Biology subjects

Savory, F. R.

Publications and source records attributed to Savory, F. R..

5 recordsLinked to original sources

bioRxiv2026

Adaptation to free-living drives loss of beneficial endosymbiosis through metabolic trade-offs

Symbioses are widespread (1) and underpin the function of diverse ecosystems (2-6), but their evolutionary stability is challenging to explain (7,8). Fitness trade-offs between contrasting intracellular and extracellular niches could act to stabilise endosymbioses because adaptation to either niche is predicted to reduce fitness in the alternate niche, thus reinforcing symbiosis (8,9). Here, we experimentally evolved four diverse Chlorella green algal endosymbionts of Paramecium bursaria to free-living conditions supplying either an amino acid, as provisioned by hosts (10,11), or nitrate, as available in freshwater (12), as the sole nitrogen source. Experimental algal populations adapted to free-living environments, generally increasing in population density and cellular chlorophyll content over time. In one of the four endosymbiont strains, adaptation to the nitrate free-living environment, but not the amino acid environments, drove the loss of fitness benefits to the host in reconstituted symbioses. This loss was not associated with reduced ability to grow on host-provisioned amino acids, nor lost ability to release the sugars provisioned to the host (10,13). Genome sequencing of evolved algal lines revealed genomic divergence between nitrate-adapted and amino acid-adapted lines, affecting genes involved with metabolic organisation and intracellular resource transport. Untargeted metabolomic profiling further showed extensive changes to membrane remodelling and turnover in N-evolved lines. Together, our data support a role for metabolic trade-offs driving divergence between contrasting intracellular and extracellular niches, with nitrogen as a key environmental axis driving divergence. Fitness trade-offs may, therefore, be a general, simple mechanism acting to reinforce symbiosis, contributing to evolutionary stability.

evolutionary biology↗

bioRxiv2026

Stable transformation of Micractinium conductrix SAG 241.80: New tools for exploring photosymbiotic interactions

Endosymbiosis played a key role in the evolution of cellular complexity, but mechanisms underpinning establishment and maintenance remain unclear. Paramecium bursaria harbours Chlorellaceae algal endosymbionts and is a valuable model system for understanding photosymbiosis. However, there are a lack of molecular tools available for exploring the association. Here we report stable transformation of the P. bursaria endosymbiont Micractinium conductrix SAG 241.80. Bioluminescent reporter assays were used to identify endogenous regulatory sequences for transgene expression and to refine a protocol for delivery of exogenous DNA. The bleomycin resistance gene Shble was then identified as an effective selectable marker for isolating transformed cell lines. We demonstrate that endogenous introns enhance transgene expression and that isolation of transformants with desirable characteristics can be achieved without extensive screening by using a 2A peptide to couple expression of an upstream non-selectable transgene to expression of the Shble selectable marker. Finally, we demonstrate that M. conductrix SAG 241.80 transformants expressing fluorescent proteins can be introduced into host cells and observed in the absence of selection, enabling distinct endosymbiont genotypes to be unambiguously identified, compared and monitored within the host environment. The development of molecular tools reported here opens new avenues for addressing unresolved questions in photosymbiosis. Significance StatementO_LIParamecium bursaria is a single-celled, mixotrophic ciliate which forms photosymbiotic interactions with Chlorellaceae green algae and is a popular model system for symbiosis research. C_LIO_LIWe established a stable transformation protocol for the P. bursaria algal endosymbiont M. conductrix SAG 241.80 and identified properties of synthetic gene constructs which facilitate isolation of transformants with robust transgene expression that can be detected within the host environment. C_LIO_LIThis marks significant progress in model system development and opens new avenues for exploring molecular and cellular mechanisms underpinning photosymbiotic interactions. C_LI

evolutionary biology↗

bioRxiv2025

De novo genome sequence assembly of the model algal endosymbiont Micractinium conductrix derived from its host Paramecium bursaria 186b

Endosymbiosis is a major driver of evolutionary innovation and underpins the function of diverse ecosystems. The origins and evolution of endosymbiosis are challenging to study experimentally due to the short-lived culturability of many microbial strains derived from endosymbiotic interactions. The facultative endosymbiosis between the ciliate, Paramecium bursaria, and the green alga, Micractinium conductrix (Chlorellaceae, Trebouxiophyceae), is ecologically widespread and has emerged as a powerful lab-tractable model system. This endosymbiosis is founded upon a reciprocal nutrient exchange, but each of the species can be cultured independently enabling quantification of symbiotic fitness effects, new partnerships to be generated in the lab, and co-associations to be subject to experimental evolution. To date, evolve-and-resequence approaches have been limited due to a lack of high-quality genome assemblies enabling gene variants to be identified. Here, we report a near telomere-to-telomere genome assembly for M. conductrix 186b, using a range of sequencing technologies. Comparative analysis shows that this is one of the most complete Chlorellaceae algal genome assemblies available to date. To aid accurate gene calling and annotation we conducted both RNAseq and Iso-Seq transcriptome sequencing experiments. Collectively these omics datasets will facilitate: i) comparative genomics studies of endosymbiont evolution, ii) evolve-and-resequence experiments, iii) genome-scale metabolic modelling studies, and iv) identification of targets for genetic modification experiments and biotechnological applications. Significance statementEndosymbiosis, where one species, the endosymbiont, lives inside the cell of another species, the host, has played a key role in evolution of complex life. However, the origins and evolution of obligate endosymbioses are often challenging to study because the key events are hidden deep in evolutionary time. Facultative microbial endosymbioses, such as between the ciliate Paramecium bursaria and the green alga Micractinium conductrix, offer experimentally tractable model systems where interacting species can be grown independently or in association allowing studies of the origin, evolution and fitness effects of symbiosis. Here we report the genome sequence for M. conductrix from P. bursaria 186b, enabling genomic studies of the evolution of endosymbiosis and simplifying gene target acquisition for microbe engineering and biotechnological applications.

genomics↗

bioRxiv2024

Immune-like glycan-sensing and horizontally-acquired glycan-processing orchestrate host control in a microbial endosymbiosis

Endosymbiosis was a key factor in the evolution of eukaryotic cellular complexity. Yet the mechanisms that allow host regulation of intracellular symbionts, a pre-requisite for stable endosymbiosis and subsequent organelle evolution, are largely unknown. Here, we describe an immune-like glycan-sensing/processing network, partly assembled through horizontal gene-transfers (HGTs), that enables Paramecium bursaria to control its algal endosymbionts. Using phylogenetics, RNA-interference (RNAi), and metabolite exposure experiments, we show that P. bursaria regulates endosymbiont destruction using glycan-sensing/processing - a system that includes a eukaryotic-wide chitin-binding chitinase-like protein (CLP) localized to the host phago-lysosome. RNAi of CLP alters expression of eight glycan-processing genes, including two prokaryote-derived HGTs, during endosymbiont destruction. Furthermore, glycan-sensing/processing dynamically regulates endosymbiont number in P. bursaria, plasticity crucial to maximize host fitness across ecological conditions. CLP is homologous to a human phagocyte-associated innate immune factor, revealing how immune functions can be alternatively adapted and expanded, partly through HGT, enabling endosymbiotic control. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=186 HEIGHT=200 SRC="FIGDIR/small/613017v2_ufig1.gif" ALT="Figure 1"> View larger version (77K): org.highwire.dtl.DTLVardef@13aeaaorg.highwire.dtl.DTLVardef@302e6dorg.highwire.dtl.DTLVardef@138224forg.highwire.dtl.DTLVardef@54aca8_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗

bioRxiv2024

De novo genome sequence assembly of the RNAi-tractable endosymbiosis model system Paramecium bursaria 186b reveals factors shaping intron repertoire

How two species engage in stable endosymbiosis is a biological quandary. The study of facultative endosymbiotic interactions has emerged as a useful approach to understand how endosymbiotic functions can arise. The ciliate protist Paramecium bursaria hosts green algae of the order Chlorellales in a facultative photo-endosymbiosis. We have recently reported RNAi as a tool for understanding gene function in Paramecium bursaria 186b, CCAP strain 1660/18 [1]. To complement this work, here we report a highly complete host genome and transcriptome sequence dataset, using both Illumina and PacBio sequencing methods to aid genome analysis and to enable the design of RNAi experiments. Our analyses demonstrate Paramecium bursaria, like other ciliates such as diverse species of Paramecia, possess numerous tiny introns. These data, combined with the alternative genetic code common to ciliates, makes gene identification and annotation challenging. To explore intron evolutionary dynamics further we show that alternative splicing leading to intron retention occurs at a higher frequency among the smaller number of longer introns, identifying a source of selection against longer introns. These data will aid the investigation of genome evolution in the Paramecia and provide additional source data for the exploration of endosymbiotic functions.

genomics↗