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Rieger J, Fitz M, Fischer SM, Wallmeroth N, Flores-Romero H, Fischer NM, Brand LH, García-Sáez AJ, Berendzen KW, Mira-Rodado V. Exploring the Binding Affinity of the ARR2 GARP DNA Binding Domain via Comparative Methods. Genes (Basel) 2023; 14:1638. [PMID: 37628689 PMCID: PMC10454580 DOI: 10.3390/genes14081638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Plants have evolved signaling mechanisms such as the multi-step phosphorelay (MSP) to respond to different internal and external stimuli. MSP responses often result in gene transcription regulation that is modulated through transcription factors such as B-type Arabidopsis response regulator (ARR) proteins. Among these proteins, ARR2 is a key component that is expressed ubiquitously and is involved in many aspects of plant development. Although it has been noted that B-type ARRs bind to their cognate genes through a DNA-binding domain termed the GARP domain, little is known about the structure and function of this type of DNA-binding domain; thus, how ARRs bind to DNA at a structural level is still poorly understood. In order to understand how the MSP functions in planta, it is crucial to unravel both the kinetics as well as the structural identity of the components involved in such interactions. For this reason, this work focusses on resolving how the GARP domain of ARR2 (GARP2) binds to the promoter region of ARR5, one of its native target genes in cytokinin signaling. We have established that GARP2 specifically binds to the ARR5 promoter with three different bi-molecular interaction systems-qDPI-ELISA, FCS, and MST-and we also determined the KD of this interaction. In addition, structural modeling of the GARP2 domain confirms that GARP2 entails a HTH motif, and that protein-DNA interaction most likely occurs via the α3-helix and the N-terminal arm of this domain since mutations in this region hinder ARR2's ability to activate transcription.
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Affiliation(s)
- Janine Rieger
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
| | - Michael Fitz
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
| | - Stefan Markus Fischer
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
| | - Niklas Wallmeroth
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
| | - Hector Flores-Romero
- Interfaculty Institute of Biochemistry (IFIB), Tübingen University, 72076 Tübingen, Germany
- CECAD Research Center, Institute of Genetics, Cologne University, 51069 Cologne, Germany
| | - Nina Monika Fischer
- Institute for Bioinformatics and Medical Informatics, Tübingen University, 72076 Tübingen, Germany
| | - Luise Helene Brand
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
| | - Ana J. García-Sáez
- Interfaculty Institute of Biochemistry (IFIB), Tübingen University, 72076 Tübingen, Germany
- CECAD Research Center, Institute of Genetics, Cologne University, 51069 Cologne, Germany
| | | | - Virtudes Mira-Rodado
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
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Schumann M, Röttig M, Fischer NM, Kohlbacher O. A framework and workflow system for virtual screening and molecular docking. J Cheminform 2011. [PMCID: PMC3083569 DOI: 10.1186/1758-2946-3-s1-p15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
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