Compartmentalized metabolic engineering in eukaryotic microbial cell factories: strategies and applications

The initial production levels of biochemicals and bioactive natural products in microbes are often too low to meet the demands of scientific research and industrial application. Constructing microbial cell factories through metabolic engineering is one of the key pathways to achieve the biomanufacturing of bio-based chemical products and bioactive natural products. Compared to prokaryotic microbes, eukaryotic microbes possess highly organized organelle structures, such as the mitochondria, peroxisome, endoplasmic reticulum, and vacuoles. These structures create physicochemical microenvironments with specific pH, redox potential, enzyme systems, and metabolite compositions, making eukaryotic microbes ideal chassis cells for the synthesis of various bioactive compounds. Compartmentalization is a cellular mechanism that utilizes specific subcellular domains or membrane-bound organelles to regulate biochemical reactions, signaling, and metabolic pathways through spatial segregation. Consequently, compartmentalization strategies for metabolic pathways offer multiple advantages, including increasing local substrate and enzyme concentrations to enhance catalytic efficiency, isolating competitive pathways through spatial isolation, and mitigating cytotoxicity of synthetic products et al. This review systematically summarizes the latest research advances in compartmentalized metabolic engineering for constructing eukaryotic cell factories, focusing on the structure and metabolic characteristics of different organelles and their applications in compartmentalization engineering. It also provides an outlook on the research and application of compartmentalized organelle engineering in bio-based chemical and natural product synthesis. Future advances in compartmental engineering will undoubtedly unlock new frontiers for biomanufacturing.