Gaowen Liu

To advance the computational simulation of cellular life, we propose a virtual yeast, an artificial intelligence (AI)-driven agent that models eukaryotic cellular behaviours by integrating multimodal biological data, mechanistic reasoning and active experimentation using Saccharomyces cerevisiae as a genetically tractable and data-rich model system. Cellular complexity is decomposed into eight function-centred modules, spanning genetic, metabolic and structural systems, each realized as a domain-specific AI tool coordinated through a large language model-based orchestration layer. Built on three data pillars, namely, mechanistic knowledge, subcellular architecture and dynamic states, the system integrates representation learning and generative modelling within a closed-loop learning pipeline that autonomously designs and executes experiments. The virtual yeast serves as both a conceptual and an operational platform to optimize biosynthetic pathways, support the generation and prioritization of hypotheses across diverse cellular processes, and accelerate target discovery. By coupling biological realism with autonomous AI reasoning, the virtual yeast establishes a generalizable blueprint for constructing virtual eukaryotic cells and advancing synthetic biology.

Summary: Investment in sexual reproduction has long been seen as a fitness cost for asexual proliferation, raising the question of how cells evolve to accommodate cyclical demands of sexual and asexual cycles. We addressed this question by evolving Schizosaccharomyces pombe lacking the critical fusion gene Prm1 through 18 cycles of alternating meiosis and mitosis. Initially, transcriptional tweaks offered a fragile means to fuse despite Prm1’s absence. However, a telomeric 1% genome deletion that epigenetically silenced Clr5 ultimately locked in a latent, Prm1-independent fusion pathway involving the mating regulator Ste11 and the pheromone-MAPK scaffold Sms1. This adaptation, though efficient at restoring sexual reproduction, came at the cost of mitotic growth. By contrast, rationally constructing mutations in a “synthetic evolution” approach bypassed the trade-off, enabling simultaneous high fusion efficiency and near–wild-type proliferation. Our findings illustrate how epigenetic de-repression and genetic assimilation converge to create innovative solutions under cyclical selection pressures with trade-offs.

To ensure genome stability, sexually reproducing organisms require that mating brings together exactly two haploid gametes and that meiosis occurs only in diploid zygotes. In the fission yeast Schizosaccharomyces pombe , fertilization triggers the Mei3-Pat1-Mei2 signaling cascade, which represses subsequent mating and initiates meiosis. Here, we establish a degron system to specifically degrade proteins post-fusion and demonstrate that mating blocks not only safeguard zygote ploidy but also prevent lysis caused by aberrant fusion attempts. Using long-term imaging and flow-cytometry approaches, we identify previously unrecognized and independent roles for Mei3 and Mei2 in zygotes. We show that Mei3 promotes premeiotic S-phase independently of Mei2 and that cell cycle progression is both necessary and sufficient to reduce zygotic mating behaviors. Mei2 imposes the meiotic program and promotes the meiotic cycle, but also blocks mating behaviors independently of Mei3 and cell cycle progression. Thus, we find that fungi preserve zygote ploidy and survival by at least two mechanisms where the zygotic fate imposed by Mei2 and the cell cycle re-entry triggered by Mei3 synergize to prevent zygotic mating.

Schizosaccharomyces pombe is a widely used model organism to study many aspects of eukaryotic cell physiology. Its popularity as an experimental system partially stems from the ease of genetic manipulations, where the innate homology-targeted repair is exploited to precisely edit the genome. While vectors to incorporate exogenous sequences into the chromosomes are available, most are poorly characterized. Here we show that commonly used fission yeast vectors, which upon integration produce repetitive genomic regions, yield unstable genomic loci. We overcome this problem by designing a new series of Stable Integration Vectors (SIV) that target four different prototrophy genes. SIV produce non-repetitive, stable genomic loci and integrate predominantly as single copy. Additionally, we develop a set of complementary auxotrophic alleles that preclude false-positive integration events. We expand the vector series to include antibiotic resistance markers, promoters, fluorescent tags and terminators, and build a highly modular toolbox to introduce heterologous sequences. Finally, as proof of concept, we generate a large set of ready-to-use, fluorescent probes to mark organelles and cellular processes with a wide range of applications in fission yeast research.

Schizosaccharomyces pombe is a widely used model organism that resembles higher eukaryotes in many aspects of cell physiology. Its popularity as an experimental system partially stems from the ease of genetic manipulations, where the innate homology-targeted repair is exploited to precisely edit the genome. While vectors to incorporate exogenous sequences into the chromosomes are available, most are poorly characterized. Here we show that commonly used fission yeast vectors, which upon integration produce repetitive genomic regions, yield unstable genomic loci. We overcome this problem by designing a new series of Stable Integration Vectors (SIV) that target four different prototrophy genes. SIV produce non-repetitive, stable genomic loci and integrate predominantly as single copy. Additionally, we develop a set of complementary auxotrophic alleles that preclude false-positive integration events. We expand the vector series to include antibiotic resistance markers, promoters, fluorescent tags and terminators, and build a highly modular toolbox to introduce heterologous sequences. Finally, as proof of concept, we generate a large set of ready-to-use, fluorescent probes to mark organelles and cellular processes with a wide range of applications in fission yeast research.