Biology subjects

Maguire, F.

Publications and source records attributed to Maguire, F..

3 recordsLinked to original sources

bioRxiv2021

Emergent RNA-RNA interactions can promote stability in a nascent phototrophic endosymbiosis

Eukaryote-eukaryote endosymbiosis was responsible for the spread of chloroplast (plastid) organelles. Stability is required for the metabolic and genetic integration that drives the establishment of new organelles, yet the mechanisms which act to stabilise nascent endosymbioses - between two fundamentally selfish biological organisms - are unclear. Theory suggests that enforcement mechanisms, which punish misbehaviour, may act to stabilise such interactions by resolving conflict. However, how such mechanisms can emerge in a nascent endosymbiosis has yet to be explored. Here, we propose that endosymbiont-host RNA-RNA interactions, arising from digestion of the endosymbiont population, can result in a cost to host growth for breakdown of the endosymbiosis. Using the model nascent endosymbiosis, Paramecium bursaria - Chlorella spp., we demonstrate that this mechanism is dependent on the host RNA-interference (RNAi) system. We reveal through small RNA (sRNA) sequencing that endosymbiont-derived mRNA released upon endosymbiont digestion can be processed by the host RNAi system into 23-nt sRNA. We predict multiple regions of shared sequence identity between endosymbiont and host mRNA, and demonstrate through delivery of synthetic endosymbiont sRNA that exposure to these regions can knock-down expression of complementary host genes, resulting in a cost to host growth. This process of host gene knock-down in response to endosymbiont-derived RNA processing by host RNAi factors, which we term RNAi-collisions, represents a mechanism which can promote stability in a nascent eukaryote-eukaryote endosymbiosis. By imposing a cost for breakdown of the endosymbiosis, endosymbiont-host RNA-RNA interactions may drive maintenance of the symbiosis across fluctuating ecological conditions and symbiotic status. SIGNIFICANCE STATEMENTStable endosymbiosis between eukaryotic microbes has driven the evolution of further cellular complexity. Yet the mechanisms which can act to stabilise a nascent eukaryote-eukaryote endosymbiosis are unclear. Using the model nascent endosymbiotic system, Paramecium bursaria-Chlorella, we demonstrate that endosymbiont-host RNA-RNA interactions can drive a cost to host growth upon endosymbiont digestion, punishing the host for misbehaviour. These RNA-RNA interactions are facilitated by the host RNA-interference system. For endosymbiont mRNA sharing a high-level of sequence identity with host transcripts, this process can result in host gene knock-down. We propose that these endosymbiont-host RNA-RNA interactions- RNAi collisions-represent a viable enforcement mechanism to sanction the host for breakdown of the endosymbiosis, promoting the stability of a nascent endosymbiotic interaction.

evolutionary biology↗

bioRxiv2020

Validation of a Core RNA-interference Pathway as a Tool for Reverse Genetics in the Emergent Model Phototrophic Endosymbiosis, Paramecium bursaria

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 phylogentics, 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 then 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 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 use of the P. bursaria-Chlorella spp. system to investigate the genetic basis of a nascent endosymbiosis.

molecular biology↗

bioRxiv2020

Metagenome-Assembled Genome Binning Methods Disproportionately Fail for Plasmids and Genomic Islands

Metagenomic methods are an important tool in the life sciences, as they enable simultaneous characterisation of all microbes in a community without time-consuming and bias-inducing culturing. Metagenome-assembled genome (MAG) binning methods have emerged as a promising approach to recover individual genomes from metagenomic data. However, MAG binning has not been well assessed for its ability to recover mobile genetic elements (MGEs), such as plasmids and genomic islands (GIs), that have very high clinical/agricultural/environmental importance. Certain antimicrobial resistance (AMR) genes and virulence factor (VF) genes are noted to be disproportionately associated with MGEs, making studying their transmission a public health priority. However, the variable copy number and sequence composition of MGEs relative to the majority of the host genome makes them potentially problematic for MAG binning methods. To systematically investigate this, we simulated a low-complexity metagenome comprising 30 GI-rich and plasmid-containing bacterial genomes. MAGs were then recovered using 12 current prediction pipelines and evaluated for recovery of MGE-associated AMR/VF genes. Here we show that while 82-94% of chromosomes could be correctly recovered and binned, only 38-44% of GIs were recovered and, even more notably, only 1-29% of plasmid sequences were found. Most strikingly, no plasmid-borne VF or AMR genes were recovered and within GIs, only between 0-45% of AMR or VF genes were identified. We conclude that short-read MAGs are largely ineffective for the analysis of mobile genes, including those of public-health importance like AMR and VF genes. We propose that microbiome researchers should instead primarily utilise unassembled short reads and/or long-read approaches to more accurately analyse metagenomic data

bioinformatics↗