Linares-Otoya Luis, Shirkey Jaden D, Chhetri Bhuwan Khatri, Mira Amira, Biswas Abhishek, Neff Samuel L, Linares-Otoya Maria V, Chen Ye, Campos-Florian Julio V, Ganoza-Yupanqui Mayar L, Jeffrey Philip D, Hughson Frederick M, Donia Mohamed S
Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
Pharmacy and Biochemistry Faculty, National University of Trujillo, Trujillo, Peru.
Nature. 2025 Aug 20. doi: 10.1038/s41586-025-09418-9.
Considerable advances have been made in characterizing bioactive molecules secreted by bacteria, yet the regulatory elements controlling their production remain largely understudied. Here we identify and characterize the N-acyl-cyclolysine (ACL) system-a cell-density-dependent chemical signalling system specific to and widespread in the phylum Bacteroidota (formerly Bacteroidetes)-and show that it regulates the expression of co-localized operons encoding diverse secreted molecules. Using genetic and biochemical analyses, combined with structural studies of a key biosynthetic enzyme, AclA, we elucidate the molecular structure of various ACLs and their complete biosynthetic pathway involving L-lysine acylation and ATP-dependent cyclization. Furthermore, we find that secreted ACLs are sensed by a dedicated transcription factor, AclR, resulting in the expression of associated operons and the autoinduction of ACL biosynthesis. Moreover, we show that different Bacteroidota strains produce structurally diverse ACLs and encode transcription factors with varying ligand specificities. Finally, we find that the acl circuit is widely distributed and transcribed in human gut and oral microbiome samples, with clear evidence for an active role in regulating associated operons under host colonization conditions. Understanding the function of the ACL system in different contexts has the potential to reveal details about the biology, ecology and chemistry of the Bacteroidota and how members of this phylum interact with their environments and hosts.
在表征细菌分泌的生物活性分子方面已经取得了相当大的进展，然而，控制其产生的调控元件在很大程度上仍未得到充分研究。在这里，我们鉴定并表征了N-酰基环赖氨酸（ACL）系统——一种特定于拟杆菌门（以前称为拟杆菌纲）并在该门中广泛存在的细胞密度依赖性化学信号系统——并表明它调节编码多种分泌分子的共定位操纵子的表达。通过遗传和生化分析，结合关键生物合成酶AclA的结构研究，我们阐明了各种ACL的分子结构及其完整的生物合成途径，该途径涉及L-赖氨酸酰化和ATP依赖性环化。此外，我们发现分泌的ACL被一种专门的转录因子AclR感知，从而导致相关操纵子的表达和ACL生物合成的自诱导。此外，我们表明不同的拟杆菌门菌株产生结构多样的ACL，并编码具有不同配体特异性的转录因子。最后，我们发现acl回路在人类肠道和口腔微生物组样本中广泛分布并转录，有明确证据表明其在宿主定殖条件下调节相关操纵子中发挥积极作用。了解ACL系统在不同背景下的功能有可能揭示拟杆菌门的生物学、生态学和化学细节，以及该门成员如何与它们的环境和宿主相互作用。
