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Phylogenomic Analysis of the Chlamydomonas Genome Unmasks Proteins Potentially Involved in Photosynthetic Function and Regulation

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Phylogenomic Analysis of the Chlamydomonas Genome Unmasks Proteins Potentially Involved in Photosynthetic Function and Regulation Photosynth Res DOI 10.1007/s11120-010-9555-7 REVIEW Phylogenomic analysis of the Chlamydomonas genome unmasks proteins potentially involved in photosynthetic function and regulation Arthur R. Grossman • Steven J. Karpowicz • Mark Heinnickel • David Dewez • Blaise Hamel • Rachel Dent • Krishna K. Niyogi • Xenie Johnson • Jean Alric • Francis-Andre´ Wollman • Huiying Li • Sabeeha S. Merchant Received: 11 February 2010 / Accepted: 16 April 2010 Ó The Author(s) 2010. This article is published with open access at Springerlink.com Abstract Chlamydomonas reinhardtii, a unicellular green performed to identify proteins encoded on the Chlamydo- alga, has been exploited as a reference organism for iden- monas genome which were likely involved in chloroplast tifying proteins and activities associated with the photo- functions (or specifically associated with the green algal synthetic apparatus and the functioning of chloroplasts. lineage); this set of proteins has been designated the Recently, the full genome sequence of Chlamydomonas GreenCut. Further analyses of those GreenCut proteins with was generated and a set of gene models, representing all uncharacterized functions and the generation of mutant genes on the genome, was developed. Using these gene strains aberrant for these proteins are beginning to unmask models, and gene models developed for the genomes of new layers of functionality/regulation that are integrated other organisms, a phylogenomic, comparative analysis was into the workings of the photosynthetic apparatus. Keywords Chlamydomonas Á GreenCut Á Chloroplast Á Phylogenomics Á Regulation A. R. Grossman (&) Á M. Heinnickel Á D. Dewez Á B. Hamel Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA Introduction e-mail: [email protected] Chlamydomonas reinhardtii as a reference organism S. J. Karpowicz Á S. S. Merchant Department of Chemistry and Biochemistry, University of for the study of photosynthesis California—Los Angeles, Los Angeles, CA 90095-1569, USA The most well-characterized photosynthetic organisms that R. Dent Á K. K. Niyogi can be probed with powerful genetic and molecular tools Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA include Synechocystis sp. PCC6803, Chlamydomonas reinhardtii (Chlamydomonas throughout) and Arabidopsis X. Johnson Á J. Alric Á F.-A. Wollman thaliana (Arabidopsis throughout). Complementary attri- Unite´ Mixte de Recherche 7141 CNRS, Institut de Biologie butes of these organisms provide a synergistic view of Physico-Chimique, Paris, France basic biological and regulatory processes that occur in X. Johnson Á J. Alric Á F.-A. Wollman photosynthetic lineages. In this article, we emphasize the UPMC Universite´ Paris 06, Paris, France ways in which Chlamydomonas has been used to elucidate photosynthesis, especially with the aid of bioinformatic H. Li Crump Institute for Molecular Imaging, Department of analyses to generate a set of proteins designated the Molecular and Medical Pharmacology, University of ‘‘GreenCut’’ (Merchant et al. 2007). California—Los Angeles, Los Angeles, CA 90095, USA Over the last half century, experimentation with Chla- mydomonas has addressed numerous biological issues and H. Li Á S. S. Merchant Institute for Genomics and Proteomics, University of elucidated mechanisms that underlie a variety of cellular California—Los Angeles, Los Angeles, CA 90095-1569, USA activities. Recently, the state of Chlamydomonas biology 123 Photosynth Res has been described in the Chlamydomonas Sourcebook to the light (Harris 1989). Hence, even mutants that are (Harris 2009), an invaluable, up-to-date resource on most extremely sensitive to light (e.g., in some photosynthetic aspects of Chlamydomonas biology. Those processes and mutants, low light triggers photo-oxidative reactions that analyses relevant to the focus of this article include char- can cause peroxidation of membranes and oxidation of acterization of the chloroplast genome (Higgs 2009) and proteins) survive when maintained in the dark or near-dark chloroplast structure and function (de Vitry and Kuras conditions. Many other photosynthetic organisms are either 2009; Finazzi et al. 2009; Gokhale and Sayre 2009; unable to use exogenous reduced carbon, or use it to some Minagawa 2009; Niyogi 2009; Redding 2009; Rochaix extent, but show diminished growth rates and/or retarded 2009), post-translation regulation of chloroplast biogenesis developmental processes. Overall, the various biological (Rochaix 2001; Bollenbach et al. 2004; Drapier et al. 2007; features of Chlamydomonas make it an important, geneti- Raynaud et al. 2007; Eberhard et al. 2008; Choquet and cally tractable eukaryote in which lesions that eliminate Wollman 2009; Goldschmidt-Clermont 2009; Herrin 2009; photosynthesis are conditional rather than lethal or severely Klein 2009; Zerges and Hauser 2009; Zimmer et al. 2009), debilitating. and elucidation of activities and regulatory circuits that While Arabidopsis does not show optimal growth or control uptake and assimilation of various macronutrients completely normal development when maintained on a (Camargo et al. 2007; Fernandez and Galvan 2007; Fern- fixed source of carbon, studies of this organism are also a´ndez and Galva´n 2008; Gonza´lez-Ballester et al. 2008; important to our understanding of photosynthesis. For Ferna´ndez et al. 2009; Gonza´lez-Ballester and Grossman example, mutations of Arabidopsis in genes encoding 2009; Moseley et al. 2009; Moseley and Grossman 2009; proteins critical for photosynthetic function can be main- Gonza´lez-Ballester et al. 2010) and micronutrients (Mer- tained in seeds as heterozygotes; these seeds can survive chant et al. 2006; Tejada-Jimenez et al. 2007; Kohinata for years when stored under appropriate conditions. This et al. 2008; Long et al. 2008). Chlamydomonas also rep- feature of vascular plants also allows recessive mutations resents an important model for studies of light-driven H2 that are lethal in the homozygous diploid state to be production (Ghirardi et al. 2007; Melis 2007; Posewitz maintained as heterozygous seeds; only when the homo- et al. 2009). zygote strain is generated through crosses would the The physiological, metabolic, and genetic characteristics mutant plant die as photosynthetic function is lost in the of Chlamydomonas make it an ideal organism for dis- developing seedlings. Furthermore, it is only in multicel- secting the structure, function, and regulation of the pho- lular organisms that one can analyze the uptake, assimila- tosynthetic apparatus. In early studies, Levine and tion, and movement of nutrients between different tissues colleagues exploited the haploid (single copy of the nuclear and organs, and elucidate various organ-specific develop- genome in each cell) genetics of Chlamydomonas, which mental and regulatory processes associated with distinct was first highlighted by Sager (Sager 1960), to elucidate plastid classes. Such processes might include temporal genes/proteins involved in photosynthetic electron trans- analyses of chromoplast and leucoplast development and port and carbon fixation (Gorman and Levine 1966, 1967; the greening of etioplasts. Also, since different organisms Givan and Levine 1967; Lavorel and Levine 1968; Levine thrive in different environments and occupy specific envi- 1969; Levine and Goodenough 1970; Moll and Levine ronmental niches, the exact mechanisms associated with 1970; Sato et al. 1971). A significant advantage of working photosynthetic function may be tailored to a specific with an organism that displays haploid genetics is that the environment. For example, while the PSBS protein, a phenotype caused by a genetic lesion is manifest almost member of the light harvesting family of proteins, may be immediately after the generation of that lesion; this affords critical for non-photochemical quenching of excess absor- researchers the opportunity to select or screen for mutants bed light energy in plants (Li et al. 2000), other light- with specific phenotypes without having to first generate harvesting family proteins, such as the LHCSRs, appear to diploid strains that are homozygous for the lesion. Another be important for non-photochemical quenching in Chla- extremely important feature of this alga is that it exhibits mydomonas (Peers et al. 2009), while the orange caroten- robust growth under heterotrophic conditions in the dark, oid protein (OCP) is critical for non-photochemical with acetate as a sole source of fixed carbon. This feature quenching in cyanobacteria (Wilson et al. 2006). Organ- of the physiology of Chlamydomonas allows for the isms adapted to different environments may also exploit identification and maintenance of mutants that are com- various electron outlets or valves to control the increased pletely blocked for photosynthetic function, as long as they excitation pressure that can occur when the photosynthetic are grown on medium supplemented with acetate. Fur- apparatus absorbs more light energy than it can use in thermore, dark-grown, wild-type Chlamydomonas cells downstream anabolic processes. For example, the flow of remain green, retain normal chloroplast structure, and electrons to O2 via the Mehler reaction (oxidation of fer- resume photosynthesis immediately following their transfer redoxin) may be significant in generating a specific redox 123 Photosynth Res poise that modulates cyclic electron flow around photo- Calvin–Benson–Bassham Cycle; this type of modulation system (PS)
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