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In the Annelid Capitella Teleta

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In the Annelid Capitella Teleta THE CYTOCHROME P450 SUPERFAMILY COMPLEMENT IN CAPITELLA TELETA THE CYTOCHROME P450 SUPERFAMILY COMPLEMENT (CYPome) IN THE ANNELID CAPITELLA TELETA By: CHRISTOPHER DEJONG, H.B.SC. A thesis Submitted to the School of Graduate Studies in Partial Fulfillment of the Requirements for the Degree Master of Science McMaster University MASTER OF SCIENCE (2013) McMaster University (Biology) Hamilton, Ontario TITLE: The Cytochrome P450 superfamily Complement (CYPome) in the annelid Capitella teleta AUTHOR: Chris A. Dejong H.B.Sc (McMaster University) SUPERVISOR: Dr. Joanna Y. Wilson NUMBER OF PAGES: iv, 116 ii Abstract CYPs are a large and diverse protein superfamily found in all domains of life and are able to metabolize a wide array of both exogenous and endogenous molecules. The CYPome of the polychaete annelid Capitella teleta has been robustly identified and annotated with the genome assembly available (version 1). Annotation of 84 full length and 12 partial CYP sequences predicted a total of 96 functional CYPs in C. teleta. A further 13 CYP fragments were found but these may be pseudogenes. The C. teleta CYPome contained 24 novel CYP families and seven novel CYP subfamilies within existing families. A phylogenetic analysis was completed, primarily with vertebrate sequences, and identified that the C teleta sequences were found in 9 of the 11 metazoan CYP clans. Clan 2 was expanded in this species with 51 CYPs in 14 novel CYP families containing 20 subfamilies. There were five clan 3, four clan 4, and six mitochondrial clan full length CYPs. Two CYPs, CYP3071A1 and CYP3072A1, did not cluster with any metazoan CYP clan. C. teleta had a CYP51A1 gene with ~65% identity to vertebrate CYP51A1 sequences and was predicted to have lanosterol 14 α-demethylase activity. Several CYPs (CYP376A1, CYP3068A1, CYP3069A1, and CYP3070A1) are discussed as candidate genes for steroidogenesis. There are two CYP1-like CYPs and a total of four CYP331s found in C. teleta, which may play a role in PAH metabolism and warrant further analysis. The sand goby, Pomatoschistus minutus, had its CYPome annotated but a majority of the CYPs could only be partially annotated because the current sand goby genome assembly was still in the contig stage. Based on the annotations, the sand goby iii CYPome is predicted to contain approximately 50 CYPs with members from all expected families and subfamilies. iv Acknowledgements I always said I'd name as few names as possible here, and I think I'll succeed in doing that. Thank you to everyone in the Wilson lab, and everyone that dealt with my loud and often crass nature around LSB, you've been great to talk to and relax with, each of you know who you are. Thank you Derek for the consistent counsel over the years I've been here. Thank you to Andrew McArthur for edits on chapter 2 and all other help along the way. Thank you to all of my housemates over the years here in Hamilton, you girls kept me alive for that last writing stretch... seriously. To my family (Mama, daddy, Yiayia and Pa, my sibs and the list keeps going) for their endless support and understanding. To Noah, my brother , thanks for keeping me sane and always being there no matter what, and listening to my endless science. To my committee - Jon Stone and Ben Evans. Thanks for the input for the project and council. And of course to Joanna Wilson, you're honestly the best supervisor a guy could ask for. You have dealt with all my crap from the very lows to the crunch-time highs. Thank you for the countless, and scarily quick and thorough edits. Thank you for being my science and life council. This work represents two years of my life. I hope you get something out of it! v Table of Contents Abstract ............................................................................................................................. iii Acknowledgements ............................................................................................................v Table of Contents ............................................................................................................. vi List of Tables and Figures ............................................................................................. viii Abbreviations ................................................................................................................... ix Chapter 1: General Introduction Cytochrome P450 .............................................................................................................1 Superfamily overview Metazoan CYP diversity General Sequence Analysis and Protein Behavior Steroidogenesis of Vertebrate-like Signaling Steroids Capitella teleta .................................................................................................................9 General Species Overview Capitella Taxonomy The Capitella Genome Research Goals ...............................................................................................................11 References ......................................................................................................................13 Figures ............................................................................................................................20 vi Chapter 2: The Cytochrome P450 Superfamily Complement (CYPome) in the annelid Capitella teleta .....................................................................................................24 Abstract ..........................................................................................................................25 Introduction ....................................................................................................................26 Methods ..........................................................................................................................29 Results ............................................................................................................................32 Discussion ......................................................................................................................35 Conclusion ......................................................................................................................47 Acknowledgements ........................................................................................................48 References ......................................................................................................................49 Tables and Figures ..........................................................................................................60 Supplementary Information ............................................................................................75 Chapter 3: General Discussion CYPome Annotations .....................................................................................................82 CYP Nomenclature based on Phylogenetic Support ......................................................86 CYPs in Metazoans ........................................................................................................88 Phylogenetics as a Tool for Raising Functional Hypotheses .........................................90 In Silico Protein 3D analysis as a Tool for Raising Functional Hypotheses ..................91 Steroidogenesis in Annelids ...........................................................................................95 References ......................................................................................................................98 Appendix I: Annotation of the Sand Goby CYPome Introduction ..................................................................................................................103 Methods ........................................................................................................................104 Results and Discussion .................................................................................................105 References ....................................................................................................................109 Tables and Figures ........................................................................................................113 vii List of Tables and Figures Chapter 1: Figure 1.1. CYP clan distribution across metazoa and fungi ........................................20 Figure 1.2. The vertebrate steroidogenesis pathway .....................................................22 Chapter 2: Table 2.1. Conserved motifs across the Capitella teleta CYPome ................................60 Table 2.2. Xenobiotic response elements upstream of C. teleta CYPs ........................65 Figure 2.1. Phylogenetic tree of Cytochrome P450s in metazoa ..................................67 Figure 2.2. Distribution of the major Cytochrome P450 clans in five different species ......................................................................................................69 Figure 2.3. Phylogenies of Cytochrome P450 clan 2, clan 3 and 4, and the mitochrondrial clan .........................................................................................................71 Supplementary Table 2.1. Cytochrome P450 superfamily complement in Capitella teleta ...............................................................................................................................75 Supplementary Table 2.2. Incomplete Cytochrome P450s in Capitella teleta ............78 Supplementary Table 2.3. Cytochrome P450 fragments in
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