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Background  Efficient light acclimation of photosynthetic cells is a basic and important property of plants. The process of acclimation depends on transformation of retrograde signals in gene expression, transcript accumulation and  de novo  protein synthesis. While signalling cues, transcriptomes and some involved players have been characterized, an integrated view is only slowly emerging, and information on the translational level is missing. Transfer of low (8 μmol quanta . m -2. s -1 ) or normal light (80 μmol quanta . m -2. s -1 ) acclimated 30 d old  Arabidopsis thaliana  plants to high light (800 μmol quanta . m -2. s -1 ) triggers retrograde signals. Using this established approach, we sought to link transcriptome data with  de novo  synthesized proteins by  in vivo  labelling with  35 S methionine and proteome composition.    Results  De novo synthesized protein and proteome patterns could reliably be matched with newly annotated master gels. Each molecular level could be quantified for a set of 41 proteins. Among the proteins preferentially synthesized in plants transferred to high light were enzymes including carbonic anhydrase, fructose-1,6-bisphosphate aldolase, O-acetyl serine thiol lyase, and chaperones, while low rates upon transfer to high light were measured for e.g. dehydroascorbate reductase, glyceraldehyde-3-phosphate dehydrogenase and CuZn superoxide dismutase, and opposite responses between 10-fold and 100-fold light increment for e.g. glutamine synthetase and phosphoglycerate kinase.    Conclusions  The results prove the hypothesis that transcript abundance is poorly linked to  de novo  protein synthesis due to profound regulation at the level of translation. This vertical systems biology approach enables to quantitatively and kinetically link the molecular levels for scrutinizing signal processing and response generation.

The link between transcript regulation and de novo protein synthesis in the retrograde high light acclimation response of Arabidopsis thaliana