SSBs bind single-stranded DNA (ssDNA) non-specifically, the others recognize and bind specific ssDNA sequences. The mechanisms underlying this binding discrepancy, however, are largely unknown. Here, we present a comparative study of protein-ssDNA interactions by annotating specific and non-specific SSBs and comparing structural features such as DNA-binding propensities and secondary structure types of residues in SSB-ssDNA interactions, protein-ssDNA hydrogen bonding and π-π interactions between specific and non-specific SSBs. Our results suggest that protein side chain-DNA base hydrogen bonds are the major contributors to protein-ssDNA binding specificity, while π-π interactions may mainly contribute to binding affinity. We also found the enrichment of aspartate in the specific SSBs, a key feature in specific protein-double-stranded DNA (dsDNA) interactions as reported in our previous study. In addition, no significant differences between specific and non-specific groups with respect of conformational changes upon ssDNA binding were found, suggesting that the flexibility of SSBs plays a lesser role than that of dsDNA-binding proteins in conferring binding specificity.
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Affiliation(s)
- Maoxuan Lin
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Fareeha K Malik
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
- Research Center of Modeling and Simulation, National University of Science and Technology, Islamabad, 44000, Pakistan
| | - Jun-tao Guo
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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19
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Dey U, Sarkar S, Teronpi V, Yella VR, Kumar A. G-quadruplex motifs are functionally conserved in cis-regulatory regions of pathogenic bacteria: An in-silico evaluation. Biochimie 2021; 184:40-51. [PMID: 33548392 DOI: 10.1016/j.biochi.2021.01.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 02/06/2023]
Abstract
The role of G-quadruplexes in the cellular physiology of human pathogenesis is an intriguing area of research. Nonetheless, their functional roles and evolutionary conservation have not been compared comprehensively in pathogenic forms of various bacterial genera and species. In the current in silico study, we addressed the role of G-quadruplex-forming sequences (G4 motifs) in the context of cis-regulation, expression variation, regulatory networks, gene orthology and ontology. Genome-wide screening across seven pathogenic genomes using the G4Hunter tool revealed the significant prevalence of G4 motifs in cis-regulatory regions compared to the intragenic regions. Significant conservation of G4 motifs was observed in the regulatory region of 300 orthologous genes. Further analysis of published ChIP-Seq data (Minch et al., 2015) of 91 DNA-binding proteins of the M. tuberculosis genome revealed significant links between G4 motifs and target sites of transcriptional regulators. Interestingly, the transcription factors entangled with virulence, in specific, CsoR, Rv0081, DevR/DosR, and TetR family are found to have G4 motifs in their target regulatory regions. Overall the current study applies positional-functional relationship computation to delve into the cis-regulation of G-quadruplex structures in the context of gene orthology in pathogenic bacteria.
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Affiliation(s)
- Upalabdha Dey
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, 784028, Assam, India
| | - Sharmilee Sarkar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, 784028, Assam, India
| | - Valentina Teronpi
- Department of Zoology, Pandit Deendayal Upadhyaya Adarsha Mahavidyalaya, Behali, Biswanath, 784184, Assam, India
| | - Venkata Rajesh Yella
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Guntur, 522502, Andhra Pradesh, India.
| | - Aditya Kumar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, 784028, Assam, India.
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20
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Tompkins KJ, Houtti M, Litzau LA, Aird EJ, Everett BA, Nelson AT, Pornschloegl L, Limón-Swanson LK, Evans RL, Evans K, Shi K, Aihara H, Gordon WR. Molecular underpinnings of ssDNA specificity by Rep HUH-endonucleases and implications for HUH-tag multiplexing and engineering. Nucleic Acids Res 2021; 49:1046-1064. [PMID: 33410911 PMCID: PMC7826260 DOI: 10.1093/nar/gkaa1248] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/08/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022] Open
Abstract
Replication initiator proteins (Reps) from the HUH-endonuclease superfamily process specific single-stranded DNA (ssDNA) sequences to initiate rolling circle/hairpin replication in viruses, such as crop ravaging geminiviruses and human disease causing parvoviruses. In biotechnology contexts, Reps are the basis for HUH-tag bioconjugation and a critical adeno-associated virus genome integration tool. We solved the first co-crystal structures of Reps complexed to ssDNA, revealing a key motif for conferring sequence specificity and for anchoring a bent DNA architecture. In combination, we developed a deep sequencing cleavage assay, termed HUH-seq, to interrogate subtleties in Rep specificity and demonstrate how differences can be exploited for multiplexed HUH-tagging. Together, our insights allowed engineering of only four amino acids in a Rep chimera to predictably alter sequence specificity. These results have important implications for modulating viral infections, developing Rep-based genomic integration tools, and enabling massively parallel HUH-tag barcoding and bioconjugation applications.
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Affiliation(s)
- Kassidy J Tompkins
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Mo Houtti
- Department of Computer Science and Engineering, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Lauren A Litzau
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Eric J Aird
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Blake A Everett
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Andrew T Nelson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Leland Pornschloegl
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Lidia K Limón-Swanson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Robert L Evans
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Karen Evans
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Wendy R Gordon
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
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21
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Lara-Gonzalez S, Dantas Machado AC, Rao S, Napoli AA, Birktoft J, Di Felice R, Rohs R, Lawson CL. The RNA Polymerase α Subunit Recognizes the DNA Shape of the Upstream Promoter Element. Biochemistry 2020; 59:4523-4532. [PMID: 33205945 DOI: 10.1021/acs.biochem.0c00571] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We demonstrate here that the α subunit C-terminal domain of Escherichia coli RNA polymerase (αCTD) recognizes the upstream promoter (UP) DNA element via its characteristic minor groove shape and electrostatic potential. In two compositionally distinct crystallized assemblies, a pair of αCTD subunits bind in tandem to the UP element consensus A-tract that is 6 bp in length (A6-tract), each with their arginine 265 guanidinium group inserted into the minor groove. The A6-tract minor groove is significantly narrowed in these crystal structures, as well as in computationally predicted structures of free and bound DNA duplexes derived by Monte Carlo and molecular dynamics simulations, respectively. The negative electrostatic potential of free A6-tract DNA is substantially enhanced compared to that of generic DNA. Shortening the A-tract by 1 bp is shown to "knock out" binding of the second αCTD through widening of the minor groove. Furthermore, in computationally derived structures with arginine 265 mutated to alanine in either αCTD, either with or without the "knockout" DNA mutation, contact with the DNA is perturbed, highlighting the importance of arginine 265 in achieving αCTD-DNA binding. These results demonstrate that the importance of the DNA shape in sequence-dependent recognition of DNA by RNA polymerase is comparable to that of certain transcription factors.
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Affiliation(s)
- Samuel Lara-Gonzalez
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Ana Carolina Dantas Machado
- Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - Satyanarayan Rao
- Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - Andrew A Napoli
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Jens Birktoft
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Rosa Di Felice
- Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States.,Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States.,CNR-NANO Modena, Via Campi 213/A, 41125 Modena, Italy
| | - Remo Rohs
- Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States.,Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States.,Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States.,Department of Computer Science, University of Southern California, Los Angeles, California 90089, United States
| | - Catherine L Lawson
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, New Jersey 08854, United States
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22
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Dantas Machado AC, Cooper BH, Lei X, Di Felice R, Chen L, Rohs R. Landscape of DNA binding signatures of myocyte enhancer factor-2B reveals a unique interplay of base and shape readout. Nucleic Acids Res 2020; 48:8529-8544. [PMID: 32738045 PMCID: PMC7470950 DOI: 10.1093/nar/gkaa642] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/16/2020] [Accepted: 07/22/2020] [Indexed: 01/08/2023] Open
Abstract
Myocyte enhancer factor-2B (MEF2B) has the unique capability of binding to its DNA target sites with a degenerate motif, while still functioning as a gene-specific transcriptional regulator. Identifying its DNA targets is crucial given regulatory roles exerted by members of the MEF2 family and MEF2B's involvement in B-cell lymphoma. Analyzing structural data and SELEX-seq experimental results, we deduced the DNA sequence and shape determinants of MEF2B target sites on a high-throughput basis in vitro for wild-type and mutant proteins. Quantitative modeling of MEF2B binding affinities and computational simulations exposed the DNA readout mechanisms of MEF2B. The resulting binding signature of MEF2B revealed distinct intricacies of DNA recognition compared to other transcription factors. MEF2B uses base readout at its half-sites combined with shape readout at the center of its degenerate motif, where A-tract polarity dictates nuances of binding. The predominant role of shape readout at the center of the core motif, with most contacts formed in the minor groove, differs from previously observed protein-DNA readout modes. MEF2B, therefore, represents a unique protein for studies of the role of DNA shape in achieving binding specificity. MEF2B-DNA recognition mechanisms are likely representative for other members of the MEF2 family.
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Affiliation(s)
- Ana Carolina Dantas Machado
- Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Brendon H Cooper
- Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Xiao Lei
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Rosa Di Felice
- Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
- Department of Physics & Astronomy, University of Southern California, Los Angeles, CA 90089, USA
| | - Lin Chen
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Remo Rohs
- Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
- Department of Physics & Astronomy, University of Southern California, Los Angeles, CA 90089, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
- Department of Computer Science, University of Southern California, Los Angeles, CA 90089, USA
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23
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Structural mechanism for replication origin binding and remodeling by a metazoan origin recognition complex and its co-loader Cdc6. Nat Commun 2020; 11:4263. [PMID: 32848132 PMCID: PMC7450096 DOI: 10.1038/s41467-020-18067-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/03/2020] [Indexed: 12/11/2022] Open
Abstract
Eukaryotic DNA replication initiation relies on the origin recognition complex (ORC), a DNA-binding ATPase that loads the Mcm2–7 replicative helicase onto replication origins. Here, we report cryo-electron microscopy (cryo-EM) structures of DNA-bound Drosophila ORC with and without the co-loader Cdc6. These structures reveal that Orc1 and Orc4 constitute the primary DNA binding site in the ORC ring and cooperate with the winged-helix domains to stabilize DNA bending. A loop region near the catalytic Walker B motif of Orc1 directly contacts DNA, allosterically coupling DNA binding to ORC’s ATPase site. Correlating structural and biochemical data show that DNA sequence modulates DNA binding and remodeling by ORC, and that DNA bending promotes Mcm2–7 loading in vitro. Together, these findings explain the distinct DNA sequence-dependencies of metazoan and S. cerevisiae initiators in origin recognition and support a model in which DNA geometry and bendability contribute to Mcm2–7 loading site selection in metazoans. The origin recognition complex (ORC) is essential for loading the Mcm2–7 replicative helicase onto DNA during DNA replication initiation. Here, the authors describe several cryo-electron microscopy structures of Drosophila ORC bound to DNA and its cofactor Cdc6 and also report an in vitro reconstitution system for Drosophila Mcm2–7 loading, revealing unexpected features of ORC’s DNA binding and remodeling mechanism during Mcm2–7 loading.
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24
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Gallego D, Darré L, Dans PD, Orozco M. VeriNA3d: an R package for nucleic acids data mining. Bioinformatics 2020; 35:5334-5336. [PMID: 31286135 DOI: 10.1093/bioinformatics/btz553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/20/2019] [Accepted: 07/06/2019] [Indexed: 11/12/2022] Open
Abstract
SUMMARY veriNA3d is an R package for the analysis of nucleic acids structural data, with an emphasis in complex RNA structures. In addition to single-structure analyses, veriNA3d also implements functions to handle whole datasets of mmCIF/PDB structures that could be retrieved from public/local repositories. Our package aims to fill a gap in the data mining of nucleic acids structures to produce flexible and high throughput analysis of structural databases. AVAILABILITY AND IMPLEMENTATION http://mmb.irbbarcelona.org/gitlab/dgallego/veriNA3d. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Diego Gallego
- Computational Biology Node, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology.,Department of Biochemistry and Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Leonardo Darré
- Computational Biology Node, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology.,Functional Genomics Laboratory and Biomolecular Simulations Laboratory, Institute Pasteur of Montevideo, Montevideo, Uruguay
| | - Pablo D Dans
- Computational Biology Node, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology
| | - Modesto Orozco
- Computational Biology Node, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology.,Department of Biochemistry and Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain
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25
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Ribeiro J, Ríos-Vera C, Melo F, Schüller A. Calculation of accurate interatomic contact surface areas for the quantitative analysis of non-bonded molecular interactions. Bioinformatics 2020; 35:3499-3501. [PMID: 30698657 PMCID: PMC6748739 DOI: 10.1093/bioinformatics/btz062] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/24/2018] [Accepted: 01/24/2019] [Indexed: 12/02/2022] Open
Abstract
Summary Intra- and intermolecular contact surfaces are routinely calculated for a large array of applications in bioinformatics but are typically approximated from differential solvent accessible surface area calculations and not calculated directly. These approximations do not properly take the effects of neighboring atoms into account and tend to deviate considerably from the true contact surface. We implemented an extension of the original Shrake-Rupley algorithm to accurately estimate interatomic contact surface areas of molecular structures and complexes. Our extended algorithm is able to calculate the contact area of an atom to all nearby atoms by directly calculating overlapping surface patches, taking into account the possible shielding effects of neighboring atoms. Here, we present a versatile software tool and web server for the calculation of contact surface areas, as well as buried surface areas and solvent accessible surface areas (SASA) for different types of biomolecules, such as proteins, nucleic acids and small organic molecules. Detailed results are provided in tab-separated values format for analysis and Protein Databank files for visualization. Direct contact surface area calculation resulted in improved accuracy in a benchmark with a non-redundant set of 245 protein–DNA complexes. SASA-based approximations underestimated protein–DNA contact surfaces on average by 40%. This software tool may be useful for surface-based intra- and intermolecular interaction analyses and scoring function development. Availability and implementation A web server, stand-alone binaries for Linux, MacOS and Windows and C++ source code are freely available from http://schuellerlab.org/dr_sasa/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Judemir Ribeiro
- Department of Molecular Genetics and Microbiology, School of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carlos Ríos-Vera
- Department of Molecular Genetics and Microbiology, School of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Francisco Melo
- Department of Molecular Genetics and Microbiology, School of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Andreas Schüller
- Department of Molecular Genetics and Microbiology, School of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
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26
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Sagendorf JM, Markarian N, Berman HM, Rohs R. DNAproDB: an expanded database and web-based tool for structural analysis of DNA-protein complexes. Nucleic Acids Res 2020; 48:D277-D287. [PMID: 31612957 PMCID: PMC7145614 DOI: 10.1093/nar/gkz889] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/22/2019] [Accepted: 10/01/2019] [Indexed: 11/24/2022] Open
Abstract
DNAproDB (https://dnaprodb.usc.edu) is a web-based database and structural analysis tool that offers a combination of data visualization, data processing and search functionality that improves the speed and ease with which researchers can analyze, access and visualize structural data of DNA–protein complexes. In this paper, we report significant improvements made to DNAproDB since its initial release. DNAproDB now supports any DNA secondary structure from typical B-form DNA to single-stranded DNA to G-quadruplexes. We have updated the structure of our data files to support complex DNA conformations, multiple DNA–protein complexes within a DNAproDB entry and model indexing for analysis of ensemble data. Support for chemically modified residues and nucleotides has been significantly improved along with the addition of new structural features, improved structural moiety assignment and use of more sequence-based annotations. We have redesigned our report pages and search forms to support these enhancements, and the DNAproDB website has been improved to be more responsive and user-friendly. DNAproDB is now integrated with the Nucleic Acid Database, and we have increased our coverage of available Protein Data Bank entries. Our database now contains 95% of all available DNA–protein complexes, making our tools for analysis of these structures accessible to a broad community.
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Affiliation(s)
- Jared M Sagendorf
- Quantitative and Computational Biology, Departments of Biological Sciences, Chemistry, Physics and Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Nicholas Markarian
- Quantitative and Computational Biology, Departments of Biological Sciences, Chemistry, Physics and Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Helen M Berman
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Remo Rohs
- Quantitative and Computational Biology, Departments of Biological Sciences, Chemistry, Physics and Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
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27
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Jha A, Saha S, Ayasolla K, Vashistha H, Malhotra A, Skorecki K, Singhal PC. MiR193a Modulation and Podocyte Phenotype. Cells 2020; 9:cells9041004. [PMID: 32316697 PMCID: PMC7226544 DOI: 10.3390/cells9041004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/08/2020] [Accepted: 04/13/2020] [Indexed: 11/16/2022] Open
Abstract
Apolipoprotein L1 (APOL1)-miR193a axis has been reported to play a role in the maintenance of podocyte homeostasis. In the present study, we analyzed transcription factors relevant to miR193a in human podocytes and their effects on podocytes’ molecular phenotype. The motif scan of the miR193a gene provided information about transcription factors, including YY1, WT1, Sox2, and VDR-RXR heterodimer, which could potentially bind to the miR193a promoter region to regulate miR193a expression. All structure models of these transcription factors and the tertiary structures of the miR193a promoter region were generated and refined using computational tools. The DNA-protein complexes of the miR193a promoter region and transcription factors were created using a docking approach. To determine the modulatory role of miR193a on APOL1 mRNA, the structural components of APOL1 3’ UTR and miR193a-5p were studied. Molecular Dynamic (MD) simulations validated interactions between miR193a and YY1/WT1/Sox2/VDR/APOL1 3′ UTR region. Undifferentiated podocytes (UPDs) displayed enhanced miR193a, YY1, and Sox2 but attenuated WT1, VDR, and APOL1 expressions, whereas differentiated podocytes (DPDs) exhibited attenuated miR193a, YY1, and Sox2 but increased WT1, VDR, APOL1 expressions. Inhibition of miR193a in UPDs enhanced the expression of APOL1 as well as of podocyte molecular markers; on the other hand, DPD-transfected with miR193a plasmid showed downing of APOL1 as well as podocyte molecular markers suggesting a causal relationship between miR193a and podocyte molecular markers. Silencing of YY1 and Sox2 in UPDs decreased the expression of miR193a but increased the expression of VDR, and CD2AP (a marker of DPDs); in contrast, silencing of WT1 and VDR in DPDs enhanced the expression of miR193a, YY1, and Sox2. Since miR193a-downing by Vitamin D receptor (VDR) agonist not only enhanced the mRNA expression of APOL1 but also of podocyte differentiating markers, suggest that down-regulation of miR193a could be used to enhance the expression of podocyte differentiating markers as a therapeutic strategy.
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Affiliation(s)
- Alok Jha
- Institute of Molecular Medicine, Feinstein Institute for Medical Research and Zucker School of Medicine at Hofstra-North well, New York, NY 11030, USA; (A.J.); (S.S.); (K.A.); (H.V.); (A.M.)
| | - Shourav Saha
- Institute of Molecular Medicine, Feinstein Institute for Medical Research and Zucker School of Medicine at Hofstra-North well, New York, NY 11030, USA; (A.J.); (S.S.); (K.A.); (H.V.); (A.M.)
| | - Kamesh Ayasolla
- Institute of Molecular Medicine, Feinstein Institute for Medical Research and Zucker School of Medicine at Hofstra-North well, New York, NY 11030, USA; (A.J.); (S.S.); (K.A.); (H.V.); (A.M.)
| | - Himanshu Vashistha
- Institute of Molecular Medicine, Feinstein Institute for Medical Research and Zucker School of Medicine at Hofstra-North well, New York, NY 11030, USA; (A.J.); (S.S.); (K.A.); (H.V.); (A.M.)
| | - Ashwani Malhotra
- Institute of Molecular Medicine, Feinstein Institute for Medical Research and Zucker School of Medicine at Hofstra-North well, New York, NY 11030, USA; (A.J.); (S.S.); (K.A.); (H.V.); (A.M.)
| | - Karl Skorecki
- Technion – Israel Institute of Technology, and Rambam Health Care Campus, Haifa 2710000, Israel;
| | - Pravin C. Singhal
- Institute of Molecular Medicine, Feinstein Institute for Medical Research and Zucker School of Medicine at Hofstra-North well, New York, NY 11030, USA; (A.J.); (S.S.); (K.A.); (H.V.); (A.M.)
- Correspondence: ; Tel.: +1-516-465-3010; Fax: +1-516-465-3011
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28
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Abstract
Circadian gene expression oscillates over a 24-h period and regulates many genes critical for growth and development in plants. A key component of the circadian clock is the Evening Complex (EC), a transcriptional repressor complex that contains the proteins LUX ARRHYTHMO, EARLY FLOWERING 3, and EARLY FLOWERING 4 (ELF4). By repressing the expression of genes such as PHYTOCHROME INTERACTING FACTOR4 (PIF4), the EC reduces elongation growth. At warmer temperatures, EC activity is lost, promoting thermomorphogenesis via PIF4 expression. The molecular mechanisms underlying EC activity are not well understood. Here, we combined structural studies with extensive in vitro assays to determine the molecular mechanisms of the temperature-dependent EC binding to DNA and demonstrate the critical role of ELF4 in this activity. The Evening Complex (EC), composed of the DNA binding protein LUX ARRHYTHMO (LUX) and two additional proteins EARLY FLOWERING 3 (ELF3) and ELF4, is a transcriptional repressor complex and a core component of the plant circadian clock. In addition to maintaining oscillations in clock gene expression, the EC also participates in temperature and light entrainment, acting as an important environmental sensor and conveying this information to growth and developmental pathways. However, the molecular basis for EC DNA binding specificity and temperature-dependent activity were not known. Here, we solved the structure of the DNA binding domain of LUX in complex with DNA. Residues critical for high-affinity binding and direct base readout were determined and tested via site-directed mutagenesis in vitro and in vivo. Using extensive in vitro DNA binding assays of LUX alone and in complex with ELF3 and ELF4, we demonstrate that, while LUX alone binds DNA with high affinity, the LUX–ELF3 complex is a relatively poor binder of DNA. ELF4 restores binding to the complex. In vitro, the full EC is able to act as a direct thermosensor, with stronger DNA binding at 4 °C and weaker binding at 27 °C. In addition, an excess of ELF4 is able to restore EC binding even at 27 °C. Taken together, these data suggest that ELF4 is a key modulator of thermosensitive EC activity.
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29
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Ray A, Di Felice R. Protein-Mutation-Induced Conformational Changes of the DNA and Nuclease Domain in CRISPR/Cas9 Systems by Molecular Dynamics Simulations. J Phys Chem B 2020; 124:2168-2179. [PMID: 32079396 DOI: 10.1021/acs.jpcb.9b07722] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Class 2 CRISPR (clustered regularly interspaced short palindromic repeats) systems offer a unique protocol for genome editing in eukaryotic cells. The nuclease activity of Cas9 has been harnessed to perform precise genome editing by creating double-strand breaks. However, the nuclease activity of Cas9 can be triggered when there is imperfect complementarity between the RNA guide sequence and an off-target genomic site, which is a major limitation of the CRISPR technique for practical applications. Hence, understanding the binding mechanisms in CRISPR/Cas9 for predicting ways to increase cleavage specificity is a timely research target. One way to understand and tune the binding strength is to study wild-type and mutant Cas9, in complex with a guide RNA and a target DNA. We have performed classical all-atom MD simulations over a cumulative time scale of 13.5 μs of CRISPR/Cas9 ternary complexes with the wild-type Cas9 from Streptococcus pyogenes and three of its mutants: K855A, H982A, and the combination K855A+H982A, selected from the outcome of experimental work. Our results reveal significant structural impact of the mutations, with implications for specificity. We find that the "unwound" part of the nontarget DNA strand exhibits enhanced flexibility in complexes with Cas9 mutants and tries to move away from the HNH/RuvC interface, where it is otherwise stabilized by electrostatic couplings in the wild-type complex. Our findings refine an electrostatic model by which cleavage specificity can be optimized through protein mutations.
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Affiliation(s)
- Angana Ray
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
| | - Rosa Di Felice
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States.,Department of Biological Sciences, Quantitative and Computational Biology Sector, University of Southern California, Los Angeles, California 90089, United States.,CNR Institute of Nanosciences, Via Campi 213/A, 41125 Modena, Italy
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30
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Kribelbauer JF, Lu XJ, Rohs R, Mann RS, Bussemaker HJ. Toward a Mechanistic Understanding of DNA Methylation Readout by Transcription Factors. J Mol Biol 2019:S0022-2836(19)30617-5. [PMID: 31689433 DOI: 10.1016/j.jmb.2019.10.021] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/23/2019] [Accepted: 10/24/2019] [Indexed: 01/09/2023]
Abstract
Epigenetic DNA modification impacts gene expression, but the underlying molecular mechanisms are only partly understood. Adding a methyl group to a cytosine base locally modifies the structural features of DNA in multiple ways, which may change the interaction with DNA-binding transcription factors (TFs) and trigger a cascade of downstream molecular events. Cells can be probed using various functional genomics assays, but it is difficult to disentangle the confounded effects of DNA modification on TF binding, chromatin accessibility, intranuclear variation in local TF concentration, and rate of transcription. Here we discuss how high-throughput in vitro profiling of protein-DNA interactions has enabled comprehensive characterization and quantification of the methylation sensitivity of TFs. Despite the limited structural data for DNA containing methylated cytosine, automated analysis of structural information in the Protein Data Bank (PDB) shows how 5-methylcytosine (5mC) can be recognized in various ways by amino acid side chains. We discuss how a context-dependent effect of methylation on DNA groove geometry can affect DNA binding by homeodomain proteins and how principled modeling of ChIP-seq data can overcome the confounding that makes the interpretation of in vivo data challenging. The emerging picture is that epigenetic modifications affect TF binding in a highly context-specific manner, with a direction and effect size that depend critically on their position within the TF binding site and the amino acid sequence of the TF. With this improved mechanistic knowledge, we have come closer to understanding how cells use DNA modification to acquire, retain, and change their identity.
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Affiliation(s)
- Judith F Kribelbauer
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Xiang-Jun Lu
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Remo Rohs
- Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA; Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA; Department of Physics & Astronomy, University of Southern California, Los Angeles, CA 90089, USA; Department of Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Richard S Mann
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA.
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31
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Aragón E, Wang Q, Zou Y, Morgani SM, Ruiz L, Kaczmarska Z, Su J, Torner C, Tian L, Hu J, Shu W, Agrawal S, Gomes T, Márquez JA, Hadjantonakis AK, Macias MJ, Massagué J. Structural basis for distinct roles of SMAD2 and SMAD3 in FOXH1 pioneer-directed TGF-β signaling. Genes Dev 2019; 33:1506-1524. [PMID: 31582430 PMCID: PMC6824466 DOI: 10.1101/gad.330837.119] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/03/2019] [Indexed: 01/08/2023]
Abstract
TGF-β receptors phosphorylate SMAD2 and SMAD3 transcription factors, which then form heterotrimeric complexes with SMAD4 and cooperate with context-specific transcription factors to activate target genes. Here we provide biochemical and structural evidence showing that binding of SMAD2 to DNA depends on the conformation of the E3 insert, a structural element unique to SMAD2 and previously thought to render SMAD2 unable to bind DNA. Based on this finding, we further delineate TGF-β signal transduction by defining distinct roles for SMAD2 and SMAD3 with the forkhead pioneer factor FOXH1 as a partner in the regulation of differentiation genes in mouse mesendoderm precursors. FOXH1 is prebound to target sites in these loci and recruits SMAD3 independently of TGF-β signals, whereas SMAD2 remains predominantly cytoplasmic in the basal state and set to bind SMAD4 and join SMAD3:FOXH1 at target promoters in response to Nodal TGF-β signals. The results support a model in which signal-independent binding of SMAD3 and FOXH1 prime mesendoderm differentiation gene promoters for activation, and signal-driven SMAD2:SMAD4 binds to promoters that are preloaded with SMAD3:FOXH1 to activate transcription.
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Affiliation(s)
- Eric Aragón
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Qiong Wang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Yilong Zou
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Sophie M Morgani
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Lidia Ruiz
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | | | - Jie Su
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Carles Torner
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Lin Tian
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Jing Hu
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Weiping Shu
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Saloni Agrawal
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Tiago Gomes
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | | | | | - Maria J Macias
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain.,ICREA, 08010 Barcelona, Spain
| | - Joan Massagué
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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32
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Comoglio F, Simonatto M, Polletti S, Liu X, Smale ST, Barozzi I, Natoli G. Dissection of acute stimulus-inducible nucleosome remodeling in mammalian cells. Genes Dev 2019; 33:1159-1174. [PMID: 31371436 PMCID: PMC6719622 DOI: 10.1101/gad.326348.119] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/03/2019] [Indexed: 12/22/2022]
Abstract
Accessibility of the genomic regulatory information is largely controlled by the nucleosome-organizing activity of transcription factors (TFs). While stimulus-induced TFs bind to genomic regions that are maintained accessible by lineage-determining TFs, they also increase accessibility of thousands of cis-regulatory elements. Nucleosome remodeling events underlying such changes and their interplay with basal positioning are unknown. Here, we devised a novel quantitative framework discriminating different types of nucleosome remodeling events in micrococcal nuclease ChIP-seq (chromatin immunoprecipitation [ChIP] combined with high-throughput sequencing) data sets and used it to analyze nucleosome dynamics at stimulus-regulated cis-regulatory elements. At enhancers, remodeling preferentially affected poorly positioned nucleosomes while sparing well-positioned nucleosomes flanking the enhancer core, indicating that inducible TFs do not suffice to overrule basal nucleosomal organization maintained by lineage-determining TFs. Remodeling events appeared to be combinatorially driven by multiple TFs, with distinct TFs showing, however, different remodeling efficiencies. Overall, these data provide a systematic view of the impact of stimulation on nucleosome organization and genome accessibility in mammalian cells.
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Affiliation(s)
- Federico Comoglio
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
- Department of Hematology, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Marta Simonatto
- Humanitas University (Hunimed), Pieve Emanuele, Milano 20090, Italy
| | - Sara Polletti
- Humanitas University (Hunimed), Pieve Emanuele, Milano 20090, Italy
| | - Xin Liu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles (UCLA), Los Angeles, California 90095, USA
| | - Stephen T Smale
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles (UCLA), Los Angeles, California 90095, USA
| | - Iros Barozzi
- Department of Surgery and Cancer, Imperial College London, London W12 00N, United Kingdom
| | - Gioacchino Natoli
- Humanitas University (Hunimed), Pieve Emanuele, Milano 20090, Italy
- Humanitas Istituto di Ricovero e Cura a Carattere Scientifico, Rozzano, Milano 20089, Italy
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33
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Ciges-Tomas JR, Alite C, Humphrey S, Donderis J, Bowring J, Salvatella X, Penadés JR, Marina A. The structure of a polygamous repressor reveals how phage-inducible chromosomal islands spread in nature. Nat Commun 2019; 10:3676. [PMID: 31417084 PMCID: PMC6695447 DOI: 10.1038/s41467-019-11504-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 07/17/2019] [Indexed: 11/10/2022] Open
Abstract
Stl is a master repressor encoded by Staphylococcus aureus pathogenicity islands (SaPIs) that maintains integration of these elements in the bacterial chromosome. After infection or induction of a resident helper phage, SaPIs are de-repressed by specific interactions of phage proteins with Stl. SaPIs have evolved a fascinating mechanism to ensure their promiscuous transfer by targeting structurally unrelated proteins performing identically conserved functions for the phage. Here we decipher the molecular mechanism of this elegant strategy by determining the structure of SaPIbov1 Stl alone and in complex with two structurally unrelated dUTPases from different S. aureus phages. Remarkably, SaPIbov1 Stl has evolved different domains implicated in DNA and partner recognition specificity. This work presents the solved structure of a SaPI repressor protein and the discovery of a modular repressor that acquires multispecificity through domain recruiting. Our results establish the mechanism that allows widespread dissemination of SaPIs in nature.
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Affiliation(s)
- J Rafael Ciges-Tomas
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Valencia, 46010, Spain
| | - Christian Alite
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Valencia, 46010, Spain
| | - Suzanne Humphrey
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - J Donderis
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Valencia, 46010, Spain
| | - Janine Bowring
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Xavier Salvatella
- ICREA and Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, 08010, Spain
| | - José R Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK.
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Valencia, 46010, Spain.
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34
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Agarwal S, Cho TY. Biochemical and structural characterization of a novel cooperative binding mode by Pit-1 with CATT repeats in the macrophage migration inhibitory factor promoter. Nucleic Acids Res 2019; 46:929-941. [PMID: 29186613 PMCID: PMC5778499 DOI: 10.1093/nar/gkx1183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/14/2017] [Indexed: 12/25/2022] Open
Abstract
Overexpression of the proinflammatory cytokine macrophage migration inhibitory factor (MIF) is linked to a number of autoimmune diseases and cancer. MIF production has been correlated to the number of CATT repeats in a microsatellite region upstream of the MIF gene. We have characterized the interaction of pituitary-specific positive transcription factor 1 (Pit-1) with a portion of the MIF promoter region flanking a microsatellite polymorphism (-794 CATT5-8). Using fluorescence anisotropy, we quantified tight complex formation between Pit-1 and an oligonucleotide consisting of eight consecutive CATT repeats (8xCATT) with an apparent Kd of 35 nM. Using competition experiments we found a 23 base pair oligonucleotide with 4xCATT repeats to be the minimum DNA sequence necessary for high affinity interaction with Pit-1. The stoichiometry of the Pit-1 DNA interaction was determined to be 2:1 and binding is cooperative in nature. We subsequently structurally characterized the complex and discovered a completely novel binding mode for Pit-1 in contrast to previously described Pit-1 complex structures. The affinity of Pit-1 for the CATT target sequence was found to be highly dependent on cooperativity. This work lays the groundwork for understanding transcriptional regulation of MIF and pursuing Pit-1 as a therapeutic target to treat MIF-mediated inflammatory disorders.
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Affiliation(s)
- Sorabh Agarwal
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Thomas Yoonsang Cho
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA.,Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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35
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Poddar S, Chakravarty D, Chakrabarti P. Structural changes in DNA-binding proteins on complexation. Nucleic Acids Res 2019. [PMID: 29534202 PMCID: PMC6283420 DOI: 10.1093/nar/gky170] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Characterization and prediction of the DNA-biding regions in proteins are essential for our understanding of how proteins recognize/bind DNA. We analyze the unbound (U) and the bound (B) forms of proteins from the protein–DNA docking benchmark that contains 66 binary protein–DNA complexes along with their unbound counterparts. Proteins binding DNA undergo greater structural changes on complexation (in particular, those in the enzyme category) than those involved in protein–protein interactions (PPI). While interface atoms involved in PPI exhibit an increase in their solvent-accessible surface area (ASA) in the bound form in the majority of the cases compared to the unbound interface, protein–DNA interactions indicate increase and decrease in equal measure. In 25% structures, the U form has missing residues which are located in the interface in the B form. The missing atoms contribute more toward the buried surface area compared to other interface atoms. Lys, Gly and Arg are prominent in disordered segments that get ordered in the interface on complexation. In going from U to B, there may be an increase in coil and helical content at the expense of turns and strands. Consideration of flexibility cannot distinguish the interface residues from the surface residues in the U form.
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Affiliation(s)
- Sayan Poddar
- Department of Biochemistry, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Devlina Chakravarty
- Bioinformatics Centre, Bose Institute, P1/12CIT Scheme VIIM, Kolkata 700054, India
| | - Pinak Chakrabarti
- Department of Biochemistry, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata 700054, India.,Bioinformatics Centre, Bose Institute, P1/12CIT Scheme VIIM, Kolkata 700054, India
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36
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Lambert SA, Yang AWH, Sasse A, Cowley G, Albu M, Caddick MX, Morris QD, Weirauch MT, Hughes TR. Similarity regression predicts evolution of transcription factor sequence specificity. Nat Genet 2019; 51:981-989. [PMID: 31133749 DOI: 10.1038/s41588-019-0411-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 04/04/2019] [Indexed: 11/09/2022]
Abstract
Transcription factor (TF) binding specificities (motifs) are essential for the analysis of gene regulation. Accurate prediction of TF motifs is critical, because it is infeasible to assay all TFs in all sequenced eukaryotic genomes. There is ongoing controversy regarding the degree of motif diversification among related species that is, in part, because of uncertainty in motif prediction methods. Here we describe similarity regression, a significantly improved method for predicting motifs, which we use to update and expand the Cis-BP database. Similarity regression inherently quantifies TF motif evolution, and shows that previous claims of near-complete conservation of motifs between human and Drosophila are inflated, with nearly half of the motifs in each species absent from the other, largely due to extensive divergence in C2H2 zinc finger proteins. We conclude that diversification in DNA-binding motifs is pervasive, and present a new tool and updated resource to study TF diversity and gene regulation across eukaryotes.
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Affiliation(s)
- Samuel A Lambert
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Ally W H Yang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Alexander Sasse
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Gwendolyn Cowley
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Mihai Albu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Mark X Caddick
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Quaid D Morris
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Canadian Institutes For Advanced Research (CIFAR) Artificial Intelligence Chair, Vector Institute, Toronto, Ontario, Canada.,Ontario Institute of Cancer Research, Toronto, Ontario, Canada
| | - Matthew T Weirauch
- Divisions of Biomedical Informatics and Developmental Biology, Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Timothy R Hughes
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. .,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada. .,CIFAR, Toronto, Ontario, Canada.
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37
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Rogers JM, Waters CT, Seegar TCM, Jarrett SM, Hallworth AN, Blacklow SC, Bulyk ML. Bispecific Forkhead Transcription Factor FoxN3 Recognizes Two Distinct Motifs with Different DNA Shapes. Mol Cell 2019; 74:245-253.e6. [PMID: 30826165 PMCID: PMC6474805 DOI: 10.1016/j.molcel.2019.01.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 12/17/2018] [Accepted: 01/11/2019] [Indexed: 12/13/2022]
Abstract
Transcription factors (TFs) control gene expression by binding DNA recognition sites in genomic regulatory regions. Although most forkhead TFs recognize a canonical forkhead (FKH) motif, RYAAAYA, some forkheads recognize a completely different (FHL) motif, GACGC. Bispecific forkhead proteins recognize both motifs, but the molecular basis for bispecific DNA recognition is not understood. We present co-crystal structures of the FoxN3 DNA binding domain bound to the FKH and FHL sites, respectively. FoxN3 adopts a similar conformation to recognize both motifs, making contacts with different DNA bases using the same amino acids. However, the DNA structure is different in the two complexes. These structures reveal how a single TF binds two unrelated DNA sequences and the importance of DNA shape in the mechanism of bispecific recognition.
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Affiliation(s)
- Julia M Rogers
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA
| | - Colin T Waters
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Tom C M Seegar
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Sanchez M Jarrett
- Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA 02138, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Amelia N Hallworth
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Stephen C Blacklow
- Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA; Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA 02138, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA.
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA; Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA 02138, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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38
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Computational approaches to macromolecular interactions in the cell. Curr Opin Struct Biol 2019; 55:59-65. [PMID: 30999240 DOI: 10.1016/j.sbi.2019.03.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 03/08/2019] [Indexed: 12/15/2022]
Abstract
Structural modeling of a cell is an evolving strategic direction in computational structural biology. It takes advantage of new powerful modeling techniques, deeper understanding of fundamental principles of molecular structure and assembly, and rapid growth of the amount of structural data generated by experimental techniques. Key modeling approaches to principal types of macromolecular assemblies in a cell already exist. The main challenge, along with the further development of these modeling approaches, is putting them together in a consistent, unified whole cell model. This opinion piece addresses the fundamental aspects of modeling macromolecular assemblies in a cell, and the state-of-the-art in modeling of the principal types of such assemblies.
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39
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Chen Y, Liu H, Yang C, Gao Y, Yu X, Chen X, Cui R, Zheng L, Li S, Li X, Ma J, Huang Z, Li J, Gan J. Structure of the error-prone DNA ligase of African swine fever virus identifies critical active site residues. Nat Commun 2019; 10:387. [PMID: 30674878 PMCID: PMC6344480 DOI: 10.1038/s41467-019-08296-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 12/27/2018] [Indexed: 11/09/2022] Open
Abstract
African swine fever virus (ASFV) is contagious and can cause highly lethal disease in pigs. ASFV DNA ligase (AsfvLIG) is one of the most error-prone ligases identified to date; it catalyzes DNA joining reaction during DNA repair process of ASFV and plays important roles in mutagenesis of the viral genome. Here, we report four AsfvLIG:DNA complex structures and demonstrate that AsfvLIG has a unique N-terminal domain (NTD) that plays critical roles in substrate binding and catalytic complex assembly. In combination with mutagenesis, in vitro binding and catalytic assays, our study reveals that four unique active site residues (Asn153 and Leu211 of the AD domain; Leu402 and Gln403 of the OB domain) are crucial for the catalytic efficiency of AsfvLIG. These unique structural features can serve as potential targets for small molecule design, which could impair genome repair in ASFV and help combat this virus in the future.
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Affiliation(s)
- Yiqing Chen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 200433, Shanghai, China
| | - Hehua Liu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 200433, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, 200433, Shanghai, China
| | - Chun Yang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 200433, Shanghai, China
| | - Yanqing Gao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 200433, Shanghai, China
| | - Xiang Yu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 200433, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, 200433, Shanghai, China
| | - Xi Chen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 200433, Shanghai, China
| | - Ruixue Cui
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, 200433, Shanghai, China
| | - Lina Zheng
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, 200433, Shanghai, China
| | - Suhua Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 200433, Shanghai, China
| | - Xuhang Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, 200433, Shanghai, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, 200433, Shanghai, China
| | - Zhen Huang
- College of Life Sciences, Sichuan University, 610041, Chengdu, China. .,Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA.
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 200433, Shanghai, China. .,Department of Neurology, Huashan Hospital, Fudan University, 200040, Shanghai, China.
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 200433, Shanghai, China.
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40
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Corona RI, Sudarshan S, Aluru S, Guo JT. An SVM-based method for assessment of transcription factor-DNA complex models. BMC Bioinformatics 2018; 19:506. [PMID: 30577740 PMCID: PMC6302363 DOI: 10.1186/s12859-018-2538-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Background Atomic details of protein-DNA complexes can provide insightful information for better understanding of the function and binding specificity of DNA binding proteins. In addition to experimental methods for solving protein-DNA complex structures, protein-DNA docking can be used to predict native or near-native complex models. A docking program typically generates a large number of complex conformations and predicts the complex model(s) based on interaction energies between protein and DNA. However, the prediction accuracy is hampered by current approaches to model assessment, especially when docking simulations fail to produce any near-native models. Results We present here a Support Vector Machine (SVM)-based approach for quality assessment of the predicted transcription factor (TF)-DNA complex models. Besides a knowledge-based protein-DNA interaction potential DDNA3, we applied several structural features that have been shown to play important roles in binding specificity between transcription factors and DNA molecules to quality assessment of complex models. To address the issue of unbalanced positive and negative cases in the training dataset, we applied hard-negative mining, an iterative training process that selects an initial training dataset by combining all of the positive cases and a random sample from the negative cases. Results show that the SVM model greatly improves prediction accuracy (84.2%) over two knowledge-based protein-DNA interaction potentials, orientation potential (60.8%) and DDNA3 (68.4%). The improvement is achieved through reducing the number of false positive predictions, especially for the hard docking cases, in which a docking algorithm fails to produce any near-native complex models. Conclusions A learning-based SVM scoring model with structural features for specific protein-DNA binding and an atomic-level protein-DNA interaction potential DDNA3 significantly improves prediction accuracy of complex models by successfully identifying cases without near-native structural models. Electronic supplementary material The online version of this article (10.1186/s12859-018-2538-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rosario I Corona
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA
| | - Sanjana Sudarshan
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA
| | - Srinivas Aluru
- School of Computational Science and Engineering, Georgia Institute of Technology, 266 Ferst Drive, Atlanta, GA, 30332, USA
| | - Jun-Tao Guo
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA.
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41
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Ray S, Tillo D, Assad N, Ufot A, Deppmann C, Durell SR, Porollo A, Vinson C. Replacing C189 in the bZIP domain of Zta with S, T, V, or A changes DNA binding specificity to four types of double-stranded DNA. Biochem Biophys Res Commun 2018; 501:905-912. [PMID: 29772230 DOI: 10.1016/j.bbrc.2018.05.080] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 05/13/2018] [Indexed: 11/15/2022]
Abstract
Zta is a bZIP transcription factor (TF) in the Epstein-Barr virus that binds unmethylated and methylated DNA sequences. Substitution of cysteine 189 of Zta to serine (Zta(C189S)) results in a virus that is unable to execute the lytic cycle, which was attributed to a change in binding to methylated DNA sequences. To learn more about the role of this position in defining sequence-specific DNA binding, we mutated cysteine 189 to four other amino acids, producing Zta(C189S), Zta(C189T), Zta(C189A), and Zta(C189V) mutants. Zta and mutants were used in protein binding microarray (PBM) experiments to evaluate sequence-specific DNA binding to four types of double-stranded DNA (dsDNA): 1) with cytosine in both strands (DNA(C|C)), 2) with 5-methylcytosine (5mC) in one strand and cytosine in the second strand (DNA(5mC|C)), 3) with 5-hydroxymethylcytosine (5hmC) in one strand and cytosine in the second strand (DNA(5hmC|C)), and 4) with both cytosines in all CG dinucleotides containing 5mC (DNA(5mCG)). Zta(C189S) and Zta(C189T) bound the TRE (AP-1) motif (TGAG/CTCA) more strongly than wild-type Zta, while binding to other sequences, including the C/EBP half site GCAA was reduced. Binding of Zta(C189S) and Zta(C189T) to DNA containing modified cytosines (DNA(5mC|C), DNA(5hmC|C), and DNA(5mCG)) was reduced compared to Zta. Zta(C189A) and Zta(C189V) had higher non-specific binding to all four types of DNA. Our data suggests that position C189 in Zta impacts sequence-specific binding to DNA containing modified and unmodified cytosine.
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Affiliation(s)
- Sreejana Ray
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Desiree Tillo
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nima Assad
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Aniekanabasi Ufot
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Christopher Deppmann
- Department of Biology, University of Virginia, Charlottesville, VA, 22903, USA; Department of Cell Biology, University of Virginia, Charlottesville, VA, 22903, USA; Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22903, USA
| | - Stewart R Durell
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Aleksey Porollo
- Center for Autoimmune Genomics and Etiology and Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Charles Vinson
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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Holden JK, Cunningham CN. Targeting the Hippo Pathway and Cancer through the TEAD Family of Transcription Factors. Cancers (Basel) 2018; 10:cancers10030081. [PMID: 29558384 PMCID: PMC5876656 DOI: 10.3390/cancers10030081] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/15/2018] [Accepted: 03/16/2018] [Indexed: 12/11/2022] Open
Abstract
The Hippo pathway is a critical transcriptional signaling pathway that regulates cell growth, proliferation and organ development. The transcriptional enhanced associate domain (TEAD) protein family consists of four paralogous transcription factors that function to modulate gene expression in response to the Hippo signaling pathway. Transcriptional activation of these proteins occurs upon binding to the co-activator YAP/TAZ whose entry into the nucleus is regulated by Lats1/2 kinase. In recent years, it has become apparent that the dysregulation and/or overexpression of Hippo pathway effectors is implicated in a wide range of cancers, including prostate, gastric and liver cancer. A large body of work has been dedicated to understanding the therapeutic potential of modulating the phosphorylation and localization of YAP/TAZ. However, YAP/TAZ are considered to be natively unfolded and may be intractable as drug targets. Therefore, TEAD proteins present themselves as an excellent therapeutic target for intervention of the Hippo pathway. This review summarizes the functional role of TEAD proteins in cancer and assesses the therapeutic potential of antagonizing TEAD function in vivo.
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Affiliation(s)
- Jeffrey K Holden
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, CA 94080, USA.
| | - Christian N Cunningham
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, CA 94080, USA.
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43
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Chiu TP, Rao S, Mann RS, Honig B, Rohs R. Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein-DNA binding. Nucleic Acids Res 2017; 45:12565-12576. [PMID: 29040720 PMCID: PMC5716191 DOI: 10.1093/nar/gkx915] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 09/28/2017] [Indexed: 12/16/2022] Open
Abstract
Protein–DNA binding is a fundamental component of gene regulatory processes, but it is still not completely understood how proteins recognize their target sites in the genome. Besides hydrogen bonding in the major groove (base readout), proteins recognize minor-groove geometry using positively charged amino acids (shape readout). The underlying mechanism of DNA shape readout involves the correlation between minor-groove width and electrostatic potential (EP). To probe this biophysical effect directly, rather than using minor-groove width as an indirect measure for shape readout, we developed a methodology, DNAphi, for predicting EP in the minor groove and confirmed the direct role of EP in protein–DNA binding using massive sequencing data. The DNAphi method uses a sliding-window approach to mine results from non-linear Poisson–Boltzmann (NLPB) calculations on DNA structures derived from all-atom Monte Carlo simulations. We validated this approach, which only requires nucleotide sequence as input, based on direct comparison with NLPB calculations for available crystal structures. Using statistical machine-learning approaches, we showed that adding EP as a biophysical feature can improve the predictive power of quantitative binding specificity models across 27 transcription factor families. High-throughput prediction of EP offers a novel way to integrate biophysical and genomic studies of protein–DNA binding.
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Affiliation(s)
- Tsu-Pei Chiu
- Computational Biology and Bioinformatics Program, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Satyanarayan Rao
- Computational Biology and Bioinformatics Program, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Richard S Mann
- Departments of Systems Biology and Biochemistry & Molecular Biophysics, Mortimer B. Zuckerman Institute, Columbia University, New York, NY 10032, USA
| | - Barry Honig
- Departments of Systems Biology and Biochemistry & Molecular Biophysics, Mortimer B. Zuckerman Institute, Columbia University, New York, NY 10032, USA.,Howard Hughes Medical Institute, New York, NY 10032, USA
| | - Remo Rohs
- Computational Biology and Bioinformatics Program, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
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44
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Tillo D, Ray S, Syed KS, Gaylor MR, He X, Wang J, Assad N, Durell SR, Porollo A, Weirauch MT, Vinson C. The Epstein-Barr Virus B-ZIP Protein Zta Recognizes Specific DNA Sequences Containing 5-Methylcytosine and 5-Hydroxymethylcytosine. Biochemistry 2017; 56:6200-6210. [PMID: 29072898 DOI: 10.1021/acs.biochem.7b00741] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The Epstein-Barr virus (EBV) B-ZIP transcription factor Zta binds to many DNA sequences containing methylated CG dinucleotides. Using protein binding microarrays (PBMs), we analyzed the sequence specific DNA binding of Zta to four kinds of double-stranded DNA (dsDNA): (1) DNA containing cytosine in both strands, (2) DNA with 5-methylcytosine (5mC) in one strand and cytosine in the second strand, (3) DNA with 5-hydroxymethylcytosine (5hmC) in one strand and cytosine in the second strand, and (4) DNA in which both cytosines in all CG dinucleotides contain 5mC. We compared these data to PBM data for three additional B-ZIP proteins (CREB1 and CEBPB homodimers and cJun|cFos heterodimers). With cytosine, Zta binds the TRE motif TGAC/GTCA as previously reported. With CG dinucleotides containing 5mC on both strands, many TRE motif variants containing a methylated CG dinucleotide at two positions in the motif, such as MGAGTCA and TGAGMGA (where M = 5mC), were preferentially bound. 5mC inhibits binding of Zta to both TRE motif half-sites GTCA and CTCA. Like the CREB1 homodimer, the Zta homodimer and the cJun|cFos heterodimer more strongly bind the C/EBP half-site tetranucleotide GCAA when it contains 5mC. Zta also binds dsDNA sequences containing 5hmC in one strand, although the effect is less dramatic than that observed for 5mC. Our results identify new DNA sequences that are well-bound by the viral B-ZIP protein Zta only when they contain 5mC or 5hmC, uncovering the potential for discovery of new viral and host regulatory programs controlled by EBV.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Aleksey Porollo
- Center for Autoimmune Genomics and Etiology and Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, and Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, Ohio 45229, United States
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology and Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, and Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, Ohio 45229, United States
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45
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Pradhan S, Mattaparthi VSK. Structural dynamics and interactions of Xeroderma pigmentosum complementation group A (XPA98–210) with damaged DNA. J Biomol Struct Dyn 2017; 36:3341-3353. [DOI: 10.1080/07391102.2017.1388285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Sushmita Pradhan
- Molecular Modelling and Simulation Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784 028, Assam, India
| | - Venkata Satish Kumar Mattaparthi
- Molecular Modelling and Simulation Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784 028, Assam, India
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46
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Li J, Dantas Machado AC, Guo M, Sagendorf JM, Zhou Z, Jiang L, Chen X, Wu D, Qu L, Chen Z, Chen L, Rohs R, Chen Y. Structure of the Forkhead Domain of FOXA2 Bound to a Complete DNA Consensus Site. Biochemistry 2017. [PMID: 28644006 DOI: 10.1021/acs.biochem.7b00211] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
FOXA2, a member of the forkhead family of transcription factors, plays essential roles in liver development and bile acid homeostasis. In this study, we report a 2.8 Å co-crystal structure of the FOXA2 DNA-binding domain (FOXA2-DBD) bound to a DNA duplex containing a forkhead consensus binding site (GTAAACA). The FOXA2-DBD adopts the canonical winged-helix fold, with helix H3 and wing 1 regions mainly mediating the DNA recognition. Although the wing 2 region was not defined in the structure, isothermal titration calorimetry assays suggested that this region was required for optimal DNA binding. Structure comparison with the FOXA3-DBD bound to DNA revealed more major groove contacts and fewer minor groove contacts in the FOXA2 structure than in the FOXA3 structure. Structure comparison with the FOXO1-DBD bound to DNA showed that different forkhead proteins could induce different DNA conformations upon binding to identical DNA sequences. Our findings provide the structural basis for FOXA2 protein binding to a consensus forkhead site and elucidate how members of the forkhead protein family bind different DNA sites.
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Affiliation(s)
- Jun Li
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China.,State Key Laboratory of Medical Genetics and College of Life Science, Central South University , Changsha, Hunan 410008, China
| | - Ana Carolina Dantas Machado
- Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States.,Department of Physics and Astronomy and Department of Computer Science, University of Southern California , Los Angeles, California 90089, United States
| | - Ming Guo
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China
| | - Jared M Sagendorf
- Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States.,Department of Physics and Astronomy and Department of Computer Science, University of Southern California , Los Angeles, California 90089, United States
| | - Zhan Zhou
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China
| | - Longying Jiang
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China
| | - Xiaojuan Chen
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China.,State Key Laboratory of Medical Genetics and College of Life Science, Central South University , Changsha, Hunan 410008, China
| | - Daichao Wu
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China
| | - Lingzhi Qu
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China
| | - Zhuchu Chen
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China
| | - Lin Chen
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China.,Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Remo Rohs
- Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States.,Department of Physics and Astronomy and Department of Computer Science, University of Southern California , Los Angeles, California 90089, United States
| | - Yongheng Chen
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China.,State Key Laboratory of Medical Genetics and College of Life Science, Central South University , Changsha, Hunan 410008, China.,Collaborative Innovation Center for Cancer Medicine , Guangzhou, Guangdong 510060, China
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