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Differences in distribution of single nucleotide polymorphisms among intracellular pattern recognition receptors in pigs

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Abstract

Pathogens localized extracellularly or incorporated into endosomes are recognized mainly by Toll-like receptors, whereas pathogens and pathogen-derived molecules that invade into the cytoplasm of host cells typically are recognized by intracellular pattern recognition receptors (PRRs), such as retinoic acid-inducible gene (RIG)-like helicases (RLHs) and nucleotide-binding oligmerization domain (NOD)-like receptors (NLRs). RIG-I and melanoma differentiation-associated gene 5 (MDA5), which belong to the RLH family, recognize viral genomic RNA, whereas NOD2, a member of the NLR family, responds to microbial peptidoglycans. These receptors may play an important role in pig opportunistic infectious diseases, such as pneumonia and diarrhea, which markedly impair livestock productivity, such that polymorphisms of these receptor genes are potential targets of pig breeding to increase disease resistance. Here, we report single nucleotide polymorphisms (SNPs) in porcine DDX58, IFIH1, and NOD2, which encode RIG-I, MDA5, and NOD2, respectively. Interestingly, compared with DDX58 and IFIH1, NOD2 abounded in nonsynonymous SNPs both throughout the coding sequence and in sequences encoding domains important for ligand recognition, such as helicase domains for RIG-I and MDA5 and leucine-rich repeats in NOD2. These differences in the distribution of SNPs in intracellular PRRs may parallel the diversity of their ligands, which include nucleic acids and peptidoglycans.

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Acknowledgments

This work was supported by the Animal Genome Research Project of the Ministry of Agriculture, Forestry and Fisheries of Japan and by a Grant-in-Aid from the Japan Racing Association.

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Authors and Affiliations

  1. Miyagi Livestock Experimental Station, Miyagi Prefecture, 1 Hiwatashi, Minamisawa, Iwadeyama, Osaki, Miyagi, 989-6445, Japan

    Chihiro Kojima-Shibata, Hiroshi Kadowaki & Eisaku Suzuki

  2. Animal Genome Research Program, NIAS/STAFF, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki, 305-0854, Japan

    Hiroki Shinkai, Takeya Morozumi, Kosuke Jozaki, Daisuke Toki, Toshimi Matsumoto & Hirohide Uenishi

  3. Second Research Division, Institute of Society for Techno-innovation of Agriculture, Forestry and Fisheries (STAFF-Institute), 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki, 305-0854, Japan

    Hiroki Shinkai, Takeya Morozumi, Daisuke Toki & Toshimi Matsumoto

  4. Division of Animal Sciences, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan

    Kosuke Jozaki & Hirohide Uenishi

  5. United Graduate School of Agricultural Sciences, Kagoshima University, 1 Honjo, Saga, 840-8502, Japan

    Kosuke Jozaki

  6. Graduate School of Agriculture, Saga University, 1 Honjo, Saga, 840-8502, Japan

    Kosuke Jozaki

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  1. Chihiro Kojima-Shibata
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  2. Hiroki Shinkai
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  9. Hirohide Uenishi
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Correspondence to Hirohide Uenishi.

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Kojima-Shibata, C., Shinkai, H., Morozumi, T. et al. Differences in distribution of single nucleotide polymorphisms among intracellular pattern recognition receptors in pigs. Immunogenetics 61, 153–160 (2009). https://doi.org/10.1007/s00251-008-0350-y

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