Genomic approaches for deciphering chloroplast biogenesis and metabolism

Chlamydomonas has served for over half a century as a reference organism for fundamental discoveries in photosynthesis. While the structural constituents of the photosynthetic apparatus are well-defined, the factors that control the abundance, stoichiometry and function of individual complexes in response to light, nutrients and other environmental cues are much less so. Genomic resources have enabled new approaches for identification these regulatory components. In one approach, we compared the protein inventory of organisms that do or do not contain plastids, resulting in a list of 597 proteins in Chlamydomonas (corresponding to 710 in Arabidopsis, which includes co-orthologs), named GreenCut2, that are found only in the plant lineage, diatoms or cyanobacteria. Manual curation of this list and reverse-genetic analysis in multiple laboratories has verified its relevance to photosynthesis and chloroplast metabolism.A subset of the proteins in the GreenCut2 is expressed preferentially in the senescent organs. Reverse genetic analysis of one of these generates a functional rather than cosmetic “stay green” phenotype, and we hypothesize that it may encode a factor required for the programmed disassembly of the thylakoid membrane. In a second project, synchronized cultures of Chlamydomonas were sampled over 2 cell / circadian cycles of growth to reveal highly coordinated expression of sets of genes encoding individual complexes or pathways. The resolution of this dataset permits the observation of transient changes that occur during the shift from dark to light.