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A channelrhodopsin is a light-gated ion channel associated with a retinal chromophore. Absorbing light changes the protein's conducting state, connecting photoreception directly with ion movement across a cell membrane. Naturally occurring members in Chlamydomonas reinhardtii participate in responses to illumination.^[ref]

The landmark channelrhodopsin-2 study expressed the protein in Xenopus laevis oocytes and mammalian cells and recorded light-evoked electric currents. Altering ionic conditions showed passage of multiple cations; continued illumination produced an initial response followed by a smaller sustained conductance. Expressing the channel in another cell type helped establish that light gating was a property of this molecular machinery.^[ref]

In an illustrative Ohmic model with outward-positive electric current, $I=g(V-E_{\mathrm{rev}})$. If light produces $g=1\mathrm{nS}$ at $V=-60\mathrm{mV}$ and $E_{\mathrm{rev}}=0$, then $I=-60\mathrm{pA}$: net inward positive electric charge. These invented values illustrate the driving force. Light opens a route whose direction depends on membrane potential and ionic conditions, a principle used in optogenetics.

Channelrhodopsin-2 is a microbial light-gated cation channel originally identified in the green alga Chlamydomonas reinhardtii. Its retinal-containing membrane protein couples light absorption to channel opening. Unlike a light-driven pump that transports charge through a directed cycle, an open Channelrhodopsin-2 provides a conductive path whose net current depends on ion concentrations and membrane potential.^[ref]

The original experiments expressed the protein in frog oocytes and mammalian cells and recorded light-induced membrane currents. Testing the isolated membrane response helped show that light directly gates the conductive protein, rather than acting only through a separate intracellular signaling cascade. Responses depended on voltage and ionic conditions, and prolonged illumination did not simply maintain an unchanged initial peak current.^[ref]

A useful conceptual example is a cell held below the channel's reversal potential: opening the channel can give net inward positive charge and depolarization. Near reversal there can be little net current despite channel opening. Consequently a blue-light pulse does not guarantee an action potential; channel abundance, ionic driving force and the cell's excitability all matter.

This direct connection between light and conductance made Channelrhodopsin-2 useful for optogenetics. The measurement logic remains important: a light-controlled current is evidence about channel function, whereas precise control of firing in a particular cell type also requires testing the resulting electrical response.

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.

Daiju Kitagawa led work explaining the ninefold organization of centrioles through interactions between SAS-6 molecules. The 2011 study combined structural analysis, biochemical assembly and cellular experiments: rod-shaped dimers associated through their ends, and disrupting the relevant association impaired centriole formation.^[ref]

A model built from the related Chlamydomonas reinhardtii protein placed nine dimers in a ring with spokes extending outward. Recombinant protein also formed cartwheel-like assemblies. The work connects a repeated protein structure to the larger geometry of an organelle, rather than treating its symmetry as an unexplained cellular pattern.^[ref]

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.

Georg Nagel studies membrane proteins that respond to light. His work on channelrhodopsin-2 helped establish the molecular basis of optogenetics, in which introduced light-sensitive proteins allow light to control cellular electrical activity.

In 2003, Nagel and colleagues expressed channelrhodopsin-2 from the microalga Chlamydomonas reinhardtii in Xenopus laevis oocytes and mammalian cells. Electrical recordings showed a rapidly opening ion channel permeable to cations. Experiments on isolated membrane patches supported direct gating by light, without requiring a freely diffusible intracellular intermediary. During sustained illumination the initial electric current declined to a lower maintained level.^[ref]

This gives a useful distinction between an ion channel and a molecular pump: an open channelrhodopsin-2 permits ions to move down their electrochemical gradient. The resulting change in membrane potential depends on the cell and its ionic conditions; a flash of light does not imply an identical electrical response in every cell.^[ref]

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]

Sabeeha S. Merchant studies photosynthesis, metabolism and how organisms manage essential metals. Her laboratory uses Chlamydomonas reinhardtii, a single-celled green alga, to investigate responses to limitations of iron and copper. Such limitations raise a concrete biochemical question: which essential tasks can a biological cell maintain when several proteins compete for a scarce chemical element? ^[ref]

Merchant is the first author of the 2007 report of the approximately 120-million-base-pair nuclear genome of Chlamydomonas reinhardtii. The team used comparative genomics to identify candidate genes associated with chloroplasts and flagella. The organism is revealing because it combines photosynthesis with motile flagella: comparisons with photosynthetic and nonphotosynthetic organisms can help distinguish these functional groups. Shared occurrence across species suggests candidate functions; experimental tests are still needed to establish what an individual protein does.^[ref]