Searching limiting steps in the expression of chloroplast‐encoded proteins: relations between gene copy number, transcription, transcript abundance and translation rate in the chloroplast of Chlamydomonas reinhardtii

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Abstract
We performed a systematic investigation of the quantitative relationship between genome copy number, transcription, transcript abundance and synthesis of photosynthetic proteins in the chloroplast of the green algae Chlamydomonas reinhardtii grown either in mixotrophic or phototrophic conditions. The chloroplast gene copy number is lower in the latter condition and the half‐life and accumulation levels of most chloroplast transcripts are significantly reduced, although the relative rates of protein synthesis remain similar. Our study shows that, in most instances, chloroplast protein synthesis is poorly sensitive to changes in gene copy number or transcript abundance in the chloroplast. Treatment with 5‐fluoro‐2′‐deoxyuridine, that inhibits chloroplast DNA replication and decreases extensively the number of copies of the chloroplast genome, had limited effects on the abundance of most chloroplast transcripts and little if any effect on the rates of protein synthesis. When using rifampicin, that selectively inhibits chloroplast transcription, we found no direct correlation between the level of transcripts remaining in the chloroplast and the rates of chloroplast protein synthesis. For two chloroplast genes, a 90% decrease in the amount of transcript did not cause a drop in the rate of synthesis of the corresponding protein product. Overall, our results demonstrate that there is no gene dosage effect in the chloroplast and that transcript abundance is not limiting in the expression of chloroplast‐encoded protein.