Transcription of photosynthetic genes in the plant chloroplast: lessons from bacteria

The RNA polymerase that transcribes photosynthetic genes in the plant chloroplast is the largest known transcription enzyme across all domains of life, comprising 21 subunits of bacterial and eukaryotic origin. Recent structural analyses revealed that the core polymerase, inherited from the cyanobacterial ancestor of the chloroplast, is encased by subunits unlike known bacterial transcription proteins. This insight into the composite nature of the complex provides clues about how the polymerase interacts with transcription regulatory elements of both bacterial and eukaryotic origin. Here, we summarize insight from recent structural and biochemical data on chloroplast and cyanobacterial transcription complexes. We analyze the available evidence on the mechanisms of chloroplast Sigma factors, NusG, mTERF proteins, kinases and alarmones, considering prevailing models of transcription control in bacteria and mitochondria to produce new hypotheses on the molecular basis of chloroplast transcription control to be characterized in the future.