Structural and dynamics studies of the TetR family protein, CprB from Streptomyces coelicolor in complex with its biological operator sequence

Bhukya, Hussain; Jana, Asis K.; Sengupta, Neelanjana; Anand, Ruchi

doi:10.1016/j.jsb.2017.03.006

Cited by 11 publications

(10 citation statements)

References 42 publications

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“…The model shows that two MmfR homodimers bind to opposite sides of the DNA duplex ( Figure 3). The obtuse angle between the planes that bisect the monomers in each homodimer is 140° ( Figure 3), consistent with that observed for other TFTRs that bind their operators as homodimeric pairs (Supplementary Figure 9) 14,15,17,18 . As in most other TFTR-DNA complexes, α-helix 2 and α-helix 3 of MmfR, encompassing the HTH-motif, serve as spacer and recognition helices, respectively.…”

Section: Cryo-em Structure Of Mmfr-dna Complexsupporting

confidence: 84%

“…Although X-ray crystal structures of CprB (a putative GBL-binding TFTR in S. coelicolor) and a CprB-DNA complex have been reported, both the structural basis for hormone recognition and the mechanism of DNA release by ArpA-like TFTRs remain poorly understood [13][14][15] . Here we report structures of MmfR bound to an AHFCA and complexed with DNA duplex containing the operator from the mmfL-mmfR intergenic region, shedding light on hormone recognition and the mechanism of DNA release.…”

Section: Introductionmentioning

confidence: 99%

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Structural basis for control of antibiotic production by bacterial hormones

Zhou¹,

Bhukya²,

Malet³

et al. 2020

Preprint

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Actinobacteria produce numerous antibiotics and other specialised metabolites with important applications in medicine and agriculture. Diffusible hormones frequently control the production of such metabolites by binding TetR family transcriptional repressors (TFTRs), but the molecular basis for this remains unclear. The production of methylenomycin antibiotics in Streptomyces coelicolor A3(2) is initiated by binding of 2-alkyl-4-hydroxymethylfuran-3-carboxylic acid (AHFCA) hormones to the TFTR MmfR. Here, we report the X-ray crystal structure of an MmfR-AHFCA complex, establishing the structural basis for hormone recognition. We also elucidate the mechanism for DNA release upon hormone binding by single particle cryo-electron microscopy of an MmfR-operator complex.Electrophoretic mobility shift assays with MmfR mutants and synthetic AHFCA analogues illuminate the role played by individual amino acid residues and hormone functional groups in ligand recognition and DNA release. These findings will facilitate the exploitation of Actinobacterial hormones and their associated TFTRs in synthetic biology and novel antibiotic discovery.

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Section: Cryo-em Structure Of Mmfr-dna Complexsupporting

confidence: 84%

Section: Introductionmentioning

confidence: 99%

Structural basis for control of antibiotic production by bacterial hormones

Zhou¹,

Bhukya²,

Malet³

et al. 2020

Preprint

Self Cite

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“…5; Arg29, Asp38, and Arg48) on the HTH domain for sitedirected mutagenesis. Similar residues have been shown to be important for DNA-protein contacts in other TFRs (43)(44)(45). The K d s of the MftR mutants and O mft were measured by FP (Table 2).…”

Section: Structural Contributions To Ligand Bindingmentioning

confidence: 99%

Biosynthesis of the redox cofactor mycofactocin is controlled by the transcriptional regulator MftR and induced by long-chain acyl-CoA species

Mendauletova

Latham

2022

Journal of Biological Chemistry

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Mycofactocin (MFT) is a ribosomally synthesized and post-translationally-modified redox cofactor found in pathogenic mycobacteria. While MFT biosynthetic proteins have been extensively characterized, the physiological conditions under which MFT biosynthesis is required are not well understood. To gain insights into the mechanisms of regulation of MFT expression in Mycobacterium smegmatis mc 2 155, we investigated the DNA-binding and ligand-binding activities of the putative TetR-like transcription regulator, MftR. In this study, we demonstrated that MftR binds to the mft promoter region. We used DNase I footprinting to identify the 27 bp palindromic operator located 5′ to mftA and found it to be highly conserved in Mycobacterium tuberculosis , Mycobacterium bovis , Mycobacterium ulcerans , and Mycobacterium marinum . To determine under which conditions the mft biosynthetic gene cluster (BGC) is induced, we screened for effectors of MftR. As a result, we found that MftR binds to long-chain acyl-CoAs with low micromolar affinities. To demonstrate that oleoyl-CoA induces the mft BGC in vivo , we re-engineered a fluorescent protein reporter system to express an MftA–mCherry fusion protein. Using this mCherry fluorescent readout, we show that the mft BGC is upregulated in M. smegmatis mc 2 155 when oleic acid is supplemented to the media. These results suggest that MftR controls expression of the mft BGC and that MFT production is induced by long-chain acyl-CoAs. Since MFT-dependent dehydrogenases are known to colocalize with acyl carrier protein/CoA-modifying enzymes, these results suggest that MFT might be critical for fatty acid metabolism or cell wall reorganization.

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“…This is also the case for SimR, an exporter of a potent DNA gyrase inhibitor from Streptomyces antibioticus , which presents an even longer N-terminus that turns back to the added “arm” between α8 and α9 of the second monomer (Le et al, 2011 ). CprB from S. coelicolor , a receptor of c-butyrolactones, a class of quorum sensing molecules (Bhukya et al, 2017 ), also takes part of this N-terminal extended sub-family. AmtR, the global nitrogen regulator of C. glutamicum that is activated by a protein instead of a small molecule (Palanca and Rubio, 2016 ), also shows an additional C-terminal helix of unclear function.…”

Section: The One-component System Regulatorsmentioning

confidence: 99%

Functional Mechanism of the Efflux Pumps Transcription Regulators From Pseudomonas aeruginosa Based on 3D Structures

Issa

Phan

Broutin

2018

Front. Mol. Biosci.

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Bacterial antibiotic resistance is a worldwide health problem that deserves important research attention in order to develop new therapeutic strategies. Recently, the World Health Organization (WHO) classified Pseudomonas aeruginosa as one of the priority bacteria for which new antibiotics are urgently needed. In this opportunistic pathogen, antibiotics efflux is one of the most prevalent mechanisms where the drug is efficiently expulsed through the cell-wall. This resistance mechanism is highly correlated to the expression level of efflux pumps of the resistance-nodulation-cell division (RND) family, which is finely tuned by gene regulators. Thus, it is worthwhile considering the efflux pump regulators of P. aeruginosa as promising therapeutical targets alternative. Several families of regulators have been identified, including activators and repressors that control the genetic expression of the pumps in response to an extracellular signal, such as the presence of the antibiotic or other environmental modifications. In this review, based on different crystallographic structures solved from archetypal bacteria, we will first focus on the molecular mechanism of the regulator families involved in the RND efflux pump expression in P. aeruginosa, which are TetR, LysR, MarR, AraC, and the two-components system (TCS). Finally, the regulators of known structure from P. aeruginosa will be presented.

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Structural and dynamics studies of the TetR family protein, CprB from Streptomyces coelicolor in complex with its biological operator sequence

Cited by 11 publications

References 42 publications

Structural basis for control of antibiotic production by bacterial hormones

Structural basis for control of antibiotic production by bacterial hormones

Biosynthesis of the redox cofactor mycofactocin is controlled by the transcriptional regulator MftR and induced by long-chain acyl-CoA species

Functional Mechanism of the Efflux Pumps Transcription Regulators From Pseudomonas aeruginosa Based on 3D Structures

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