A photoconversion model for full spectral programming and multiplexing of optogenetic systems

Optogenetics combines externally applied light signals and genetically engineered photoreceptors to control cellular processes with unmatched precision. Here, we develop a mathematical model of wavelength‐ and intensity‐dependent photoconversion, signaling, and output gene expression for our two previously engineered light‐sensing Escherichia coli two‐component systems. To parameterize the model, we develop a simple set of spectral and dynamical calibration experiments using our recent open‐source “Light Plate Apparatus” device. In principle, the parameterized model should predict the gene expression response to any time‐varying signal from any mixture of light sources with known spectra. We validate this capability experimentally using a suite of challenging light sources and signals very different from those used during the parameterization process. Furthermore, we use the model to compensate for significant spectral cross‐reactivity inherent to the two sensors in order to develop a new method for programming two simultaneous and independent gene expression signals within the same cell. Our optogenetic multiplexing method will enable powerful new interrogations of how metabolic, signaling, and decision‐making pathways integrate multiple input signals.     

微生物金属响应蛋白研究进展

微生物金属响应蛋白(Metal responsive proteins)是一类具有金属传感效应的DNA转录调节因子。目前,已研究的该调节因子家族有7个(Ars R-Smt B等)。每个响应蛋白家族的不同代表都可以调节基于不同金属效应物的基因表达,它们不仅调节微生物细胞内与金属内稳态直接相关的基因表达,还可以调节细胞代谢以减少细胞对供应短缺的金属的需求。目前,金属响应蛋白的研究已有一定成果,部分金属响应结合位点的氨基酸残基及调节机制都被确定。本综述总结了不同金属响应蛋白家族的金属转录调节因子,介绍了关于金属调节基因表达机制的现有研究进展,并以Ars R-Smt B家族和Fur家族为例,详细介绍了金属响应结合位点的结构特征与相关表达调控机制。此外,还介绍了不同响应蛋白控制微生物细胞金属水平作用方面的最新进展,以及在生物冶金与微生物环境治理方面的应用前景。     

Principles of redox control in photosynthesis gene expression

Light is one of the most important environmental factors influencing gene expression in photosynthetic organisms. In particular, genes for components of the photosynthetic machinery show light-dependent expression. In recent years, it has become clear that photosynthesis itself contributes important signals to this light control of gene expression by means of changes in the reduction/oxidation (redox) state of signalling molecules. Such changes in redox state are induced by changes in quality and quantity of the incident light. Redox signalling mechanisms therefore provide photosynthesis with the possibility of acclimational changes in the structure of the photosynthetic apparatus via a feedback control of photosynthesis gene expression. The great variety of these signalling mechanisms is summarised under the term 'redox control'. In some cases, oxygen acts as a different environmental, light-independent stimulus of photosynthetic gene expression, providing an additional redox signal and a different kind of redox control. In this review, we summarise present knowledge about such redox control mechanisms and analyse common properties as well as differences in the various signalling pathways. We suggest that there is an urgent need for a clear distinction between different kinds of redox control. Accordingly, we propose a categorisation into perceptional and transductional redox control. These categories are defined and examples given. The generalisation and comparability of results obtained in different physiological test systems and species are critically discussed.