Structome of Yeast Cells Determined by Freeze-Substitution and Serial Ultrathin Sectioning Electron Microscopy

Abstract

True understanding of cell structure comes only from quantitative three-dimensional structural analysis. The term “structome”, coined by combining “structure” and “-ome”, is defined as quantitative three-dimensional structural information of whole cells at the electron microscopic level. We report here, for the first time, the structome of the cells of yeast Exophiala dermatitidis in the G1 phase determined using freeze-substitution and serial ultrathin sectioning electron microscopy. The cell wall and the nucleus occupied ～22% and ～7% of the cell volume respectively. There were 17-52 mitochondria per cell, occupying 7-12% of the cell volume. Five to ten endoplasmic reticula were present in a cell, occupying ～0.2% of the cell volume: they did not form a network in the cell. There were 1-4 vacuoles in a cell, occupying 4-10% of the cell volume. The Golgi apparatus, spindle pole body, autophagosomes, multivesicular bodies, lipid bodies, microtubules and microfilaments occupied ～1% of the cell volume in total. About 200,000 ribosome particles and 1,000 glycogen granules were present per cell. The cytosol occupied 43-53% of the cell volume. The membranes of cells of this yeast could be classified into three groups by their appearance and thickness.