Chakraborty Udit Kumar, Park Youngchan, Sengupta Kushal, Jung Won, Joshi Chandra P, Francis Danielle H, Chen Peng
Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany.
Nat Commun. 2024 Dec 4;15(1):10555. doi: 10.1038/s41467-024-55017-z.
Transition metals like Zn are essential for all organisms including bacteria, but fluctuations of their concentrations in the cell can be lethal. Organisms have thus evolved complex mechanisms for cellular metal homeostasis. One mechanistic paradigm involves pairs of transcription regulators sensing intracellular metal concentrations to regulate metal uptake and efflux. Here we report that Zur and ZntR, a prototypical pair of regulators for Zn uptake and efflux in E. coli, respectively, can coordinate their regulation through DNA, besides sensing cellular Zn concentrations. Using a combination of live-cell single-molecule tracking and in vitro single-molecule FRET measurements, we show that unmetallated ZntR can enhance the unbinding kinetics of Zur from DNA by directly acting on Zur-DNA complexes, possibly through forming heteromeric ternary and quaternary complexes that involve both protein-DNA and protein-protein interactions. This 'through-DNA' mechanism may functionally facilitate the switching in Zn-uptake regulation when bacteria encounter changing Zn environments, such as facilitating derepression of Zn-uptake genes upon Zn depletion; it could also be relevant for regulating the uptake-vs.-efflux of various metals across different bacterial species and yeast.
像锌这样的过渡金属对包括细菌在内的所有生物体都是必不可少的，但细胞内其浓度的波动可能是致命的。因此，生物体进化出了复杂的细胞金属稳态机制。一种机制模式涉及一对转录调节因子，它们感知细胞内金属浓度以调节金属的摄取和外排。在这里我们报告，Zur和ZntR分别是大肠杆菌中锌摄取和外排的一对典型调节因子，除了感知细胞内锌浓度外，它们还可以通过DNA协调它们的调节。通过结合活细胞单分子追踪和体外单分子荧光共振能量转移测量，我们表明未金属化的ZntR可以通过直接作用于Zur-DNA复合物来增强Zur从DNA上的解离动力学，可能是通过形成涉及蛋白质-DNA和蛋白质-蛋白质相互作用的异源三聚体和四聚体复合物。当细菌遇到变化的锌环境时，这种“通过DNA”的机制可能在功能上促进锌摄取调节的转换，例如在锌耗尽时促进锌摄取基因的去阻遏；它也可能与调节不同细菌物种和酵母中各种金属的摄取与外排有关。
