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Rajasekar KV, Lovering AL, Dancea F, Scott DJ, Harris SA, Bingle LEH, Roessle M, Thomas CM, Hyde EI, White SA. Flexibility of KorA, a plasmid-encoded, global transcription regulator, in the presence and the absence of its operator. Nucleic Acids Res 2016; 44:4947-56. [PMID: 27016739 PMCID: PMC4889941 DOI: 10.1093/nar/gkw191] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 03/08/2016] [Accepted: 03/11/2016] [Indexed: 12/03/2022] Open
Abstract
The IncP (Incompatibility group P) plasmids are important carriers in the spread of antibiotic resistance across Gram-negative bacteria. Gene expression in the IncP-1 plasmids is stringently controlled by a network of four global repressors, KorA, KorB, TrbA and KorC interacting cooperatively. Intriguingly, KorA and KorB can act as co-repressors at varying distances between their operators, even when they are moved to be on opposite sides of the DNA. KorA is a homodimer with the 101-amino acid subunits, folding into an N-terminal DNA-binding domain and a C-terminal dimerization domain. In this study, we have determined the structures of the free KorA repressor and two complexes each bound to a 20-bp palindromic DNA duplex containing its consensus operator sequence. Using a combination of X-ray crystallography, nuclear magnetic resonance spectroscopy, SAXS and molecular dynamics calculations, we show that the linker between the two domains is very flexible and the protein remains highly mobile in the presence of DNA. This flexibility allows the DNA-binding domains of the dimer to straddle the operator DNA on binding and is likely to be important in cooperative binding to KorB. Unexpectedly, the C-terminal domain of KorA is structurally similar to the dimerization domain of the tumour suppressor p53.
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Affiliation(s)
- Karthik V Rajasekar
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Andrew L Lovering
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Felician Dancea
- School of Cancer Studies, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - David J Scott
- School of Biosciences, Sutton Bonington Campus, University of Nottingham, Nottingham LE12 5RD, UK
| | - Sarah A Harris
- School of Physics and Astronomy and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Lewis E H Bingle
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | | | - Christopher M Thomas
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Eva I Hyde
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Scott A White
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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Bingle LEH, Rajasekar KV, Muntaha ST, Nadella V, Hyde EI, Thomas CM. A single aromatic residue in transcriptional repressor protein KorA is critical for cooperativity with its co-regulator KorB. Mol Microbiol 2008; 70:1502-14. [PMID: 19019158 PMCID: PMC2680271 DOI: 10.1111/j.1365-2958.2008.06498.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2008] [Indexed: 01/08/2023]
Abstract
A central feature of broad host range IncP-1 plasmids is the set of regulatory circuits that tightly control plasmid core functions under steady-state conditions. Cooperativity between KorB and either KorA or TrbA repressor proteins is a key element of these circuits and deletion analysis has implicated the conserved C-terminal domain of KorA and TrbA in this interaction. By NMR we show that KorA and KorB interact directly and identify KorA amino acids that are affected on KorB binding. Studies on mutants showed that tyrosine 84 (or phenylalanine, in some alleles) is dispensable for repressor activity but critical for the specific interaction with KorB in both in vivo reporter gene assays and in vitro electrophoretic mobility shift and co-purification assays. This confirms that direct and specific protein-protein interactions are responsible for the cooperativity observed between KorB and its corepressors and lays the basis for determining the biological importance of this cooperativity.
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Affiliation(s)
| | | | - Sidra tul Muntaha
- School of Biosciences, University of Birmingham, EdgbastonBirmingham B15 2TT, UK
| | - Vinod Nadella
- School of Biosciences, University of Birmingham, EdgbastonBirmingham B15 2TT, UK
| | - Eva I Hyde
- School of Biosciences, University of Birmingham, EdgbastonBirmingham B15 2TT, UK
| | - Christopher M Thomas
- School of Biosciences, University of Birmingham, EdgbastonBirmingham B15 2TT, UK
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