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Vertebrate P450s with emphasis on the land vertebrates

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Presentation on theme: "Vertebrate P450s with emphasis on the land vertebrates"— Presentation transcript:

1 Vertebrate P450s with emphasis on the land vertebrates
David Nelson Dec. 7, 2015

2 Progress in acquiring and naming the vertebrate P450s
Sources of sequences: Ensembl Pfam Datamining genomes

3 Download options from Pfam

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5 Use of FamAln data to supplement Ensembl genes downloaded via BioMart
Dr. Osamu Gotoh’s algorithm for searching and assembling P450s from genomic data finds more genes and pseudogenes than are annotated in Ensembl. For example 83 seqs vs 70 seqs in cow. 11 of the 13 were pseudogenes, two of the 13 were intact genes (CYP2J8 and CYP4F46). The FamAln data give enhanced gene collections. Dr. Gotoh has run his algorithm on 84 vertebrate genomes finding 5859 seqs.

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7

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9 The origin of the CYP2D subfamily

10 diverge from CYP2P to CYP2J
fish HOOK1, CYP2P, CYP2P, SERBP1, HSD17B7, DDR2 Split the locus HOOK1, CYP2P CYP2P, SERBP1, HSD17B7, DDR2 diverge from CYP2P to CYP2J Rearrange, diverge from CYP2P to CYP2D amphibians HOOK1, CYP2J HSD17B7, CYP2D, DDR2 (CYP2J lost in frogs, present in other tetrapods) Seed new locus Xenopus HSD17B7, CYP2D53, CYP2D54 DDR2 WBP2NL, CYPD, SREBF2 Migrate 5 genes to the right reptiles SREBF2 SHISA9 CENPM SEPT3 WBP2NL NAGA FAM109B SMDT1 NDUFA6 CYP2D6 Move TCF20 in to join the cluster SREBF2 SHISA9 CENPM SEPT3 WBP2NL NAGA FAM109B SMDT1 NDUFA6 CYP2D6 TCF20

11 CYP3A Synteny COW HUMAN HORSE PIKA CPSF4 ZKSCAN5 ZFN655 CYP3A24
GJC3 ATP5J2 ZSCAN25 CYP3A76 ORA2AE1 TRIM4 AZGP1 HUMAN ZFN789 ZKSCAN5 ZFN655 CYP3A5 CYP3A4 ORA2AE1 GJC3 ZFN394 FAM200A ZSCAN25 CYP3A7 CYP3A43 TRIM4 AZGP1 HORSE ZFN789 ZKSCAN5 ZFN655 CYP3A93 CYP3A95 CYP3A96 CYP3A128P ORA2AE1 GJC3 ZFN394 ZSCAN25 CYP3A94 CYP3A89 CYP3A97 CYP3A129 TRIM4 AZGP1 FUS PRSS8 AKRIE2 ORA2AE1 GJC3 PIKA PRSS36 BCKDK CYP3A TRIM4 AZGP1

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13 New CYP2 subfamily found in mammals
CYP2AR1P is present in cow as a pseudogene and in 13-lined ground squirrel and star-nosed mole as whole genes. Subsequent searches found pseudogenes In many mammals from armadillo (Xenarthra), manatee (Afrotheria), carnivora, insectivora. The gene has been lost in human, mouse, rat, and opossum, so it was not discovered before now. The synteny is preserved next to CYP2S1 and a CYP2B sequence all the way back to reptiles. Xenopus has a CYP2AR1 gene flanked by divergent CYPs near the edge of a large cluster syntenic with the CYP2ABFGST cluster.

14 9% 16% 14% 11% 61,879 known vertebrates ca 80,000 estimated total
Fish species number ~ 31500 Fish ecotype diversity is huge (salt vs fresh, deep vs shallow, veg vs pisc vs omin vs crust, toxin exposure,) Closely related species may live in diff env, eat diff foods 61,879 known vertebrates ca 80,000 estimated total Fish species number ~ 31500

15 Tetrapods Koepfli et al The Genome 10K Project: A Way Forward (2015)

16 55 55-59 65-70 53-71 49 51 110 75-94 94 60 55 46

17 Tetraodon nigroviridis Danio rerio Oryzias latipes
Previously annotated Newly annotated or ongoing Next genomes Takifugu rubripes Tetraodon nigroviridis Danio rerio Oryzias latipes Fundulus heteroclitus Gasterosteus aculeatus Gadus morhua Lepisosteus oculatus Astyanaxa mexicanus Latimeria chalumnae Xiphophorus maculatus Oreochromis niloticus Salmo salar Oncorhynchus mykiss Clupea harenga Poecilia formosa Esox lucius Austrofundulus limnaeus Cynoglossus semilaevis Notothenia coriiceps Physter macrocephalus Cyprinus carpio Pseudopleuronectes yokohamae Anguila japonica Cichlid (6 spp)

18 Tilapia Killifish Zebrafish Coelacanth Human Gar Stickleback Medaka Fugu Elephant shark Cavefish Platyfish

19 The CYP2 family in fish exhibits “blooms”

20 The CYP2 family in fish exhibits “blooms”

21 Lineage-specific expansions (blooms) are evident in different fish genomes
Cavefish CYP2AA Zebrafish CYP2AA

22 PXR and CYP2AA genes Tandem duplications CYP2AA2 CYP2AA1 podn 2AA7
CYP2AE1 zcchc11 2AA11 2AA8 2AA6 2AA3 2AA1 CYP2AA2 CYP2AA1

23 PXR and CYP2AA genes 3 uM PN Tandem duplications n.s. n.s. n.s. n.s.
podn 2AA7 2AA2 2AA9 2AA4 2AA12 CYP2AE1 zcchc11 2AA11 2AA8 2AA6 2AA3 2AA1 3 uM PN n.s. n.s. n.s. n.s. n.s. n.s. n.s. Fold change

24 Questions for SAB Homeologs (X. laevis example)
Genome collection and annotation Standardized pipelines for gene calls?

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26 Homeologs – naming convention from Xenbase
Xenopus laevis homeologs (duplicate laevis genes that arose from a genome polyploidization event) should be indicated with a "-L" or "-S" to distinguish between the two sub-genomes. In cases where the sub-genome determination has not been determined, the original "-a" or "-b" designation will stand. Example: laevis wnt3 homeologs are wnt3-L, wnt3-S, laevis wnt3a homeologs are wnt3a-L, wnt3a-S

27 Questions for SAB Homeologs (X. laevis example)
Genome collection and annotation Standardized pipelines for gene calls? Currently ENSEMBL > NCBI BioProject > individual genome pages

28 Future plans

29 27 REMAINING PROTEOMES IN THE RP75 SET (2221 SEQUENCES)

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