ORIGINAL RESEARCH article
Front. Cell. Infect. Microbiol.
Sec. Adaptive & Innate Immunity in Infection
This article is part of the Research TopicRole of Immune Effectors in Microbial Settlement and Host-Microbiota InteractionsView all 3 articles
Redefinition of the Toll-like Receptor Repertoire in Ciona robusta Through Genomic, Structural, and Expression Analyses
Provisionally accepted
Akira Shiraishi1
Shin Matsubara1
Sakura Kikuchi2
Kanako Hisata2
Nori Satoh2
Larry J. Dishaw3*
Honoo Satake1*- 1Division of Molecular Biology, Suntory Foundation for Life Sciences, Kyoto, Japan
- 2Okinawa Kagaku Gijustu Daigakuin Daigaku Marine Genomics Unit, Onna, Japan
- 3University of South Florida, Tampa, United States
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Toll-like receptors (TLRs) are essential components of innate immunity, mediating the recognition of pathogen-associated molecular patterns (PAMPs) through extracellular leucine-rich repeat (LRR) domains and initiating signaling via intracellular Toll/interleukin-1 receptor (TIR) domains. In the ascidian Ciona robusta, two canonical TLRs (CiTLR1 and CiTLR2) and several putative TLR-like genes (TLR3, -4, -6, -7, -13) have been annotated; however, their authenticity has remained uncertain due to limited structural and functional validation. In this study, we systematically reanalyzed the Ciona genome using the latest nearly complete assembly (HT genome) in combination with domain prediction, three-dimensional structural modeling, and transcriptomic expression profiling. Genomic mapping and sequence comparison demonstrated that TLR13 is identical to CiTLR1, while TLR3, -6, and -7 lack a complete TIR domain, indicating that these are not canonical TLRs. We further identified a novel TLR gene, CiTLRs1, located approximately 42 kb from CiTLR1 on chromosome 14, which encodes all essential structural features including LRR and TIR domains. AlphaFold3 structural predictions confirmed that CiTLR1, CiTLR2, and CiTLRs1 possess canonical solenoid LRR folds and typical TIR domain architectures. In addition, we found no convincing evidence that CiTLR3, CiTLR6, or CiTLR7 function as soluble TLRs. Transcriptomic analyses revealed distinct tissue-specific expression profiles of these genes, suggesting nonredundant immune functions. Our findings revise the repertoire of bona fide TLRs in Ciona to three (CiTLR1, CiTLR2, CiTLRs1) and emphasize the risk of overestimating TLR diversity based solely on sequence homology without domain and functional validation. This work refines the structural and functional landscape of ascidian TLRs.
Keywords: ascidian, Ciona robusta, domain, Structure, Toll-like receptor
Received: 30 Sep 2025; Accepted: 04 Dec 2025.
Copyright: © 2025 Shiraishi, Matsubara, Kikuchi, Hisata, Satoh, Dishaw and Satake. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Larry J. Dishaw
Honoo Satake
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