Ruiz Nestor, Xing Jiawei, Zhulin Igor B, Brautigam Chad A, Hendrixson David R
Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
Department of Microbiology, The Ohio State University, Columbus, Ohio, USA.
mBio. 2025 Feb 5;16(2):e0327824. doi: 10.1128/mbio.03278-24. Epub 2024 Dec 13.
Two-component signal transduction systems (TCSs) are nearly ubiquitous across bacterial species and enable bacteria to sense and respond to specific cues for environmental adaptation. The BumSR TCS is unusual in that the BumS sensor exclusively functions as a phosphatase rather than a kinase to control phosphorylated levels of its cognate BumR response regulator (P-BumR). We previously found that BumSR directs a response to the short-chain fatty acid butyrate generated by resident microbiota so that identifies ideal lower intestinal niches in avian and human hosts for colonization. However, butyrate is an indirect cue for BumS and did not inhibit BumS phosphatase activity for P-BumR. In this work, we expanded the repertoire of lower intestinal metabolites that are cues sensed by BumS that modulate the expression of genes required for colonization to include the branched short-chain fatty acids isobutyrate and isovalerate. Unlike butyrate, isobutyrate and isovalerate inhibited BumS phosphatase activity for P-BumR, indicating that these metabolites are direct cues for BumS. Isobutyrate and isovalerate reduced the thermostability of BumS and caused a reorganization of protein structure to suggest how sensing these cues inhibits phosphatase activity. We also identified residues in the BumS sensory domain required to detect isobutyrate, isovalerate, and butyrate and for optimal colonization of hosts to reveal how gut bacteria can recognize these intestinal metabolites. Our work reveals how this unusual bacterial sensor phosphatase senses a repertoire of intestinal metabolites and how cues alter BumSR signal transduction to influence colonization of hosts.IMPORTANCETCSs are prevalent in many bacteria, but the cues sensed by each are not actually known for many of these systems. Microbiota-generated butyrate in human and avian hosts is detected by the BumS sensor phosphatase so that the bacterium identifies ideal lower intestinal niches for colonization. However, BumS only indirectly senses butyrate to inhibit dephosphorylation of its cognate BumR response regulator. Here, we expanded the repertoire of cues sensed by BumS to the branched-short chain fatty acids isobutyrate and isovalerate that are also abundant in the lower intestines. Both isobutyrate and isovalerate are potent, direct cues for BumS, whereas butyrate is an indirect cue. Leveraging isobutyrate and isovalerate as direct cues, we reveal BumS structure is altered upon cue detection to inhibit its phosphatase activity. We provide an understanding of the mechanics of an unusual mode of signal transduction executed by BumSR and other bacterial sensor phosphatase-driven TCSs.
双组分信号转导系统（TCSs）几乎在所有细菌物种中都存在，使细菌能够感知并响应特定线索以适应环境。BumSR TCS不同寻常之处在于，BumS传感器仅作为磷酸酶而非激酶发挥作用，以控制其同源BumR反应调节蛋白（P-BumR）的磷酸化水平。我们之前发现，BumSR引导对常驻微生物群产生的短链脂肪酸丁酸的响应，从而在禽类和人类宿主中识别出理想的下肠道生态位以供定殖。然而，丁酸是BumS的间接线索，且不会抑制BumS对P-BumR的磷酸酶活性。在这项研究中，我们扩展了BumS所感知的下肠道代谢物种类，这些代谢物作为线索调节定殖所需基因的表达，包括支链短链脂肪酸异丁酸和异戊酸。与丁酸不同，异丁酸和异戊酸抑制BumS对P-BumR的磷酸酶活性，表明这些代谢物是BumS的直接线索。异丁酸和异戊酸降低了BumS的热稳定性并导致蛋白质结构重组，从而揭示了感知这些线索如何抑制磷酸酶活性。我们还确定了BumS传感结构域中检测异丁酸、异戊酸和丁酸以及宿主最佳定殖所需的残基，以揭示肠道细菌如何识别这些肠道代谢物。我们的研究揭示了这种不寻常的细菌传感器磷酸酶如何感知一系列肠道代谢物，以及这些线索如何改变BumSR信号转导以影响宿主定殖。
重要性
TCSs在许多细菌中普遍存在，但其中许多系统实际所感知的线索尚不清楚。人类和禽类宿主中微生物群产生的丁酸由BumS传感器磷酸酶检测到，从而使该细菌识别出理想的下肠道生态位以供定殖。然而，BumS仅间接感知丁酸以抑制其同源BumR反应调节蛋白的去磷酸化。在此，我们将BumS所感知的线索种类扩展到下肠道中也大量存在的支链短链脂肪酸异丁酸和异戊酸。异丁酸和异戊酸都是BumS的有效直接线索，而丁酸是间接线索。利用异丁酸和异戊酸作为直接线索，我们揭示了在检测到线索后BumS结构发生改变以抑制其磷酸酶活性。我们对BumSR以及其他细菌传感器磷酸酶驱动的TCSs所执行的一种不寻常信号转导模式的机制有了理解。
