Calcium starvation leads to strain-specific gene regulation of lipid and carotenoid production in Mucor circinelloides

Fungi are pivotal in transitioning to a bio-based, circular economy due to their ability to transform organic material into valuable products such as organic acids, enzymes, and drugs. Mucor circinelloides is a model organism for studying lipogenesis and is particularly promising for its metabolic capabilities in producing oils like TAGs and carotenoids, influenced by environmental factors such as nutrient availability. Notably, strains VI04473 and FRR5020 have been identified for their potential in producing single-cell oils and carotenoids, respectively. Calcium starvation has previously been shown to have strain-specific effects, with VI04473 accumulating more lipids and FRR5020 producing more carotenoids. Here, we used genome sequencing, comparative genomics, transcriptomics, and metabolite phenotyping to explore the genetic basis of lipid and carotenoid production under calcium starvation in these strains. We found extensive genomic rearrangements between these strains, as well as low conservation of gene regulatory responses to calcium depletion. This lack of conservation also applies to genes involved in lipid and carotenoid production, ie the lipidome. Crucially, we identified several metabolic pathways with distinct transcriptional responses to calcium depletion, suggesting the existence of a previously unrecognized, strain-dependent mechanism by which calcium signaling modulates metabolite production. This points to a potentially novel regulatory pathway linking calcium homeostasis to secondary metabolism in fungi, which may be linked to the complex gene family evolution of several lipidome-genes. Our study sheds light on the complexity of the evolution of metabolic networks in M. circinelloides. Understanding these genetic underpinnings can optimize the industrial use of M. circinelloides, enhancing lipid productivity and stress tolerance, and tailoring metabolic profiles for specific applications.