PIF1 Regulates Plastid Development by Repressing Photosynthetic Genes in the Endodermis

Mutations in Phytochrome Interacting Factors （PIFs） induce a conversion of the endodermal amyloplasts necessary for gravity sensing to plastids with developed thylakoids accompanied by abnormal activation of photosynthetic genes in the dark. In this study, we investigated how PIFs regulate endodermal plastid development by performing comparative transcriptome analysis. We show that both endodermal expression of PIF1 and global expression of the PIF quartet induce transcriptional changes in genes enriched for nuclear-encoded photosynthetic genes such as LHCA and LHCB. Among the 94 shared differentially expressed genes identified from the comparative transcriptome analysis, only 14 genes are demonstrated to be direct targets of PIF1, and most photosynthetic genes are not. Using a co-expression analysis, we identified a direct target of PIF, whose expression pattern shows a strong negative correlation with many photo- synthetic genes. We have named this gene REPRESSOR OF PHOTOSYNTHETIC GENES1 （RPGE1）. Endodermal expression of RPGE1 rescued the elevated expression of photosynthetic genes found in the pff quadruple （pifQ） mutant and partly restored amyloplast development and hypocotyl negative gravitropism. Taken together, our results indicate that RPGE1 acts downstream of PIF1 in the endodermis to repress photosynthetic genes and regulate plastid development.

The Dof transcription factor COG1 acts as a key regulator of plant biomass by promoting photosynthesis and starch accumulation

Photosynthetic efficiency is the primary determinant of crop yield,including vegetative biomass and grain yield.Manipulation of key transcription factors known to directly control photosynthetic machinery can be an effective strategy to improve photosynthetic traits.In this study,we identified an Arabidopsis gain-of-function mutant,cogwheel1-3D,that shows a significantly enlarged rosette and increased biomass compared with wild-type plants.Overexpression of COG1,a Dof transcription factor,recapitulated the phenotype of cogwheel1-3D,whereas knocking out COG1 and its six paralogs resulted in a reduced rosette size and decreased biomass.Transcriptomic and quantitative reverse transcription polymerase chain reaction analyses demonstrated that COG1 and its paralogs were required for light-induced expression of genes involved in photosynthesis.Further chromatin immunoprecipitation and electrophoretic mobility shift assays indicated that COG1 can directly bind to the promoter regions of multiple genes encoding light-harvesting antenna proteins.Physiological,biochemical,and microscopy analyses revealed that COG1 enhances photosynthetic capacity and starch accumulation in Arabidopsis rosette leaves.Furthermore,combined results of bioinformatic,genetic,and molecular experiments suggested that the functions of COG1 in increasing biomass are conserved in different plant species.These results collectively demonstrated that COG1 acts as a key regulator of plant biomass by promoting photosynthesis and starch accumulation.Manipulating COG1 to optimize photosynthetic capacity would create new strategies for future crop yield improvement.