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Chlamydomonas reinhardtii is a unicellular green member of the algae used as a model organism for photosynthesis and for the structure and function of eukaryotic flagella. A typical motile vegetative cell has two anterior flagella, a large cup-shaped chloroplast and a light-sensing eyespot. These features bring propulsion, light sensing and photosynthesis together in one experimentally tractable cell.^[ref]

Its flagella contain the same basic microtubule machinery as motile cilia in animals. This is an evolutionary relationship between organelles; bacterial flagella use a different construction. In the genome study published in 2007, researchers sequenced its nuclear genome and compared predicted proteins across organisms with different cellular capabilities. Genes shared by organisms with flagella, but absent from comparison organisms lacking them, supplied candidates for flagellar assembly and function. Comparisons with proteins experimentally found in flagella helped test those candidates.^[ref]

A photosynthetic alga can therefore illuminate defects in human cilia, while also providing a system for studying chloroplast biology.

An eyespot is a subcellular light-sensing apparatus that helps a motile organism determine the direction of illumination. In Chlamydomonas reinhardtii, it combines carotenoid-rich granules in the chloroplast with channelrhodopsin proteins in the adjacent cell membrane. Its optical arrangement gives the light-sensitive machinery a directional response; it does not form a visual image.^[ref]

During swimming, flagella propel the rotating biological cell, so the eyespot samples changing orientations to the light. Differences in light response can then guide phototaxis. Experiments with mutants lacking the visible pigment layers found that they could still show phototaxis, but with the direction reversed under the tested conditions. Optical observations showed that the cell body could concentrate light onto the rear of the receptors; pigment-layer shielding helps determine the direction of the response.^[ref] This distinguishes detecting light from correctly interpreting its direction.

Noriko Ueki investigates how swimming green algae respond to light. A 2016 study led by Ueki examined Chlamydomonas reinhardtii mutants lacking a normal eyespot and found that their direction of phototaxis could reverse relative to normal cells under the same chemical conditions. The result made the optical arrangement of the biological cell part of the explanation for its behavior.^[ref]

The carotenoid layers of an eyespot help control which direction of illumination reaches light-sensitive channelrhodopsins. Without that shielding, the cell body can act as a convex lens, concentrating light arriving from the rear. The investigators demonstrated the lens effect by imaging a small letter through the cells with a microscope. This is an illuminating example of a physical structure changing the meaning of a sensory signal: the same light-sensitive machinery can receive its strongest illumination from a different direction. Comparing mutants, a rescued strain and normal cells connected the optical effect with the observed phototaxis.^[ref]