Department of Biology, York University, Toronto, ON, M3J1P3, Canada.
Department of Molecular Biology, University of Gdańsk, 80-308, Gdańsk, Poland.
Sci Rep. 2024 Feb 15;14(1):3793. doi: 10.1038/s41598-024-54508-9.
The orf63 gene resides in a region of the lambda bacteriophage genome between the exo and xis genes and is among the earliest genes transcribed during infection. In lambda phage and Shiga toxin (Stx) producing phages found in enterohemorrhagic Escherichia coli (EHEC) associated with food poisoning, Orf63 expression reduces the host survival and hastens the period between infection and lysis thereby giving it pro-lytic qualities. The NMR structure of dimeric Orf63 reveals a fold consisting of two helices and one strand that all make extensive intermolecular contacts. Structure-based data mining failed to identify any Orf63 homolog beyond the family of temperate bacteriophages. A machine learning approach was used to design an amphipathic helical ligand that bound a hydrophobic cleft on Orf63 with micromolar affinity. This approach may open a new path towards designing therapeutics that antagonize the contributions of Stx phages in EHEC outbreaks.
orf63 基因位于 lambda 噬菌体基因组 exo 和 xis 基因之间的区域，是感染过程中最早转录的基因之一。在 lambda 噬菌体和产志贺毒素（Stx）的噬菌体中，这些噬菌体存在于与食物中毒相关的肠出血性大肠杆菌（EHEC）中，Orf63 的表达降低了宿主的存活率，并加速了感染和裂解之间的时间，从而使其具有促裂解的特性。二聚体 Orf63 的 NMR 结构揭示了一个由两个螺旋和一个链组成的折叠，这些都与分子间广泛的接触。基于结构的数据挖掘未能在温和噬菌体家族之外发现任何 Orf63 同源物。使用机器学习方法设计了一种两亲性螺旋配体，该配体以微摩尔亲和力结合 Orf63 上的疏水裂缝。这种方法可能为设计对抗 EHEC 爆发中 Stx 噬菌体作用的治疗方法开辟了一条新途径。
