In many ways, Escherichia coli can be considered the universal model organism. Anything that can be studied with E. coli is studied with E. coli. It is simple, sequenced, and very well established. Beyond prokaryotes, the budding yeast, Saccharomyces cerevisiae, seems the predominant eukaryotic model. For understanding the cell cycle, basic physiology and metabolism, and principles of eukaryotic genetics, yeast has been incredibly useful. Moving down the list of models, the mouse, Mus musculus, is the most commonly used mammalian model and a frequent stand-in for humans. Other groups of organisms have their own premier models, such as Arabidopsis for plants.

The Chlamydomonas stt7 mutant, which is defective in a photosynthetic regulatory mechanism called state transition, provides a specific example of how Chlamydomonas can drive discovery in Arabidopsis and beyond. State transition involves the reversible reallocation of the light-harvesting complex proteins ordinarily associated with photosystem II (PSII) toward PSI in response to a shift in incident wavelengths of light (Wollman, 2001). Chlamydomonas exhibits a particularly large, and thus easily detectable, shift in chlorophyll fluorescence during state transition, making Chlamydomonas the initial experimental organism of choice for studying state transition. The stt7 mutant was identified in a video imaging screen for mutants that were incapable of making the fluorescence shift (Fleischmann et al., 1999). Using traditional complementation and molecular biology techniques, STT7 was cloned and found to encode a chloroplast-localized Ser/Thr protein kinase (Depège et al., 2003). It has been implicated in phosphorylating, either directly or indirectly, light-harvesting complex II proteins, a process shown to be involved in state transition. STT7 has two homologs that can be recognized in the Arabidopsis genome (Depège et al., 2003). These genes, which would have been much more difficult to recognize and isolate directly among the plethora of kinases in the Arabidopsis genome (Wang et al., 2003), can now be targeted and studied in both organisms.

Mutants defective in a protective response to excess light called nonphotochemical quenching have been isolated and studied in our laboratory, and they provide a good example of the parallel utility of Chlamydomonas and Arabidopsis. The npq1 mutant, which is defective in the high-light-dependent synthesis of zeaxanthin via the xanthophyll cycle, was isolated first in Chlamydomonas (Niyogi et al., 1997) and subsequently in Arabidopsis, where it proved easier to identify the mutated gene (Niyogi et al., 1998). Although the phenotypes of the npq1 mutants are broadly similar, there is a difference in the relative contributions of the xanthophyll cycle to nonphotochemical quenching (Niyogi et al., 1998) that underscores the value of comparative studies using Chlamydomonas and Arabidopsis. Working in the opposite direction, the critical role of the PsbS protein of PSII was first identified and characterized using an Arabidopsis mutant (Li et al., 2000). It was only recently through genome sequencing that a Chlamydomonas homolog of PsbS was found (X.P. Li, D.A. Martinez, and K.K. Niyogi, unpublished data). Now there are two fronts on which to attack this protein and get at the other components of this important physiological process. It will be exciting to see not only where PsbS fits in the overall framework of PSII, and what other factors work with it, but also how the process differs between photosynthetic organisms.

Studies of chloroplast-localized RecA have also shown how these two models, Chlamydomonas and Arabidopsis, work well as companions. A RecA homolog was first identified and cloned in Arabidopsis (Cerutti et al., 1992). However, because Chlamydomonas has an easily transformable chloroplast, the function of the RecA homolog could be tested much more easily in Chlamydomonas than in Arabidopsis. By transforming a known dominant-negative form of the E. coli protein into the Chlamydomonas chloroplast genome, Cerutti et al. (1995) were able to show that recombination in the chloroplast was impaired, as was viability in the presence of DNA-damaging agents. A RecA homolog (REC1) has now been cloned from Chlamydomonas too and shown to have a functional chloroplast-targeting peptide as well as expression patterns that are consistent with roles in chloroplast DNA replication and repair (Nakazato et al., 2003).

One area in which the unique attributes of Chlamydomonas as a photosynthetic model have proven especially fruitful is that of nucleus-encoded factors involved in translation of chloroplast-encoded photosynthetic proteins. A great number of such factors, often specific to a single chloroplast gene, have been identified genetically in Chlamydomonas. In Arabidopsis, investigation of these chloroplast-nucleus interactions lags behind because of the relative difficulty in isolating nonphotosynthetic mutants (Barkan and Goldschmidt-Clermont, 2000). Going forward, as one organism informs the other, it will be interesting to see how conserved these factors and regulatory processes are across the green plants. Variety might be expected, as there are significant differences in chloroplast genome organization and gene structure (Maul et al., 2002).