Ancestral sequence reconstruction as a tool for structural analysis of modular polyketide synthases

Taichi Chisuga, Shota Takinami, Zengwei Liao, Masayuki Karasawa, Naruhiko Adachi, Masato Kawasaki, Toshio Moriya, Toshiya Senda, Tohru Terada, Fumitaka Kudo, Tadashi Eguchi, Shogo Nakano (), Sohei Ito () and Akimasa Miyanaga ()
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Taichi Chisuga: University of Shizuoka
Shota Takinami: University of Shizuoka
Zengwei Liao: The University of Tokyo
Masayuki Karasawa: The University of Tokyo
Naruhiko Adachi: High Energy Accelerator Research Organization (KEK)
Masato Kawasaki: High Energy Accelerator Research Organization (KEK)
Toshio Moriya: High Energy Accelerator Research Organization (KEK)
Toshiya Senda: High Energy Accelerator Research Organization (KEK)
Tohru Terada: The University of Tokyo
Fumitaka Kudo: Tokyo Institute of Technology (Institute of Science Tokyo)
Tadashi Eguchi: Tokyo Institute of Technology (Institute of Science Tokyo)
Shogo Nakano: University of Shizuoka
Sohei Ito: University of Shizuoka
Akimasa Miyanaga: Tokyo Institute of Technology (Institute of Science Tokyo)

Nature Communications, 2025, vol. 16, issue 1, 1-13

Abstract: Abstract Modular polyketide synthases (PKSs) are large multi-domain enzymes critical for the biosynthesis of polyketide antibiotics. However, challenges with structural analysis limits our mechanistic understanding of modular PKSs. In this report, we explore the potential of ancestral sequence reconstruction (ASR) for structure analysis of target proteins. As a model, we focus on the FD-891 PKS loading module composed of ketosynthase-like decarboxylase (KSQ), acyltransferase (AT) and acyl carrier protein (ACP) domains. We construct a KSQAncAT chimeric didomain by replacing the native AT with an ancestral AT (AncAT) using ASR. After confirming that KSQAncAT chimeric didomain retains similar enzymatic function to the native KSQAT didomain, we successfully determine a high-resolution crystal structure of the KSQAncAT chimeric didomain and cryo-EM structures of the KSQ–ACP complex. These cryo-EM structures, which could not be determined for the native protein, exemplify the utility of ASR to enable cryo-EM single-particle analysis. Our findings demonstrate that integrating ASR with structural analysis provides deeper mechanistic insight into modular PKSs. Furthermore, applying ASR to a partial region of the targeted multi-domain proteins could expand the potential of ASR and may serve as a valuable framework for investigating the structure and function of various multi-domain proteins.

Date: 2025
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DOI: 10.1038/s41467-025-62168-0

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