Ubilla-Rodriguez Natalia C, Andreas Michael P, Giessen Tobias W
bioRxiv. 2024 Dec 3:2024.11.27.625667. doi: 10.1101/2024.11.27.625667.
Encapsulins are self-assembling protein compartments found in prokaryotes and specifically encapsulate dedicated cargo enzymes. The most abundant encapsulin cargo class are Dye-decolorizing Peroxidases (DyPs). It has been previously suggested that DyP encapsulins are involved in oxidative stress resistance and bacterial pathogenicity due to DyPs' inherent ability to reduce and detoxify hydrogen peroxide while oxidizing a broad range of organic co-substrates. Here, we report the structural and biochemical analysis of a DyP encapsulin widely found across enterobacteria. Using bioinformatic approaches, we show that this DyP encapsulin is encoded by a conserved transposon-associated operon, enriched in enterobacterial pathogens. Through low pH and peroxide exposure experiments, we highlight the stability of this DyP encapsulin under harsh conditions and show that DyP catalytic activity is highest at low pH. We determine the structure of the DyP-loaded shell and free DyP via cryo-electron microscopy, revealing the structural basis for DyP cargo loading and peroxide preference. Our work lays the foundation to further explore the substrate range and physiological functions of enterobacterial DyP encapsulins.
内膜蛋白是原核生物中发现的自组装蛋白隔室，专门包裹特定的货物酶。内膜蛋白最丰富的货物类别是染料脱色过氧化物酶（DyP）。此前有研究表明，由于DyP具有还原和解毒过氧化氢的固有能力，同时能氧化多种有机共底物，因此DyP内膜蛋白与氧化应激抗性和细菌致病性有关。在此，我们报告了一种在肠杆菌中广泛发现的DyP内膜蛋白的结构和生化分析。通过生物信息学方法，我们表明这种DyP内膜蛋白由一个保守的转座子相关操纵子编码，在肠道病原菌中富集。通过低pH和过氧化物暴露实验，我们突出了这种DyP内膜蛋白在恶劣条件下的稳定性，并表明DyP催化活性在低pH时最高。我们通过冷冻电子显微镜确定了装载DyP的外壳和游离DyP的结构，揭示了DyP货物装载和过氧化物偏好的结构基础。我们的工作为进一步探索肠道细菌DyP内膜蛋白的底物范围和生理功能奠定了基础。
