The pyrenoid matrix of the marine dinoflagellate Prorocentrum micans is shown to consist of regular close-packed units, which form a cubic face-centred lattice. Numerous lamellae usually consisting of two apposed thylakoids traverse the pyrenoid matrix. They normally run strikingly parallel to each other, with an average distance of 139 nm between each stack. The three-layered unit membrane of the thylakoids penetrating the pyrenoid is 70 Å thick, the same as the unit membrane of the chloroplast thylakoids. The total thickness of one thylakoid measures 190-220 Å.

The globular units of the pyrenoid matrix have a calculated mean diameter of 232 Å, forming different line and dot patterns (hexagonal and cubic arrays) due to different section angles. Hexagonal patterns on prints result from projections of superimposed close-packed layers; they do not belong to one close-packing. Line patterns parallel to the thylakoid direction are composed without exception of 11 contrasted lines (6 and 5 alternating). This fact suggests that a definite number of units is arranged between the thylakoid stacks, thus producing the constant matrix thickness. Comparable regions in the chloroplast matrix cannot be confused with the pyrenoid matrix, as they never display an ordered structure. A three-dimensional model of the matrix is presented.

Starch is stored only in the cytoplasm; there is no visible connexion with the pyrenoid. On the evidence of protein storage in similar crystal lattices both in plants and animals it is suggested that the pyrenoid may also be an organelle for protein storage in some groups of algae.

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