Palomar, M. | bioRxiv Science

bioRxiv2024

pTAC3 and pTAC14 are required for binding of plastid-encoded RNA polymerase to DNA

Plastid-encoded RNA polymerase (PEP) is a bacterial-type multisubunit RNA polymerase responsible for the majority of transcription in chloroplasts. PEP consists of four core subunits, which are orthologs of their cyanobacterial counterparts. In Arabidopsis thaliana, PEP associates with 12 PEP-associated proteins (PAPs), which serve as peripheral subunits of the RNA polymerase. The exact contributions of PAPs to PEP function are still poorly understood. We use ptChIP-seq to show that PAP1/pTAC3, a peripheral subunit of PEP, binds to the same genomic loci as RpoB, a core subunit of PEP. The pap1/ptac3 mutant shows a complete loss of RpoB binding to DNA throughout the genome, indicating that PAP1/pTAC3 is necessary for RpoB binding to DNA. A similar loss of RpoB binding to DNA is observed in the pap7/ptac14 mutant, which is defective in another peripheral PEP subunit. We propose that the peripheral subunits of PEP are required for the recruitment of core PEP subunits to DNA. KEY MESSAGEThe peripheral subunits of plastid-encoded RNA polymerase play a crucial role in recruiting the core PEP subunits to DNA in Arabidopsis chloroplasts.

plant biology↗

bioRxiv2022

High-resolution map of plastid encoded polymerase binding patterns demonstrates a major role of transcription in chloroplast gene expression

Plastids are endosymbiotic organelles containing their own genomes, which are transcribed by two types of RNA polymerases. One of those enzymes is a bacterial-type, multi-subunit polymerase encoded by the plastid genome. The plastid encoded RNA polymerase (PEP) is required for efficient expression of genes encoding proteins involved in photosynthesis. Despite the importance of PEP, its DNA binding locations have not been studied on the genome-wide scale at high resolution. We established a highly specific approach to detect the genome-wide pattern of PEP binding to chloroplasts DNA using ptChIP-seq. We found that in mature Arabidopsis thaliana chloroplasts, PEP has a complex DNA binding pattern with preferential association at genes encoding rRNA, tRNA, and a subset of photosynthetic proteins. Sigma factors SIG2 and SIG6 strongly impact PEP binding to a subset of tRNA genes and have more moderate effects on PEP binding throughout the rest of the genome. PEP binding is commonly enriched on gene promoters, around transcription start sites. Finally, the levels of PEP binding to DNA are correlated with the levels of RNA accumulation, which allowed estimating the quantitative contribution of transcription to RNA accumulation.

plant biology↗