Thermal protection of the plastid-encoded RNA polymerase complex by PAP9 ensures chloroplast function in Arabidopsis

The Plastid-encoded RNA polymerase (PEP) complex is a multi-subunit machinery essential for chloroplast biogenesis and photosynthetic gene transcription. Its structural integrity and enzymatic activity rely critically on a suite of PEP-associated proteins (PAPs). Mutations in most PAP-encoding genes typically lead to severe albinism and developmental arrest in Arabidopsis thaliana. However, the pap9 mutant exhibits phenotype closely resembling the wild type under standard growth conditions. In this study, we demonstrate that pap9 mutants display impaired chloroplast development, reduced photosynthetic efficiency (with a 35 % decrease in Fv/Fm, P < 0.001), and increased reactive superoxide anion (O₂^-) accumulation specifically at 27 °C. Yeast two-hybrid assays identified a specific interaction between PAP9 and PAP4, which is consistent with recent structural insights. Complementation with PAP9-OE restored both PEP-dependent gene expression and chloroplast ultrastructure. Overexpression lines exhibited enhanced thermotolerance, with a 28 % increase in fresh weight at 27 °C (P < 0.01). Together, our results demonstrate that PAP9, a crucial component of the PEP complex, protects it from thermal oxidative stress, ensuring chloroplast development and function at elevated temperatures. These findings provide novel insights into chloroplast adaptation to warming temperatures.