Marine medaka ATP-binding cassette (ABC) superfamily and new insight into teleost Abch nomenclature

Transcription

1 Supplementary file for: Marine medaka ATP-binding cassette (ABC) superfamily and new insight into teleost Abch nomenclature Chang-Bum Jeong a,b,#, Bo-Mi Kim a,#, Hye-Min Kang a, Ik-Young Choi c, Jae-Sung Rhee d,*, Jae-Seong Lee a,* a Department of Biological Science, College of Science, Sungkyunkwan University, Suwon , South Korea b Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul , South Korea c National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul , South Korea d Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon , South Korea # These authors contributed equally to this manuscript. *Corresponding authors: jslee2@skku.edu (J.-S. Lee a ), jsrhee@inu.ac.kr (J.-S. Rhee d )

2 Table S1. Information on the putative abcb1/4 genes in teleosts registered in GenBank database and/or Ensembl genome browser. Species Gene name Ensembl Gene ID GenBank No. Astyanax mexicanus Abcb4 ENSAMXG Danio rerio Abcb4 ENSDARG AFR69055 Gadus morhua Abcb4 ENSGMOG Gasterosteus aculeatus Abcb4 ENSGACP Ictalurus punctatus Abcb1 JT Latimeria chalumnae Abcb4 ENSLACG Lepisosteus oculatus Abcb4 ENSLOCG Oncorhynchus mykiss Abcb1 AAW56424 Oreochromis niloticus 1 P-glycoprotein BAM36701 Abcb4 ENSONIP Oryzias latipes 2 Abcb Abcb4 ENSORLP Petromyzon marinus 3 Abcb1 AKC42134 Abcb4 ENSPMAG Poecilia formosa Abcb4 ENSPFOG Poeciliopsis lucida Abcb1 ADQ20481 Scleropages formosus Abcb4 KKX05686 Takifugu rubripes Abcb4 ENSTRUG Tetraodon nigroviridis 4 Abcb4-1 Abcb4-2 Abcb4-3 ENSTNIG ENSTNIG ENSTNIG CAG11904 CAG11905 CAG11906 Trematomus bernacchii Abcb1 ACX30417 Xiphophorus maculatus Abcb4 ENSXMAG A single gene annotated with different names. 2 A single gene annotated with different names. 3 A single gene annotated with different names. 4 Three genes annotated individually.

3 Identity (%) Table S2. Amino acid similarity and identity comparisons for Oryzias melastigma and Ictalurus punctatus abcc5 genes, which are separated into distinctive clades. Abbreviations: Om, Oryzias melastigma; Ip, Ictalurus punctatus. Similarity (%) -like like

4 Identity (%) Table S3. Amino acid similarity and identity comparisons for Oryzias melastigma, Oryzias latipes, and Danio rerio abcg2 genes, which are separated into distinctive clades. Abbreviations: Om, Oryzias melastigma; Ol, Oryzias latipes; Dr, Danio rerio. Similarity (%) OmAbcg2-1 OmAbcg2-2 OmAbcg2-like OlAbcg2-1 OlAbcg2-2 OlAbcg2-like DrAbcg2a DrAbcg2b DrAbcg2c DrAbcg2d OmAbcg OmAbcg OmAbcg2-like OlAbcg OlAbcg OlAbcg2-like DrAbcg2a DrAbcg2b DrAbcg2c DrAbcg2d

5 Supplementary Figure Legends Figure S1. Schematic representation of the conserved domain analysis of 50 O. melastigma ABC transporters. NBD in an ellipse indicates nucleotide binding domains (also referred to as an ATP-binding cassette), and TM in a rectangle represents transmembrane domains (TMDs). Numbers in brackets refer to the number of ABC proteins in each subfamily. Figure S2. Phylogenetic analysis of the O. melastigma Abca subfamily, compared with those of other species, using the Bayesian method. Numbers at branch nodes represent the confidence level of posterior probability. Species abbreviations: Dr, Danio rerio; Hs, Homo sapiens; Ip, Ictalurus punctatus; Mm, Mus musculus; Ol, Oryzias latipes; Om, Oryzias melastigma; On, Oreochromis niloticus; Tn, Tetraodon nigroviridis. Figure S3. Phylogenetic analysis of the O. melastigma Abcb subfamily, compared with those of other species, using the Bayesian method. Numbers at branch nodes represent the confidence level of posterior probability. Dr, Danio rerio; Hs, Homo sapiens; Ip, Ictalurus punctatus; Mm, Mus musculus; Ol, Oryzias latipes; Om, Oryzias melastigma; On, Oreochromis niloticus; Tn, Tetraodon nigroviridis. Figure S4. Phylogenetic analysis of the O. melastigma Abcc subfamily, compared with those of other species, using the Bayesian method. Numbers at branch nodes represent the confidence level of posterior probability. Dr, Danio rerio; Hs, Homo sapiens; Ip, Ictalurus punctatus; Mm, Mus musculus; Ol, Oryzias latipes; Om, Oryzias melastigma; On, Oreochromis niloticus; Tn, Tetraodon nigroviridis. Figure S5. Phylogenetic analysis of the O. melastigma Abcd subfamily, compared with those of other species, using the Bayesian method. In the case of Danio rerio abcd2-2 and Ictalurus punctatus abcd2, the sequences were excluded as they disrupt overall distance values in the phylogenetic branches due to the partial cdna sequences registered in GenBank. Numbers at branch nodes represent the confidence level of posterior probability. Dr, Danio rerio; Hs, Homo sapiens; Ip, Ictalurus punctatus; Mm,

6 Mus musculus; Ol, Oryzias latipes; Om, Oryzias melastigma; On, Oreochromis niloticus; Tn, Tetraodon nigroviridis. Figure S6. Phylogenetic analysis of the O. melastigma Abce and Abcf subfamilies, compared with those of other species, using the Bayesian method. Numbers at branch nodes represent the confidence level of posterior probability. Dr, Danio rerio; Hs, Homo sapiens; Ip, Ictalurus punctatus; Mm, Mus musculus; Ol, Oryzias latipes; Om, Oryzias melastigma; On, Oreochromis niloticus; Tn, Tetraodon nigroviridis. Figure S7. Phylogenetic analysis of the O. melastigma Abcg and Abch subfamilies, compared with those of other species, using the Bayesian method. Numbers at branch nodes represent the confidence level of posterior probability. Dr, Danio rerio; Hs, Homo sapiens; Ip, Ictalurus punctatus; Mm, Mus musculus; Ol, Oryzias latipes; Om, Oryzias melastigma; On, Oreochromis niloticus; Tn: Tetraodon nigroviridis. Figure S8. Amino acid similarity of Oryzias melastigma and Ictalurus punctatus abcc5 genes, which are separated into distinctive clades. Abbreviations: Om, Oryzias melastigma; Ip, Ictalurus punctatus. Figure S9. An updated phylogenetic analysis of 50 O. melastigma ABC proteins with other species including arthropod abch genes, and three abch genes of invertebrates; Pacific oyster abch gene (Crassostrea gigas; EKC37771), acorn worm (Saccoglossus kowalevskii; XP_ ), and sea urchin (Strongylocentrotus purpuratus; XP_ ; also registered in the Sea urchin genome database ( ID: SPU_026438). In addition, three putative ABCH/Abch members were incorporated to analyze their phylogenetic locations (highlighted with yellow color; sea urchin ABC transporter H family member 2-like (S. purpuratus; LOC889169), the dolphin ABC transporter H family member 2-like (Lipotes vexillifer; LOC ), and the Tibetan antelope ABC transporter H family member 2-like (Pantholops hodgsonii; LOC ). Species abbreviations: Cg, Crassostrea gigas; Dm, Drosophila melanogaster; Dp, Daphnia pulex; Dr, Danio rerio; Hs, Homo sapiens; Ip, Ictalurus punctatus; Mm, Mus musculus; Ol, Oryzias latipes; Om, Oryzias melastigma; On, Oreochromis niloticus; Sk, Saccoglossus

7 kowalevskii; Sp, Strongylocentrotus purpuratus; Tb, Tribolium castaneum; Tj, Tigriopus japoncus; Tn, Tetraodon nigroviridis. Figure S10. Enlarged phylogenetic clade of the Abch subfamily from Fig. S9. Species abbreviations: Cg, Crassostrea gigas; Dm, Drosophila melanogaster; Dp, Daphnia pulex; Dr, Danio rerio; Om, Oryzias melastigma; Sk, Saccoglossus kowalevskii; Sp, Strongylocentrotus purpuratus; Tb, Tribolium castaneum; Tj, Tigriopus japoncus; Tn, Tetraodon nigroviridis. Figure S11. Enlarged phylogenetic clade of the Abcf and Abcg subfamilies from Fig. S9. Species abbreviations: Dr, Danio rerio; Hs, Homo sapiens; Ip, Ictalurus punctatus; Mm, Mus musculus; Ol, Oryzias latipes; Om, Oryzias melastigma; On, Oreochromis niloticus; Tn, Tetraodon nigroviridis.

8 Fig. S1 Subfamily A TMD NBD TMD NBD (10) Subfamily B TMD TMD NBD NBD TMD (7) NBD (3) Subfamily C TMD NBD TMD NBD (13) Subfamily D TMD NBD (4) Subfamily E NBD NBD (1) Subfamily F NBD NBD (3) Subfamily G NBD (8) TMD Subfamily H NBD TMD (1)

9 Subfamily A Hs: Homo sapiens Mm: Mus musculus Dr: Danio rerio Ip: Ictalurus punctatus Tn: Tetraodon nigroviridis On: Oreochromis niloticus Ol: Oryzias latipes Om: Oryzias melastigma IpAbca OlAbca1-2 OnAbca1-2 TnAbca1-2 IpAbca1a DrAbca1a DrAbca1b IpAbca1b OlAbca1-like OmAbca1-2 OmAbca1-1 OlAbca1-1 OnAbca1-1 TnAbca1-1 HsABCA1 MmAbca1 HsABCA7 MmAbca7 IpAbca7 TnAbca7 OlAbca7 OmAbca7 IpAbca1-like OmAbca1-like HsABCA4 MmAbca4 OmAbca4-1 OlAbca4-1 OnAbca4-1 DrAbca4A DrAbca4-1 TnAbca4 OnAbca4-2 OlAbca4-2 OmAbca4-2 HsABCA2 MmAbca2 DrAbca2 IpAbca2 OlAbca2 OmAbca2 HsABCA3 MmAbca3 DrAbca3 IpAbca3 TnAbca3 OnAbca3 OlAbca3 OmAbca3 HsABCA13 MmAbca13 HsABCA12 MmAbca12 DrAbca12 IpAbca12 OnAbca12 OlAbca12 OmAbca12 MmAbca5 HsABCA5 DrAbca5 IpAbca5 TnAbca5 OnAbca5 OlAbca5 OmAbca5 HsABCA6 MmAbca6 HsABCA10 HsABCA9 MmAbca9 MmAbca8a HsABCA8 MmAbca8b Fig. S2

10 Subfamily B Full transporters Half transporters Fig. S3 OlAbcb4 OmAbcb4 OnABCB4 TnAbcb1-1 TnAbcb1-2 IpAbcb1 DrAbcb4 MmAbcb4 HsABCB4 MmAbcb1b MmAbcb1a HsABCB1 IpAbcb5 DrAbcb5 MmAbcb5 HsABCB5 HsABCB11 MmAbcb11 OlAbcb11b OmAbcb11b DrAbcb11a DrAbcb1b IpAbcb11 TnAbcb11 OlAbcb11a OmAbcb11a OmAbcb10 OlAbcb10 OnABCB10 TnAbcb10 IpAbcb10 DrAbcb10 MmAbcb10 HsABCB10 MmAbcb8 HsABCB8 DrAbcb8 IpAbcb8 TnAbcb8 OnABCB8 OmAbcb8 OlAbcb8 OlAbcb2 OmAbcb2 OnABCB2 TnAbcb2 IpAbcb2 DrAbcb2 HsABCB2 MmAbcb2 OmAbcb9 OlAbcb9 TnAbcb9 IpAbcb9 DrAbcb9 MmAbcb9 HsABCB9 MmAbcb3 HsABCB3 IpAbcb3-like DrAbcb3-like IpAbcb3 OlAbcb3 OmAbcb3 OlAbcb7 OmAbcb7 OnABCB7 TnAbcb7 DrAbcb7 IpAbcb7 HsABCB7 MmAbcb7 HsABCB6 MmAbcb6 IpAbcb6-2 DrAbcb6-2 TnAbcb6-2 DrAbcb6 IpAbcb6-1 TnAbcb6-1 OnABCB6-1 OnABCB6-2 OmAbcb6 OlAbcb

11 OmAbcc4-1 OlAbcc4-1 OnAbcc4-1 TnAbcc4-2 TnAbcc4-3 OnAbcc4-3 TnAbcc4-1 OnAbcc4-2 OlAbcc4-2 OmAbcc4-2 IpAbcc4 DrAbcc4 MmAbcc4 HsABCC4 HsABCC7 MmAbcc7 DrAbcc7 IpAbcc7 OnAbcc7 TnAbcc7 OlAbcc7 OmAbcc7 HsABCC10 MmAbcc10 DrAbcc10 IpAbcc10 TnAbcc10 OnAbcc10 OlAbcc10 OmAbcc10 OmAbcc12 OlAbcc12 TnAbcc12 DrAbcc12 IpAbcc12 HsABCC12 MmAbcc12 HsABCC11 OlAbcc5b TnAbcc5 -like HsABCC5 MmAbcc5 DrAbcc5 OnAbcc5-1 OnAbcc5-2 OlAbcc5a DrAbcc8-1 DrAbcc8-2 DrAbcc8 IpAbcc8 OlAbcc8 OmAbcc8 TnAbcc8 OnAbcc8 DrAbcc8-like HsABCC8 MmAbcc8 HsABCC9 MmAbcc9 DrAbcc9 IpAbcc9 OmAbcc9 OlAbcc9 DrAbcc13 OmAbcc2 OlAbcc2 OnAbcc2 TnAbcc2 IpAbcc2 DrAbcc2 HsABCC2 MmAbcc2 OmAbcc6 OlAbcc6 TnAbcc6 OnAbcc6 DrAbcc6-1 IpAbcc6 DrAbcc6-2 DrAbcc6-3 HsABCC6 MmAbcc6 OmAbcc3 OlAbcc3 IpAbcc3 DrAbcc3 HsABCC3 MmAbcc3 HsABCC1 MmAbcc1 TnAbcc1 DrAbcc1 IpAbcc1 OnAbcc1 OlAbcc1 OmAbcc Subfamily C Fig. S4

12 Subfamily D OmAbcd1 OlAbcd1 OnAbcd1 TnAbcd1 DrAbcd1 IpAbcd1 HsABCD1 MmABCD1 HsABCD2 MmABCD2 DrAbcd2-1 OnAbcd2 OlAbcd2 OmAbcd2 HsABCD3 MmABCD3 IpAbcd3b DrAbcd3b DrAbcd3a IpAbcd3a TnAbcd3 OnAbcd3 OlAbcd3 OmAbcd3 HsABCD4 MmABCD4 IpAbcd4 DrAbcd4 TnAbcd4 OnAbcd4 OlAbcd4 OmAbcd Fig. S5

13 Subfamily E and F Fig. S OmAbcf2 OlAbcf2 OnAbcf2 TnAbcf2 IpAbcf2-2 DrAbcf2a IpAbcf2-1 DrAbcf2-1 HsABCF2 MmABCF2 HsABCF3 MmABCF3 DrAbcf3 IpAbcf OnAbcf3 TnAbcf3 OlAbcf3 OmAbcf3 HsABCF1 MmABCF1 DrAbcf1 IpAbcf1 OnAbcf1 TnAbcf1-1 OlAbcf1 OmAbcf HsABCE1 MmABCE1 DrAbce1 IpAbce1-1 IpAbce1-2 TnAbce1 OnAbce1 OlAbce1 OmAbce1 Subfamily F Subfamily E

14 OlAbcg2-2 OmAbcg2-2 OnAbcg2-1 TnAbcg2-1 IpAbcg2-2 DrAbcg2d DrAbcg2a IpAbcg2-1 OnAbcg2-2 OlAbcg2-1 OmAbcg2-1 MmABCG3 HsABCG2 MmABCG2 DrAbcg2c DrAbcg2b OlAbcg2-like OmAbcg2-like OlAbcg5 OmAbcg5 OnAbcg5 TnAbcg5 IpAbcg5 DrAbcg5 HsABCG5 MmABCG5 HsABCG8 MmABCG8 DrAbcg8 IpAbcg8 TnAbcg8 OnAbcg8 OmAbcg8 OlAbcg8 OlAbcg1 OmAbcg1 TnAbcg1 OnAbcg1 DrAbcg1 HsABCG1 MmABCG1 HsABCG4 MmABCG4 OlAbcg4-1 OmAbcg4-1 TnAbcg4 OnAbcg4-2 DrAbcg4b IpAbcg4 DrAbcg4a OnAbcg4-1 OlAbcg4-2 OmAbcg4-2 DrABCH1 OmABCH1 TnABCH Subfamily G Subfamily H Subfamily G and H Fig. S7

15 Fig. S8 -like -like -like -like -like -like -like -like -like -like 1,383 1,384 1,423 1,3

16 Fig. S9

17 Fig. S10 Other invertebrates Fish Arthropods ABCH

18 Fig. S11 ABCG ABCF