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Defensive Symbiosis in Drosophila: from Multiple Infections to Mechanism of Defense

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Defensive Symbiosis in Drosophila: from Multiple Infections to Mechanism of Defense Defensive symbiosis in Drosophila: from multiple infections to mechanism of defense by Phineas T. Hamilton B.Sc., University of Victoria, 2006 M.Sc., University of Victoria, 2010 ADissertationSubmittedinPartialFulfillmentofthe Requirements for the Degree of DOCTOR OF PHILOSOPHY in the Department of Biology c Phineas Hamilton, 2015 University of Victoria All rights reserved. This dissertation may not be reproduced in whole or in part, by photocopying or other means, without the permission of the author. ii Defensive symbiosis in Drosophila: from multiple infections to mechanism of defense by Phineas T. Hamilton B.Sc., University of Victoria, 2006 M.Sc., University of Victoria, 2010 Supervisory Committee Dr. Steve Perlman, Supervisor (Department of Biology) Dr. Brad Anholt, Departmental Member (Department of Biology) Dr. Ben Koop, Departmental Member (Department of Biology) Dr. Brian Starzomski, Outside Member (Department of Environmental Studies) iii Supervisory Committee Dr. Steve Perlman, Supervisor (Department of Biology) Dr. Brad Anholt, Departmental Member (Department of Biology) Dr. Ben Koop, Departmental Member (Department of Biology) Dr. Brian Starzomski, Outside Member (Department of Environmental Studies) ABSTRACT Multiple infections within the same host are now understood to be common and important determinants of the outcomes of disease processes. Multiple infections are particularly important in insects, which are often infected by vertically transmitted symbionts that are passed from the mother to her o↵spring. In many cases, these symbionts have evolved to confer high levels of protection against co-infecting para- sites, pathogens, or other natural enemies. Despite widespread examples of symbiont- mediated defense, there are key outstanding questions in the ecology and evolution of defensive symbiosis. These include the mechanisms through which protection is conferred, the specificity of defensive e↵ects against di↵erent parasites and pathogens, and the overall roles of defensive and other symbioses in host communities and ecosys- tems. To address these questions, I used a model of defensive symbiosis in which the bacterium Spiroplasma protects the woodland fly Drosophila neotestacea from the ne- matode parasite Howardula aoronymphium. First, I conducted a series of experiments iv that included transcriptome sequencing of D. neotestacea infected by Howardula and Spiroplasma to uncover the mechanistic basis of defense in this symbiosis. Through these experiments, I found evidence of a putative protein toxin encoded by Spiro- plasma that might contribute to defense. Following this, we characterized the protein as a novel member of a class of toxins known as ribosome-inactivating proteins (RIPs). RIPs are important virulence factors in bacteria such as enterohemorrhagic E. coli; IexploitedrecentapproachesforquantifyingRIPactivitytodesignsensitiveassays that demonstrate that Howardula su↵ers a high degree of ribosome cleavage specific to RIP attack during Spiroplasma-mediated defense. This is among the first demon- strations of a mechanism of defense against a specific enemy in an insect defensive symbiosis. Inextworkedwithcollaboratorstocultureandcharacterizeanoveltrypanoso- matid parasite of Drosophila that I uncovered during the above transcriptome se- quencing. Trypanosomatids are protist parasites that are common in insects, and the causes of important human diseases that include Chagas disease and African sleeping sickness. Despite Drosophila’s history as an important model of infection and immu- nity, little is known of its trypanosomatid parasites, and we describe this parasite as anewgenusandspecies:Jaenimonas drosophilae,thefirsttrypanosomatidformally described from a Drosophila host. We conduct a series of experiments to understand infection dynamics, immune responses and interactions with other parasites and sym- bionts within the host, beginning to establish Drosophila-Jaenimonas infections as a tractable model of trypanosomatid infection in insects. Finally, though examples of ecologically important defensive symbioses accumu- late, an understanding of their overall roles in ecosystems is lacking. I close with a synthesis of the ways in which symbioses - defensive or otherwise - can a↵ect ecosys- tem structure and function through their e↵ects on food webs. This work will help to develop a conceptual framework to link reductionist findings on specific symbioses to larger scale processes. v Contents Supervisory Committee ii Abstract iii Table of Contents v List of Tables vi List of Figures vii Acknowledgements xiii 1 An introduction: from multiple infections to defensive symbiosis 1 2 Transcriptional responses in a Drosophila defensive symbiosis 7 3 A novel ribosome-inactivating protein in a Drosophila defensive symbiont 27 4 Infection dynamics and immune response in a newly described Drosophila-trypanosomatid association 44 5 Symbiosis in ecological networks 72 A Supplementary Information 90 vi List of Tables Table 4.1 Gene Ontology Enrichment analysis for genes up- and down- regulated in response to Jaenimonas exposure in D. melanogaster larvae. Selected gene ontology terms are shown to limit redun- dancy. Analysis was based on genes identified as di↵erentially expressed by Cu✏inks (Q < 0.05) and conducted using the on- line tool DAVID against a D. melanogaster background. 55 Table A.1 Targets, primer sequences, and reaction conditions for PCR and qPCR reactions of Chapter 2 . 90 Table A.2 Selected Gene Ontology categories significantly enriched in tran- scripts responding to Howardula and Spiroplasma infection. *** Padj < 0.01, ** Padj < 0.05, * Padj < 0.1. 91 Table A.3 Efficiencies of primers used for all assays in Chapter 3. Efficiency and specificity were validated on standard curves of 5 10-fold ⇥ serial dilutions of synthetic DNA (IDT gBlocks) for all primer sets, except for the primer pair for the Howardula normalizing primer set, which was tested using a dilution series of cDNA re- verse transcribed from Howardula-infected flies. Bases specific to sites of depurination are in bold, and deliberate mismatches underlined. 92 vii List of Figures Figure 2.1 Spiroplasma infection intensity (mean SE of log of Spiro- ± 2 plasma dnaA normalized against host tpi) over the development of Drosophila neotestacea.Errorbarsarestaggeredforclarity. There were no discernible e↵ects of Howardula exposure or in- fection status on Spiroplasma infection (N = 69). 16 Figure 2.2 Raw expression levels of assembled transcripts in the reduced transcriptome, with taxonomy assigned by BLASTx against the non-redundant database. Treatments containing both host and parasites are shown (S-HA+ and S+HA+), with total numbers of contigs for the host and parasites presented in legend. Nematode transcript abundance is 10foldlowerintheS+line. 17 ⇠ Figure 2.3 Heatmap of expression levels of transcripts with immune, stress or defense function, based on Gene Ontology. Transcripts are clustered on the y-axis based on similarity in expression lev- els across treatments (Euclidean distance of scaled responses), with the blue trace reflecting the relative magnitude of expres- sion across transcripts (as Z-scores). Expression patterns demon- strate a large immune gene response to Howardula (HA) exposure but little response to Spiroplasma (S-); note that most of these transcripts are not statistically significant in their responses to treatments. 19 Figure 2.4 Expression of the putative Spiroplasma ribosome-inactivating protein in one-day (n=31) and seven-day (n=14) old flies. Exper- imental treatments are unexposed (control), nematode-exposed and uninfected (HA -), and nematode exposed and infected (HA +). Expression is significantly higher in day-old nematode - flies. Flies in the seven-day experiment were also screened for trypanosomatid infection; all flies tested negative . 22 viii Figure 3.1 Spiroplasma strains encode divergent RIP-like sequences. Maximum- likelihood phylogeny of SpRIP from the defensive D. neotestacea strain of Spiroplasma,alignedwithotherputativeSpiroplasma RIPs and selected RIP seed sequences from the PFAM database (PF00161). Support values are calculated based on 1000 boot- straps using FastTree; the scale bar denotes substitutions per site. Single and double asterisks represent >70% and 90% boot- strap support, respectively. 31 Figure 3.2 Purified recombinant SpRIP degrades into a stable product over two weeks time at 4◦C. (A) Schematic of SpRIP domain pre- diction. SP, signal peptide. The black horizontal line a repre- sents the recombinant protein (Ala31 to His403) produced in this study. b represents the stable degradation product from purified recombinant SpRIP. (B) SDS-PAGE analysis of SpRIP (44 kDa) incubated at 4◦C.FigurecourtesyofFangniPeng. 32 Figure 3.3 SpRIP depurinates rabbit 28S rRNA at the site of RIP attack in cell-free assays. Abundance of cDNA representing intact (A) and depurinated (B) rRNA template after incubation with 5.25 µMofrecombinantSpRIP for 30 min at 30◦C(N=6). SpRIP significantly decreases the abundance of intact template and in- creases the abundance of depurinated template (P < 0.001 for both)................................. 33 Figure 3.4 SpRIP causes dose-dependent depurination of rabbit 28S rRNA in cell free assays (N = 14). 34 Figure 3.5 SpRIP depurinates Howardula 28S rRNA at the site of RIP at- tack in assays with live Howardula. Abundance of cDNA rep- resenting intact (A) and depurinated (B) rRNA template after incubation with 5.25 µMofrecombinantSpRIP for 4 hours at 21◦C (N = 6). While abundance
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