Cis-acting signals modulate the efficiency of programmed DNA elimination in Paramecium tetraurelia

One Cell, Two Gears: Extensive Somatic Genome Plasticity Accompanies High Germline Genome Stability in Paramecium

Mutation accumulation (MA) experiments are conventionally employed to study spontaneous germline mutations. However, MA experiments can also shed light on somatic genome plasticity in a habitual and genetic drift-maximizing environment. Here, we revisit an MA experiment that uncovered extraordinary germline genome stability in Paramecium tetraurelia, a single-celled eukaryote with nuclear dimorphism. Our re-examination of isogenic P. tetraurelia MA lines propagated in nutrient-rich medium for >40 sexual cycles reveals that their polyploid somatic genome accrued hundreds of intervening DNA segments (IESs), which are normally eliminated during germline-soma differentiation. These IESs frequently occupy a fraction of the somatic DNA copies of a given locus, producing IES excision/retention polymorphisms, and preferentially fall into a class of epigenetically controlled sequences. Relative to control lines, retained IESs are flanked by stronger cis-acting signals and interrupt an excess of highly expressed coding exons. These findings suggest that P. tetraurelia’s elevated germline DNA replication fidelity is associated with pervasive somatic genome plasticity. They show that MA regimes are powerful tools for investigating the role that developmental plasticity, somatic mutations, and epimutations have in ecology and evolution.

Cross-Generational Effects and Non-random Developmental Response to Temperature Variation in Paramecium

Unicellular organisms such as ciliates are largely neglected in research on adaptive developmental plasticity, although their nuclear dualism offers ideal circumstances to study development outside an embryonic context. Here, we gain first insights into the ability of the ciliate Paramecium to develop potentially adaptive phenotypic changes in response to early-life adversity. We show that, upon exposure to unconventional culture temperatures, germ line-to-soma differentiation gives rise to coordinated molecular changes that may help attune the number of functional gene copies to the new external conditions. The non-random somatic heterogeneity that developmental plasticity generates is largely epigenetically controlled, shaped by the parental experience, and may prompt a stress response. These findings establish Paramecium as a new model system to study the molecular basis and evolutionary significance of developmental plasticity. In echoing previous indications in mammals, they call for an incorporation of intergenerational effects in adaptation studies.

Environmentally induced plasticity of programmed DNA elimination boosts somatic variability in Paramecium tetraurelia

Can ecological changes impact somatic genome development? Efforts to resolve this question could reveal a direct link between environmental changes and somatic variability, potentially illuminating our understanding of how variation can surface from a single genotype under stress. Here, we tackle this question by leveraging the biological properties of ciliates. When Paramecium tetraurelia reproduces sexually, its polyploid somatic genome regenerates from the germline genome through a developmental process that involves the removal of thousands of ORF-interrupting sequences known as internal eliminated sequences (IESs). We show that exposure to nonstandard culture temperatures impacts the efficiency of this process of programmed DNA elimination, prompting the emergence of hundreds of incompletely excised IESs in the newly developed somatic genome. These alternative DNA isoforms display a patterned genomic topography, impact gene expression, and might be inherited transgenerationally. On this basis, we conclude that environmentally induced developmental thermoplasticity contributes to genotypic diversification in Paramecium.