Characterization of the RNA-interference pathway as a tool for reverse genetic analysis in the nascent phototrophic endosymbiosis, Paramecium bursaria.

Benjamin H Jenkins,Guy Leonard,Joshua D Eaton,Thomas A Richards,Benjamin E Housden,David S Milner,Steven West,Finlay Maguire

doi:10.1098/rsos.210140

Benjamin H Jenkins, Guy Leonard + Show 6 more

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https://doi.org/10.1098/rsos.210140

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Abstract

Endosymbiosis was fundamental for the evolution of eukaryotic complexity. Endosymbiotic interactions can be dissected through forward- and reverse-genetic experiments, such as RNA-interference (RNAi). However, distinguishing small (s)RNA pathways in a eukaryote–eukaryote endosymbiotic interaction is challenging. Here, we investigate the repertoire of RNAi pathway protein-encoding genes in the model nascent endosymbiotic system, Paramecium bursaria–Chlorella spp. Using comparative genomics and transcriptomics supported by phylogenetics, we identify essential proteome components of the small interfering (si)RNA, scan (scn)RNA and internal eliminated sequence (ies)RNA pathways. Our analyses reveal that copies of these components have been retained throughout successive whole genome duplication (WGD) events in the Paramecium clade. We validate feeding-induced siRNA-based RNAi in P. bursaria via knock-down of the splicing factor, u2af1, which we show to be crucial to host growth. Finally, using simultaneous knock-down ‘paradox’ controls to rescue the effect of u2af1 knock-down, we demonstrate that feeding-induced RNAi in P. bursaria is dependent upon a core pathway of host-encoded Dcr1, Piwi and Pds1 components. Our experiments confirm the presence of a functional, host-derived RNAi pathway in P. bursaria that generates 23-nt siRNA, validating the use of the P. bursaria–Chlorella spp. system to investigate the genetic basis of a nascent endosymbiosis.

Highlights

Endosymbiosis was fundamental for the evolution of eukaryotic cellular complexity [1,2,3,4]
We found that P. bursaria encodes a total of five Dicer or Dicer-like endonucleases (Dcr1, Dcr2/3—electronic supplementary material, dataset S1; Dcl1/2, Dcl3/4 and Dcl5—electronic supplementary material, dataset S2), three RdRPs (Rdr1/4, Rdr2 and Rdr3—electronic supplementary material, dataset S3), six AGO-Piwi components (PiwiA1, PiwiA2, PiwiB, PiwiC1, PiwiC2 and PiwiD— electronic supplementary material, dataset S4), a single Paramecium-specific Pds1 (Pds1—electronic supplementary material, dataset S5), and two nucleotidyl transferase (Cid1/3 and Cid2—electronic supplementary material, dataset S6) genes
We show that P. bursaria encodes homologues for components of the transgene-induced siRNA pathway, as well as the endogenous ciliate-specific scnRNA and iesRNA pathways involved in nuclear reorganization and development

Summary

Introduction

Endosymbiosis was fundamental for the evolution of eukaryotic cellular complexity [1,2,3,4]. In order to investigate the genetic basis of an emergent endosymbiotic system, we must develop experimentally tractable endosymbiotic model species [5,6,7]. Paramecium bursaria is a ciliate protist which harbours several hundred cells of the green algae, Chlorella spp., in a nascent and facultative photoendosymbiosis [8,9,10,11,12]. While the interaction is heritable, the P. bursaria–Chlorella spp. system is described as a ‘nascent’ or ‘facultative’ endosymbiosis, as both host and endosymbiont can typically survive independently [10,20,21,22,23]. Paramecium bursaria represents a potentially tractable model system with which to investigate the genetic basis of a nascent endosymbiotic cell–cell interaction

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