Interpretation of the Genome in Synchronized Chlamydomonas Cells

Abstract

Chlamydomonas has served for over half a century as a reference organism for fundamental discoveries in photosynthesis. Cultures of Chlamydomonas are readily synchronized by alternating light‐dark cycles. We sampled synchronized cultures of Chlamydomonas over a 24 h period to reveal highly coordinated expression of sets of genes encoding individual complexes or pathways. The density of sampling permits us to resolve closely spaced events to reveal that the expression of the nucleus‐encoded subunits of the proton pumping complexes precedes the expression of the photosynthetic reaction centers and their associated light harvesting complexes, which are themselves very tightly coordinated. The separation of expression of genes encoding photosynthetic metabolism from those encoding respiratory metabolism allows us to assign function in the Calvin‐Benson vs. oxidative pentose phosphate pathway to genes encoding isoforms of the same enzyme. The expression profile shows evidence for transient photo‐oxidative stress at the transition from dark to light and more sustained stress towards the end of the light cycle. Candidate regulatory RNAs have been identified as well.