title: Phylogenomic analysis of the Chlamydomonas genome unmasks proteins potentially involved in photosynthetic function and regulation.
abstract: Chlamydomonas reinhardtii, a unicellular green alga, has been exploited as a reference organism for identifying proteins and activities associated with the photosynthetic apparatus and the functioning of chloroplasts. Recently, the full genome sequence of Chlamydomonas was generated and a set of gene models, representing all genes on the genome, was developed. Using these gene models, and gene models developed for the genomes of other organisms, a phylogenomic, comparative analysis was performed to identify proteins encoded on the Chlamydomonas genome which were likely involved in chloroplast functions (or specifically associated with the green algal lineage); this set of proteins has been designated the GreenCut. Further analyses of those GreenCut proteins with uncharacterized functions and the generation of mutant strains aberrant for these proteins are beginning to unmask new layers of functionality/regulation that are integrated into the workings of the photosynthetic apparatus.
authors.affiliation: Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA. arthurg@stanford.edu
authors.forename: Arthur R
authors.initials: AR
authors.lastname: Grossman
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Karpowicz
authors.forename: Mark
authors.initials: M
authors.lastname: Heinnickel
authors.forename: David
authors.initials: D
authors.lastname: Dewez
authors.forename: Blaise
authors.initials: B
authors.lastname: Hamel
authors.forename: Rachel
authors.initials: R
authors.lastname: Dent
authors.forename: Krishna K
authors.initials: KK
authors.lastname: Niyogi
authors.forename: Xenie
authors.initials: X
authors.lastname: Johnson
authors.forename: Jean
authors.initials: J
authors.lastname: Alric
authors.forename: Francis-André
authors.initials: FA
authors.lastname: Wollman
authors.forename: Huiying
authors.initials: H
authors.lastname: Li
authors.forename: Sabeeha S
authors.initials: SS
authors.lastname: Merchant
mesh_terms: D000064:Acclimatization / Q000235:genetics; D001483:Base Sequence; D016825:Chlamydomonas reinhardtii / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics* / Q000502:physiology; D023281:Genomics / Q000379:methods*; D009154:Mutation / Q000235:genetics; D010641:Phenotype; D010788:Photosynthesis / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*
chemical_list: D010940:Plant Proteins