Much like the cytostome, a set of microtubules form an association with the cytopharynx. Two sets of microtubules follow the path of the cytopharynx in cells. These sets of microtubules form a gutter like structure that surrounds the cytopharynx. One side of the cytopharynx is not associated with these microtubules and is deemed the "naked side".
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Equally as important in the function of endocytosis is the structure known as the cytopharynx. The cytopharynx is a long, tube-like structure that forms the invagination associated with the cytostome. While the shape of the cytopharynx is not constant, it is typically directed towards the posterior of the cell, often hooking around a central nucleus. The length of the cytopharynx varies during the cell cycle, however the average length is 8 μm.
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The cytostome-cytopharynx complex functions as follows: macromolecules to be taken up by a cell enter the cytostome. Macromolecules then pass into the lumen of the cytopharynx and are transported to the posterior end of the cell where they are put into budding vesicles that are transported to others parts of the cell. The cytopharynx in this way acts much like a straw that sucks macromolecules to the posterior end of the cell. The passage of macromolecules from the entrance of the cytostome to the posterior end of the cytopharynx takes at least 2 minutes.
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The cytopharynx works in conjunction with the cytostome in order to import macromolecules into the cell. This strong association between the cytostome and cytopharynx is often called the cytostome-cytopharynx complex or the cytopharyngeal apparatus. However, in a small number of cases the cytostome works independently in order to import macromolecules. In these instances, the cytostome imports macromolecules by directly forming vesicles that are imported into the interior of the cell.
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Another team used ion beam scanning electron microscopy, also known as FIB-SEM followed by three dimensional reconstruction in order to create a 3-dimensional model of the cytostome-cytopharynx complex.
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The new genus Neobodo is characterized as solitary phagotrophic flagellates with a single discrete eukinetoplast. They are known for having an apical cytostome and cytopharynx supported by a prismatic rod of microtubules. Neobodo cells are usually elongate and elliptical in shape and somewhat inflexible. They range from 4 to 12 microns long, but are mostly 6 to 9 microns.
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The cytostome is often labeled as the entire invagination, but in fact the cytostome only constitutes the opening of the invagination at the surface of the cell. The rest of the invagination is classified as the cytopharynx.Preston, T. M. "The Form and Function of the Cytostome-Cytopharynx of the Culture Forms of the Elasmobranch Haemoflagellate Trypanosoma raiae Laveran & Mesnil." The Journal of protozoology 16.2 (1969): 320-333.
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Many methods have been used in order to visualize the cytostome. Eger et al. used gold labeled transferrin molecules in combination with confocal microscopy in order to visualize the cytostome. This experiment showed that labeling with the gold particles was evident at two locations in the cells; one of the locations was the bottom of the cytopharynx, and the other location was in reservosomes in the cell.
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Nassula is a genus of unicellular ciliates, belonging to the class Nassophorea. Like other members of the class, Nassula possesses a basket-like feeding apparatus (nasse, or cyrtos) made up of cytopharyngeal rods (nematodesmata), which are themselves composed of closely packed microtubules. Nassula use this structure to ingest filamentous cyanobacteria, drawing individual strands of blue-green algae through the cytopharynx and into the body of the cell, where they are digested. As the algae are broken down, they can take on a variety of bright colours, which give Nassula a distinctive, variegated appearance under the microscope.
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Some early researchers speculated that it might assist Peranema in tearing up and consuming its food; while others held that it was actually a tubular construction, serving as a cytopharynx. In 1950, Y. T. Chen accurately identified it as a structure separate from the reservoir, which could be used by Peranama to cut and pierce its prey. Brenda Nisbet questioned this, on the grounds that, when examined closely with an electron microscope, the rod-organ is blunt, and therefore an improbable instrument for either cutting or piercing. Since the rod-organ had been seen to move back and forth during feeding, Nisbet argued that its primary function is to create suction, drawing prey into the cytostome.
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