Loss of the plastidial signaling molecule, ppGpp, accumulation alters nuclear gene expression during nitrogen starvation
Nitrogen deficiency triggers major transcriptional reprogramming in plants. The chloroplast alarmone guanosine tetraphosphate, ppGpp, synthesized and hydrolyzed by RelA-SpoT homologs, has been proposed to regulate cellular metabolism. Here, we characterized an Arabidopsis mutant lacking all RSHs, referred to as the quadruple mutant, which accumulates no detectable ppGpp. Transcriptome analysis showed that 774 and 2,928 nuclear-encoded genes were differentially expressed in the quadruple mutant compared with the wild type under nitrogen-sufficient and nitrogen-deficient conditions, respectively. Upon transition from nitrogen-sufficient to nitrogen-deficient conditions, 2,387 nuclear genes in the wild type and 1,505 genes in the quadruple mutant, primarily associated with cell wall biosynthesis and defense responses, were differentially expressed, suggesting that plastidial ppGpp is involved in the reprogramming of nuclear gene expression in response to nitrogen availability. Network analysis of transcription factors indicated that ppGpp alters transcription factor expression and identified 11 candidates as master regulators of transcription factor expression in a ppGpp-dependent manner during nitrogen starvation. Transcript levels of several plastid-encoded genes were higher in the quadruple mutant compared to the wild type under nitrogen-deficient conditions, whereas mitochondrial transcripts were less affected. Together, these findings suggest that ppGpp acts as both a regulator and a key component of retrograde signaling, coordinating nuclear transcription and metabolic adaptation in response to nitrogen availability.