A research group led by ZHANG Yu from the Center for Excellence in Molecular Plant Science of the Chinese Academy of Sciences has determined plant plastid-encoded RNA polymerase supercomplex in apo and transcription elongation state, which provides a structural basis for the mechanistic and functional study of transcription regulation in plant chloroplasts. The study was published in Cell. 

The plastid-encoded RNA polymerase (PEP) plays an essential role during chloroplast biogenesis from proplastids and functions as the predominant RNA polymerase (RNAP) in mature chloroplasts. The PEP-centered transcription apparatus comprises a bacterial-origin PEP core and more than a dozen eukaryotic-origin PEP-associated proteins (PAPs) encoded in the nucleus. However, how the eukaryotic-origin PAPs and prokaryotic-origin RNAP assemble into a PEP-PAP supercomplex and what roles the eukaryotic-origin PAPs play in PEP transcription remain elusive. 

In this study, the researchers incorporated an affinity-purification tag into the chloroplast genome of Nicotiana tabacum and purified the plant plastid-encoded RNA polymerase supercomplex. And they subsequently determined the cryo-EM structures of the supercomplex in its apo form and its transcription elongation state. 

The structures revealed the composition, assembly, function, and evolution of the chloroplast transcription apparatus. The PEP-PAP apoenzyme showed that the bacterial-origin subunits of PEP fold into a typical structure as bacterial RNAP and a total of fifteen PAPs bind at the periphery of the PEP core. The interactions of PAPs with the PEP core facilitate assembling the PEP-PAP supercomplex, protect the complex from oxidation damage, and couple gene transcription with RNA processing. The PEP-PAP transcription elongation complex revealed interactions of the PEP-PAP core, DNA, and RNA during transcription elongation.  

In addition, the evolution analysis of the chloroplast transcription apparatus revealed that the emergence of PEP-PAP supercomplex coincides with the appearance of the land plants, and the recruitment of additional subunits helps land plants survive in the harsh land environment and adapt to the new life cycles.