title: Clustered Xenopus keratin genes: A genomic, transcriptomic, and proteomic analysis.
abstract: Keratin genes belong to the intermediate filament superfamily and their expression is altered following morphological and physiological changes in vertebrate epithelial cells. Keratin genes are divided into two groups, type I and II, and are clustered on vertebrate genomes, including those of Xenopus species. Various keratin genes have been identified and characterized by their unique expression patterns throughout ontogeny in Xenopus laevis; however, compilation of previously reported and newly identified keratin genes in two Xenopus species is required for our further understanding of keratin gene evolution, not only in amphibians but also in all terrestrial vertebrates. In this study, 120 putative type I and II keratin genes in total were identified based on the genome data from two Xenopus species. We revealed that most of these genes are highly clustered on two homeologous chromosomes, XLA9_10 and XLA2 in X. laevis, and XTR10 and XTR2 in X. tropicalis, which are orthologous to those of human, showing conserved synteny among tetrapods. RNA-Seq data from various embryonic stages and adult tissues highlighted the unique expression profiles of orthologous and homeologous keratin genes in developmental stage- and tissue-specific manners. Moreover, we identified dozens of epidermal keratin proteins from the whole embryo, larval skin, tail, and adult skin using shotgun proteomics. In light of our results, we discuss the radiation, diversification, and unique expression of the clustered keratin genes, which are closely related to epidermal development and terrestrial adaptation during amphibian evolution, including Xenopus speciation.
authors.affiliation: Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan. Electronic address: suzuk107@hiroshima-u.ac.jp.
authors.forename: Ken-Ichi T
authors.initials: KT
authors.lastname: Suzuki
authors.affiliation: Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan.
authors.forename: Miyuki
authors.initials: M
authors.lastname: Suzuki
authors.affiliation: Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan.
authors.forename: Mitsuki
authors.initials: M
authors.lastname: Shigeta
authors.affiliation: Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
authors.forename: Joshua D
authors.initials: JD
authors.lastname: Fortriede
authors.affiliation: Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan.
authors.forename: Shuji
authors.initials: S
authors.lastname: Takahashi
authors.affiliation: Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan.
authors.forename: Shuuji
authors.initials: S
authors.lastname: Mawaribuchi
authors.affiliation: Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Yamamoto
authors.affiliation: Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
authors.forename: Masanori
authors.initials: M
authors.lastname: Taira
authors.affiliation: Laboratory of Tissue and Polymer Sciences, Faculty of Advanced Life Science, Hokkaido University, N10W8, Sapporo 060-0810, Japan. Electronic address: afukui@sci.hokudai.ac.jp.
authors.forename: Akimasa
authors.initials: A
authors.lastname: Fukui
mesh_terms: D000818:Animals; D004171:Diploidy; D004817:Epidermis / Q000254:growth & development / Q000378:metabolism; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D016678:Genome; D023281:Genomics; D007633:Keratins / Q000235:genetics*; D005810:Multigene Family / Q000235:genetics*; D010802:Phylogeny; D040901:Proteomics / Q000379:methods; D013045:Species Specificity; D021241:Spectrometry, Mass, Electrospray Ionization; D057891:Tetraploidy; D059467:Transcriptome; D014981:Xenopus / Q000235:genetics* / Q000378:metabolism; D029867:Xenopus Proteins / Q000235:genetics*; D014982:Xenopus laevis / Q000235:genetics / Q000378:metabolism
chemical_list: D029867:Xenopus Proteins; D007633:Keratins
keywords: Genome; Keratin; Proteome; Transcriptome; Xenopus laevis; Xenopus tropicalis