Plastid-encoded RNA polymerase (PEP) forms a multisubunit complex in operating chloroplasts, where PEP subunits and a sigma factor are tightly associated with 12 additional nuclear-encoded proteins. Mutants with disrupted genes encoding PEP-associated proteins (PAPs) provide unique tools for deciphering mutual relationships among phytohormones. A block of chloroplast biogenesis in Arabidopsis pap mutants specifying highly altered metabolism in white tissues induced dramatic fluctuations in the content of major phytohormones and their metabolic genes, whereas hormone signaling circuits mostly remained functional. Reprogramming of the expression of biosynthetic and metabolic genes contributed to a greatly increased content of salicylic acid (SA) and a concomitant decrease in 1-aminocyclopropane-1-carboxylic acid (ACC) and oxophytodienoic acid (OPDA), precursors of ethylene and jasmonic acid, respectively, in parallel to reduced levels of abscisic acid (ABA). The lack of differences in the free levels of indole-3-acetic acid (IAA) between the pap mutants and wild-type plants was accompanied by fluctuations in the contents of IAA precursors and conjugated forms as well as multilayered changes in the expression of IAA metabolic genes. Along with cytokinin (CK) overproduction, all of these compensatory changes aim to balance plant growth and defense systems to ensure viability under highly modulated conditions.

Plants harbor a large diversity of endophytic microbes. Meadow fescue (Festuca pratensis) is a cool-season grass known for its symbiotic relationship to the systemic and vertically- via seeds - transmitted fungal endophyte Epichloë uncinata but the effect of the endophyte on the microbial endophyte community and phytohormones is largely unexplored. Here, we sequenced the endophytic bacterial and fungal communities in the leaves and roots, analyzed phytohormone concentrations and plant performance parameters in Epichloë-symbiotic (E+) and Epichloë-free (E-) individuals of two meadow fescue cultivars. The endophytic leaf microbial community differed between leaf and root tissues independent of endophyte symbiosis while the fungal community was different in leaves of Epichloë-symbiotic and Epichloë-free plants in both cultivars. At the same time, endophyte symbiosis decreased salicylic acid and increased auxin concentrations in leaves. Epichloë-symbiotic plants showed a higher biomass, chlorophyll content (SPAD) and higher seed mass at the end of the season. Our results demonstrate that Epichloë-symbiosis alters the leaf fungal microbiome, which coincides with changes in phytohormone concentrations, indicating that Epichloë endophytes affect both, plant immune responses and other fungal endophytes. Whether the effect of Epichloë endophytes on other fungal endophytes is connected to changes in the phytohormone concentrations remains to be elucidated.