Signal Transduction

5% of the genes in humans are different variants of these receptors. 50% of the drugs used in medicine act at these gene products. Consequently understanding how these proteins activate is particularly important. Particularly exciting, as we first showed with the green sensitive rhodopsin of Chlamydomonas, is that unexpectedly it is the electronic motion of charge triggered by light that flips amino acids within the binding pocket for the chromophore for vision and not the steric motion of the chromophore as was once thought. Much still remains to be done however in learning how these early changes lead to activation at the millisecond time scale.

Our group is interested in the mechanisms of activation and evolution of membrane receptors. Our model is rhodopsin, the visual pigment of green algae, fungi and animals. When a chromophore such as N-retinylidene absorbs light, its excitation causes it to change shape and move charges within rhodopsin. Short chromophores such as N-hexenylidene (four fewer double bonds than the native pigment) and N-napthalylidene (double ring system instead of polyene chain) strongly activate rhodopsin suggest that the shape change of the chromophore may not be important. The particular isomer is equally not important or whether the chromophore is attached to the protein. What seems important is the asymmetric pi-bonded conjugated chain. Chromophores demonstrated in the green alga Chlamydomonas and the fungus Allomyces are illustrated at the right.

Evolution of this family of receptors with particular emphasis on the evolution of visual receptors. All the major domains of life have rhodopsin receptors. We were the first to identify rhodopsins in three kingdoms of eukaryotes, Euglenoids, fungi, and green algae. Understanding the step by step evolution in these different groups teaches us how our visual molecules became the way they are today. Using bioinformatics (see below also) we are mapping the molecular changes in their evolution.

Flavin/pterin-based vision

Dominates free-swimming phototaxis in the Euglenoid and Stramenopile Kingdoms and phototropism responses in the Fungal and Plant Kingdoms. They probably affect many responses in Animals as well.

Like us, these organisms have eyes (or shaped-beam dielectric electromagnetic-wave antennas). These typically use interference and diffraction rather than geometrical optics to optimize their light reception. Tiny toroidal quarter-wave stack mirrors, multiple antenna arrays, or curved antennas are part of the variety. Such designs (evolved by the selection algorithm) may prove useful to engineers.

To learn how the “eye” of Chlamydomonas is optimized in its role of determining the orientation of the cell to the light, the field of view of its antenna’s is being analyzed in detail.

Bioinformatics

Our primary interest is in application of nonlinear molecular clocks to combine the phylogenetic data from data sets corresponding to different homologous molecular families. Our main effort is to constrain phylogenies by incorporating geological and fossil evidence in the analysis of the molecular sequence data. We are also developing ways to remove time-rate degeneracy from use of “distance” methods of phylogenetic reconstruction and to statistically validate phylogeny. Presently our focus is applying our methods to determining the connections in the network of eukaryotic divergences and lateral transfers that took place more than a billion years ago.

Action Spectroscopy

While we normally associate rhodopsin with vision, it also controls gene expression within the photoreceptor cell. In fact, there are many different photoreceptors in cells responsible for the selective activation of different genes. In Chlamydomonas rhodopsin controls synthesis of retinal, a far-red absorbing phytochrome-like pigment controls the enzyme isocitrate lyase, (more in progress). One approach employed to suggest the nature of the pigments is to use action spectroscopy, measurement of the wavelength dependence of response for a behavior or expressed gene. This may be combined in favorable circumstances with modifications of chromophores, use of specific inhibitors and mutations that enable specific identification of the chromophore and hence type of photoreceptor involved.

We remain strong advocates of action spectroscopy as an extremely sensitive approach to learn about cell behavior and receptor behavior. See Foster (2001) for details.

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Foster, K.W., Saranak, J., Patel, N., Zarrilli, G., Okabe, M., Kline, T. and Nakanishi K. A rhodopsin is the functioning photoreceptor for phototaxis unicellular eukaryote Chlamydomonas. Nature 311:7567-759 (1984).

Foster, K.W., Saranak, J. and Zarrilli, G. Autoregulation of rhodopsin synthesis in Chlamydomonas reinhardtii. Proc. Natl. Acad. Sci. U.S.A. 85:6379-6383 (1988).

Smyth, R.D., Saranak, J. and Foster, K.W. Algal visual systems and their photoreceptor pigments. Prog. Phycol. Res. 6:255-286 (1988).

Foster, K.W., Saranak, J., Derguini, F., Zarrilli, G.R., Johnson, R., Okabe, M. and Nakanishi, K. Activation of Chlamydomonas rhodopsin in vivo does not require isomerization of retinal. Biochemistry 28: 819-824 (1989).

Foster, K.W. and Saranak, J. The Chlamydomonas (Chlorophyceae) eye as a model of cellular structure, intracellular signaling and rhodopsin activation. In: Algae as Experimental Systems (Coleman, A., Goff, L., and Stein-Taylor, J.R. eds.) (1989), p. 215-230.

Saranak, J. and Foster K.W. Activation of Chlamydomonas rhodopsin by reducing agents in the dark. 10th International Biophysics Congress Abstracts. (1990) p.482.

Foster, K.W., Saranak, J. and Dowben, P.A. Spectral sensitivity, structure, and activation of eukaryotic rhodopsins: Activation spectroscopy of rhodopsin analogs in Chlamydomonas. J. Photochem. Photobiol. B: Biol. 8:385-408 (1991).

Saranak, J. and Foster, K.W. The in vivo cleavage of carotenoids into retinoids in Chlamydomonas reinhardtii. J. Exp. Bot., 45:505-511 (1994).

Saranak, J. and Foster, K.W. Rhodopsin guides fungal phototaxis. Nature 387:465-466 (1997).

Petridou, S., Foster, K. and Kindle, K. Light induces accumulation of isocitrate lyase mRNA in a carotenoid-deficient mutant of Chlamydomonas reinhardtii. Plant Molecular Biology 33:381-392 (1997).

Saranak, J. and Foster, K.W. Reducing Agents and Light Break an S-S Bond Activating Rhodopsin In Vivo in Chlamydomonas. Biochem. Biophys. Res. Comm. 275:286-291 (2000).

Foster, K.W. Making the biomolecular time scale more robust for
phylogenetic studies. Protist. (in press).

Foster, K.W. Action spectroscopy of photomovement. In: Photomovement, eds. D-P Hader & M. Lebert, Comprehensive Series in the Photosciences, 1: pp. 51-115, (2001).