Disruption of lysine biosynthesis modulates DNA methylation and developmental programs in Arabidopsis thaliana

Lysine metabolism is a central determinant of plant growth, coupling amino acid biosynthesis to mitochondrial electron transport and the tricarboxylic acid (TCA) cycle to sustain cellular energy homeostasis. However, whether perturbation of lysine biosynthesis reshapes developmental transitions through epigenetic regulatory pathways remains unknown. Here, we show that reduced activity of L,L -diaminopimelate aminotransferase (DAPAT), a key enzyme in lysine biosynthesis, markedly reprograms growth and developmental timing in Arabidopsis thaliana . The lysine biosynthesis-deficient mutant dapat exhibits severe development constraints, displaying a pronounced flowering delay under long-day conditions accompanied by reduced shoot branching, fewer siliques, lower seed number per silique, decreased seed biomass, and reduced leaf production, a comprehensive developmental phenotype that underscores the critical role of lysine metabolism in orchestrating plant growth. Strikingly, neutral-day conditions partially rescue the flowering delay in dapat plants, revealing an unexpected environmental plasticity that positions lysine biosynthesis at the intersection of metabolic regulation, epigenetic remodeling, and developmental timing. Gene expression analysis of key flowering-time regulators that control the photoperiodic and vernalization pathways in Arabidopsis revealed upregulation of CONSTANS ( CO ) and FLOWERING LOCUS C ( FLC ), downregulation of FRIGIDA ( FRI ), and unaltered FLOWERING LOCUS T ( FT ), suggesting that lysine deficiency modulates flowering through a CO / FLC -dependent regulatory framework. Using whole-genome bisulfite sequencing (WGBS) we identified 957 genes with altered methylation patterns across the plant's five chromosomes. These changes occurred in three different DNA sequence contexts: 749 genes showed differences in CpG sites, while 104 genes each showed changes in CHG and CHH contexts. These epigenetic changes coincide with altered expression of genes involved in S -adenosyl-methionine metabolism and chromatin regulation, including upregulation of S -adenosyl-methionine synthase 2 ( MAT2 ), S -adenosyl-methionine synthase 4 ( MAT4 ), and histone methyltransferase SU(VAR)3–9 HOMOLOG 4 ( SUVH4 ), whereas SUVH5 is downregulated and SUVH6 remains unchanged. These findings uncover a previously unrecognized role for lysine biosynthesis via DAPAT enzyme in coordinating plant growth, flowering time, and reproductive output through metabolic-epigenetic regulation.