The Four FAD-Dependent Histone Demethylases of Arabidopsis Are Differently Involved in the Control of Flowering Time

Abstract

In Arabidopsis thaliana , four FAD-dependent lysine-specific histone demethylases (LDL1, LDL2, LDL3, and FLD) are present, bearing both a SWIRM and an amine oxidase domain. In this study, a comparative analysis of gene structure, evolutionary relationships, tissue- and organ-specific expression patterns, physiological roles and target genes for the four Arabidopsis LDL/FLDs is reported. Phylogenetic analysis evidences a different evolutionary history for the four LDL/FLDs , while promoter activity data show that LDL/FLDs are strongly expressed during plant development and embryogenesis, with some gene-specific expression patterns. Furthermore, phenotypical analysis of loss-of-function mutants indicates a role of all four Arabidopsis LDL/FLD genes in the control of flowering time, though for some of them with opposing effects. This study contributes toward a better understanding of the LDL/FLD physiological roles and may provide biotechnological strategies for crop improvement.

Advances in Plant Regeneration: Shake, Rattle and Roll

“…LYSINE-SPECIFIC DEMETHYLASE 1, LSD1 (also known as KDM1A), is a conserved histone demethylase in metazoans that specifically removes H3K4me1/me2 or H3K9me1/me2 marks, and can function as a transcriptional repressor or activator [22]. The Arabidopsis genome contains four LSD1 paralogs, FLOWERING LOCUS D (FLD), LDL1, LDL2 and LDL3, which have been linked to seed dormancy, circadian clock and flowering time regulation [23][24][25]. In a recent report, LDL3 was found upregulated on CIM and presumably removes H3K4me2 during callus formation, which then may allow the genes for shoot initiation to be expressed after SIM treatment [26].…”

Two Arabidopsis Homologs of Human Lysine-Specific Demethylase Function in Epigenetic Regulation of Plant Defense Responses

“…Therefore, Arabidopsis LDLs may fine-tune plant immune responses in a sophisticated manner by targeting different genes. Indeed, ldl1 , ldl2 , and ldl4 / fld exhibit a late-flowering phenotype, although the tissue- and organ-specific expression patterns of these genes and the targets of the encoded proteins are different ( Greenberg et al, 2013 ; Yu et al, 2016 ; Hung et al, 2018 ; Martignago et al, 2019 ). For example, 2.3% of DEGs (60 genes out of 2539 DEGs) and 5.8% of DEGs (17 genes out of 273) appear to be involved in biotic stress responses in ldl4 / fld and ldl1 ldl2 , respectively ( Yu et al, 2016 ; Supplementary Figure 5A ).…”

“…Among the four homologous LDL group members, LDL1 and LDL2 are highly similar to LDL4/FLD structurally, with an N-terminal SWIRM domain and an amine oxidase domain, while the structure of LDL3 is different from the others ( Martignago et al, 2019 ). Like the ldl4 / fld mutant, mutations of LDL1 and LDL2 result in late flowering due to high expression of FLC and FWA , but the ldl3 mutants flower earlier and express FLC at lower levels than WT plants ( Martignago et al, 2019 ).…”

“…Therefore, human LSD1 is a proposed target for therapeutic purposes ( Ellis and Loda, 2018 ; Tu et al, 2020 ). In plants, methyl groups of H3K4 are erased by Jumonji C domain-containing demethylases and plant LSD1-like (LDL) proteins ( Spedaletti et al, 2008 ; Martignago et al, 2019 ).…”

“…The Arabidopsis thaliana genome contains four LDL genes [ At1g62830 ( LDL1 ), At3g13682 ( LDL2 ), At4g16310 (LDL3), and At3g10390 ( LDL4 )], which are engaged in flowering time control, circadian clock regulation, homologous recombination repair, hormone responses, and systemic resistance ( Jiang et al, 2007 ; Krichevsky et al, 2009 ; Singh et al, 2012 , 2013 ; Shafiq et al, 2014 ; Zhao et al, 2015 ; Hung et al, 2018 , 2019 ; Hirakawa et al, 2019 ; Martignago et al, 2019 ). For example, Arabidopsis LDL1/SWIRM domain PAO PROTEIN1 (LDL1/SWP1) represses the expression of FLOWERING LOCUS C ( FLC ), encoding a floral repressor, and LATERAL ROOT PRIMODIUM1 , encoding a transcriptional activator, to promote auxin homeostasis-regulated gene expression in root primordia during early root development.…”