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Richardson W, Kang GW, Lee HJ, Kwon KM, Kim S, Kim HJ. Chasing the structural diversity of the transcription regulator Mycobacterium tuberculosis HigA2. IUCRJ 2021; 8:823-832. [PMID: 34584743 PMCID: PMC8420761 DOI: 10.1107/s2052252521007715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/28/2021] [Indexed: 06/13/2023]
Abstract
Transcription factors are the primary regulators of gene expression and recognize specific DNA sequences under diverse physiological conditions. Although they are vital for many important cellular processes, it remains unclear when and how transcription factors and DNA interact. The antitoxin from a toxin-antitoxin system is an example of negative transcriptional autoregulation: during expression of the cognate toxin it is suppressed through binding to a specific DNA sequence. In the present study, the antitoxin HigA2 from Mycobacterium tuberculosis M37Rv was structurally examined. The crystal structure of M. tuberculosis HigA2 comprises three sections: an N-terminal autocleavage region, an α-helix bundle which contains an HTH motif, and a C-terminal β-lid. The N-terminal region is responsible for toxin binding, but was shown to cleave spontaneously in its absence. The HTH motif performs a key role in DNA binding, with the C-terminal β-lid influencing the interaction by mediating the distance between the motifs. However, M. tuberculosis HigA2 exhibits a unique coordination of the HTH motif and no DNA-binding activity is detected. Three crystal structures of M. tuberculosis HigA2 show a flexible alignment of the HTH motif, which implies that the motif undergoes structural rearrangement to interact with DNA. This study reveals the molecular mechanisms of how transcription factors interact with partner proteins or DNA.
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Affiliation(s)
- William Richardson
- Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
| | - Gyun Won Kang
- College of Pharmacy, Woosuk University, Wanju 55338, Republic of Korea
| | - Hee Joong Lee
- College of Pharmacy, Woosuk University, Wanju 55338, Republic of Korea
| | - Kang Mu Kwon
- College of Pharmacy, Woosuk University, Wanju 55338, Republic of Korea
| | - Saron Kim
- College of Pharmacy, Woosuk University, Wanju 55338, Republic of Korea
| | - Hyo Jung Kim
- Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
- College of Pharmacy, Woosuk University, Wanju 55338, Republic of Korea
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Kushwaha R, Downie AB, Payne CM. Uses of phage display in agriculture: sequence analysis and comparative modeling of late embryogenesis abundant client proteins suggest protein-nucleic acid binding functionality. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2013; 2013:470390. [PMID: 23956788 PMCID: PMC3727180 DOI: 10.1155/2013/470390] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 04/02/2013] [Indexed: 11/17/2022]
Abstract
A group of intrinsically disordered, hydrophilic proteins-Late Embryogenesis Abundant (LEA) proteins-has been linked to survival in plants and animals in periods of stress, putatively through safeguarding enzymatic function and prevention of aggregation in times of dehydration/heat. Yet despite decades of effort, the molecular-level mechanisms defining this protective function remain unknown. A recent effort to understand LEA functionality began with the unique application of phage display, wherein phage display and biopanning over recombinant Seed Maturation Protein homologs from Arabidopsis thaliana and Glycine max were used to retrieve client proteins at two different temperatures, with one intended to represent heat stress. From this previous study, we identified 21 client proteins for which clones were recovered, sometimes repeatedly. Here, we use sequence analysis and homology modeling of the client proteins to ascertain common sequence and structural properties that may contribute to binding affinity with the protective LEA protein. Our methods uncover what appears to be a predilection for protein-nucleic acid interactions among LEA client proteins, which is suggestive of subcellular residence. The results from this initial computational study will guide future efforts to uncover the protein protective mechanisms during heat stress, potentially leading to phage-display-directed evolution of synthetic LEA molecules.
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Affiliation(s)
- Rekha Kushwaha
- Agricultural Science Center, Department of Horticulture, University of Kentucky, Lexington, KY 40546, USA
- Seed Biology Group, University of Kentucky, Lexington, KY 40546, USA
| | - A. Bruce Downie
- Seed Biology Group, University of Kentucky, Lexington, KY 40546, USA
- Plant Science Building, Department of Horticulture, University of Kentucky, Lexington, KY 40546, USA
| | - Christina M. Payne
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY 40506, USA
- Center for Computational Sciences, University of Kentucky, Lexington, KY 40506, USA
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Wang HC, Wu ML, Ko TP, Wang AHJ. Neisseria conserved hypothetical protein DMP12 is a DNA mimic that binds to histone-like HU protein. Nucleic Acids Res 2013; 41:5127-38. [PMID: 23531546 PMCID: PMC3643605 DOI: 10.1093/nar/gkt201] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 03/04/2013] [Accepted: 03/04/2013] [Indexed: 12/16/2022] Open
Abstract
DNA mimic proteins are unique factors that control the DNA-binding activity of target proteins by directly occupying their DNA-binding sites. To date, only a few DNA mimic proteins have been reported and their functions analyzed. Here, we present evidence that the Neisseria conserved hypothetical protein DMP12 should be added to this list. Our gel filtration and analytical ultracentrifugation results showed that the DMP12 monomer interacts with the dimeric form of the bacterial histone-like protein HU. Subsequent structural analysis of DMP12 showed that the shape and electrostatic surface of the DMP12 monomer are similar to those of the straight portion of the bent HU-bound DNA and complementary to those of HU protein dimer. DMP12 also protects HU protein from limited digestion by trypsin and enhances the growth rate Escherichia coli. Functionally, HU proteins participate in bacterial nucleoid formation, as well as recombination, gene regulation and DNA replication. The interaction between DMP12 and HU protein might, therefore, play important roles in these DNA-related mechanisms.
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Affiliation(s)
- Hao-Ching Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan, Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei 115, Taiwan, and Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
| | - Mao-Lun Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan, Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei 115, Taiwan, and Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan, Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei 115, Taiwan, and Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
| | - Andrew H.-J. Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan, Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei 115, Taiwan, and Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
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Wang HC, Ko TP, Wu ML, Ku SC, Wu HJ, Wang AHJ. Neisseria conserved protein DMP19 is a DNA mimic protein that prevents DNA binding to a hypothetical nitrogen-response transcription factor. Nucleic Acids Res 2012; 40:5718-30. [PMID: 22373915 PMCID: PMC3384305 DOI: 10.1093/nar/gks177] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 02/01/2012] [Accepted: 02/03/2012] [Indexed: 11/14/2022] Open
Abstract
DNA mimic proteins occupy the DNA binding sites of DNA-binding proteins, and prevent these sites from being accessed by DNA. We show here that the Neisseria conserved hypothetical protein DMP19 acts as a DNA mimic. The crystal structure of DMP19 shows a dsDNA-like negative charge distribution on the surface, suggesting that this protein should be added to the short list of known DNA mimic proteins. The crystal structure of another related protein, NHTF (Neisseria hypothetical transcription factor), provides evidence that it is a member of the xenobiotic-response element (XRE) family of transcriptional factors. NHTF binds to a palindromic DNA sequence containing a 5'-TGTNAN(11)TNACA-3' recognition box that controls the expression of an NHTF-related operon in which the conserved nitrogen-response protein [i.e. (Protein-PII) uridylyltransferase] is encoded. The complementary surface charges between DMP19 and NHTF suggest specific charge-charge interaction. In a DNA-binding assay, we found that DMP19 can prevent NHTF from binding to its DNA-binding sites. Finally, we used an in situ gene regulation assay to provide evidence that NHTF is a repressor of its down-stream genes and that DMP19 can neutralize this effect. We therefore conclude that the interaction of DMP19 and NHTF provides a novel gene regulation mechanism in Neisseria spps.
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Affiliation(s)
| | | | | | | | | | - Andrew H.-J. Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
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