Form and Function: Development and Application Of a 3D Rendering-Based Method for Analysis of Mitochondrial Morphology and Subcellular Architecture

Abstract

Classical images of subcellular architecture depict organelles as discrete and static compartments, not unlike the organs of the human body. Mitochondria, for example, are displayed as double membrane half-cylinders inside a cytoplasmic soup of vesicles and other organelles while the endoplasmic reticulum (ER) is depicted as an orderly labyrinth abutting a central nucleus. The reality of the subcellular environment, however, is far more complex. Mitochondria, for instance, can exist as multiple individual subcellular compartments or as one expansive tubular network while the ER is often found as a complex mesh throughout the cytoplasm rather than merely surrounding the nucleus. These organelles are also dynamic and can interact with other subcellular components to participate in various metabolic pathways. The study of mitochondrial morphology and its implications in human disease and microbial engineering have gained significant attention over the past decade. Saccharomyces cerevisiae, more commonly known as baker’s yeast, offers a valuable model system for studying mitochondria due to its ability to survive without respiring, its genetic tractability, and the high degree of mitochondrial similarity across eukaryotic species. Renewed recognition of the importance of mitochondrial morphology studies in yeast calls attention to our need for precise classifications of mitochondrial phenotypes and for new methods to analyze our growing base of high-quality data. In this work, we design and apply a novel and versatile method to analyze yeast subcellular architecture, with an emphasis on mitochondrial morphology. This 3D rendering-based approach is first applied to quantify changes in mitochondrial morphology, distribution, and mitochondrial-ER contacts in fermenting and respiring wild-type yeast. Next, we use this method to identify differences in mitochondrial morphology between cells with and without mitochondrial pyruvate carriers – heterodimeric proteins responsible for transporting pyruvate across the inner mitochondrial membrane and a drug target in the treatment of both type 2 diabetes and Parkinson's disease. Lastly, this method is employed to investigate mitochondrial morphology in yeast strains engineered to produce valuable biofuels, demonstrating the broad applicability and versatility of our approach.