Molecular basis for control of antibiotic production by a bacterial hormone

Abstract

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Using cryo-EM to uncover mechanisms of bacterial transcriptional regulation

“…The lower-order NanR-dimer 1 /DNA complex (70.5 kDa) was also resolved within the study at near atomic resolution, demonstrating the power of cryo-EM in this so-called ‘resolution revolution’ ( Figure 2E , inset). Similarly, cooperative binding was also observed for the TetR-type regulator, MmfR, where two dimers bound DNA at an obtuse angle of 140° in the cryo-EM structure [ 29 ].…”

“…These sources include variations in the stoichiometry of the interaction partners, partially assembled complexes or the presence of assembly intermediates [75,76,80]. At the biochemical level, these phenomena can be addressed through sample preparation procedures, mostly commonly via size exclusion chromatography to remove aggregates or unbound components and isolate a target complex [22,23,26,29]. If complexes are inherently fragile, researchers have successfully employed a fractionation technique, named GraFix, to prepare homogeneous cryo-EM samples [39,[84][85][86].…”

“…Following 3D reconstruction, atomic models provide the basis to structurally and functionally interpret the cryo-EM density maps. Most commonly, this process involves the input of existing X-ray or NMR structures from the PDB [22,[26][27][28][29], however in their absence, the neural network-based, structure prediction programs, AlphaFold [109] or RoseTTA [110] now offer an alternative. To guide this initial structure into the target density map, various flexible fitting tools, such as cryo_fit within phenix [70], ISOLDE [71] or iMODFIT [72] in Chimera, Namdinator [73] among others [29,111] can be used to accommodate conformational heterogeneity by utilising molecular dynamics simulations or normal mode analysis [112].…”

“…Most commonly, this process involves the input of existing X-ray or NMR structures from the PDB [22,[26][27][28][29], however in their absence, the neural network-based, structure prediction programs, AlphaFold [109] or RoseTTA [110] now offer an alternative. To guide this initial structure into the target density map, various flexible fitting tools, such as cryo_fit within phenix [70], ISOLDE [71] or iMODFIT [72] in Chimera, Namdinator [73] among others [29,111] can be used to accommodate conformational heterogeneity by utilising molecular dynamics simulations or normal mode analysis [112]. In scenarios where it is difficult to annotate protein and DNA in the density maps, the recent tools Haruspex [68] and Emap2sec+ [69] can be employed to detect these structures in high-resolution maps (>4 Å) and lower resolution maps 5-10 Å, respectively using neural networks.…”

Polyketide Starter and Extender Units Serve as Regulatory Ligands to Coordinate the Biosynthesis of Antibiotics in Actinomycetes

“…Both the onset and yield of antibiotic biosynthesis are modulated by different regulatory factors, some of which respond to diverse physiological or environmental signals ( 3 ). These specialized metabolites, such as hormone-like autoregulators ( 4 – 7 ), antibiotics themselves, or their biosynthetic intermediates ( 8 – 14 ), modulate the DNA-binding activity of these allosteric regulators ( 3 ). However, due to the difficulties in identifying novel ligands and characterizing their receptors, the underlying mechanisms of ligand-mediated regulation remain poorly understood.…”