Quantitative three-dimensional structural analysis of Exophiala dermatitidis yeast cells by freeze-substitution and serial ultrathin sectioning

The morphologies, numbers, sizes and volumes of all organelles and cell components identified on ultrathin sections of aerobically grown exponential phase yeast cells of Exophiala dermatitidis in G1 phase were examined by freeze-substitution fixation and serial ultrathin sectioning. The cell wall consisted of three layers and occupied ∼22% of the cell volume. The nucleus was ∼1.8 µm in diameter and occupied ∼7% of the cell volume. There was only one nucleolus in the nucleus and it occupied ∼16% of the nuclear volume. There were 17–52 mitochondria per cell, occupying 7–12% of the cell volume. Five to ten endoplasmic reticula were present per cell; these occupied only 0.2% of the cell volume and did not form a network. There were 1–4 vacuoles per cell and they occupied 4–10% of the cell volume. Storage material was round and electron transparent and occupied 4–11% of the cell volume. The cytosol occupied 43–53% 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, 1000 glycogen granules and several tens of microtubules (average length 0.78 µm) were present per yeast cell. The membranes of this yeast could be classified into three groups by their appearance and thickness. This is the first report, to our knowledge, that analysed all the components in the yeast cell quantitatively and in three dimensions, and provides fundamental information for understanding various aspects of cell biology.