Xi Chenggang, Ma Yuefeng, Amrofell Matthew B, Moon Tae Seok
Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
These authors contributed equally.
Cell Rep Phys Sci. 2024 Oct 16;5(10). doi: 10.1016/j.xcrp.2024.102211. Epub 2024 Sep 16.
Tryptophan and its metabolites, produced by the gut microbiota, are pivotal for human physiological and mental health. Yet, quantifying these structurally similar compounds with high specificity remains a challenge, hindering point-of-care diagnostics and targeted therapeutic interventions. Leveraging the innate specificity and adaptability of biological systems, we present a biosensing approach capable of identifying specific metabolites in complex contexts with minimal cross-activity. This study introduces a generalizable strategy that combines evolutionary analysis, key ligand-binding residue identification, and mutagenesis scanning to pinpoint ligand-specific transcription factor variants. Furthermore, we uncover regulatory mechanisms within uncharacterized ligand-binding domains, whether in homodimer interfaces or monomers, through structural prediction and ligand docking. Notably, our "plug-and-play" strategy broadens the detection spectrum, enabling the exclusive biosensing of indole-3-acetic acid (an auxin), tryptamine, indole-3-pyruvic acid, and other tryptophan derivatives in engineered probiotics. This groundwork paves the way to create highly specific transcriptional biosensors for potential clinical, agricultural, and industrial use.
由肠道微生物群产生的色氨酸及其代谢产物对人类生理和心理健康至关重要。然而，以高特异性定量这些结构相似的化合物仍然是一项挑战，这阻碍了即时诊断和靶向治疗干预。利用生物系统固有的特异性和适应性，我们提出了一种生物传感方法，能够在复杂环境中以最小的交叉活性识别特定代谢产物。本研究介绍了一种通用策略，该策略结合进化分析、关键配体结合残基鉴定和诱变扫描，以确定配体特异性转录因子变体。此外，我们通过结构预测和配体对接，揭示了未表征的配体结合域内的调控机制，无论是在同二聚体界面还是单体中。值得注意的是，我们的“即插即用”策略拓宽了检测范围，能够在工程益生菌中对吲哚-3-乙酸（一种生长素）、色胺、吲哚-3-丙酮酸和其他色氨酸衍生物进行专属生物传感。这项基础工作为创建用于潜在临床、农业和工业用途的高度特异性转录生物传感器铺平了道路。
