The MADS-domain factor AGAMOUS-Like18 promotes somatic embryogenesis

Abstract

AGAMOUS-Like 18 (AGL18) is a MADS domain transcription factor (TF) that is structurally related to AGL15. Here we show that, like AGL15, AGL18 can promote somatic embryogenesis (SE) when ectopically expressed in Arabidopsis (Arabidopsis thaliana). Based on loss-of-function mutants, AGL15 and AGL18 have redundant functions in developmental processes such as SE. To understand the nature of this redundancy, we undertook a number of studies to look at the interaction between these factors. We studied the genome-wide direct targets of AGL18 to characterize its roles at the molecular level using chromatin immunoprecipitation (ChIP)-SEQ combined with RNA-SEQ. The results demonstrated that AGL18 binds to thousands of sites in the genome. Comparison of ChIP-SEQ data for AGL15 and AGL18 revealed substantial numbers of genes bound by both AGL15 and AGL18, but there were also differences. Gene ontology analysis revealed that target genes were enriched for seed, embryo, and reproductive development as well as hormone and stress responses. The results also demonstrated that AGL15 and AGL18 interact in a complex regulatory loop, where AGL15 inhibited transcript accumulation of AGL18, while AGL18 increased AGL15 transcript accumulation. Co-immunoprecipitation revealed an interaction between AGL18 and AGL15 in somatic embryo tissue. The binding and expression analyses revealed a complex crosstalk and interactions among embryo TFs and their target genes. In addition, our study also revealed that phosphorylation of AGL18 and AGL15 was crucial for the promotion of SE.

AGL15 Promotion of Somatic Embryogenesis: Role and Molecular Mechanism

“…This would be consistent with AGL15 recruitment of histone deacetylase complexes to repress gene expression (discussed further below) (Hill et al, 2008 ). Neither SERRATE nor HEN1 were found as targets in our ChIP studies (Zheng et al, 2009 ; Paul et al, 2021 ).…”

“…These include a set of WRKY, NAC, and bZIP TFs that have been associated with dedifferentiation (Grafi et al, 2011 ). A more recent ChIP-seq study for Arabidopsis AGL15 revealed that regulatory regions corresponding to genes encoding nearly all of these TFs are directly bound by AGL15, which seems quite extraordinary (Paul et al, 2021 ). When comparing the percentage of genes encoding these TFs bound by AGL15 to the percentage of genes bound overall compared to the whole genome, a significant enrichment in the dedifferentiation-related (DD) TFs potentially directly regulated by AGL15 is observed ( Table 1 ).…”

“…Some AGPs have been found to be important in the conditioned medium to promote SE, and at least some are expressed in the non-embryogenic cells in embryogenic cultures (reviewed in Von Arnold et al, 2002 ). Interestingly, AGPs, including the subgroup of fasciclin-like AGPs, (FLAs) were prevalent on the AGL15 direct repressed list (Zheng et al, 2009 ), a list that became longer with the ChIP-seq data (Paul et al, 2021 ) ( Table 2 ). Only one ( AGP14 ) showed direct expression in response to AGL15 accumulation, with one additional ( FLA10 ) showing reduced transcript in both comparisons.…”

“… Chip-chip is from Zheng et al ( 2009 ), but allowing transcript change of 0.67–1.5. ChIP-seq is from Paul et al ( 2021 ), analyzed by CLC Genomics Workbench, but also including the three sets of data analyzed by CisGenome (Ji et al, 2008 ). The transcriptomic data is from Zheng et al ( 2009 ) .…”

“…Ectopic constitutive expression of AGL15 promotes SE in Arabidopsis, Glycine max (soybean), and Gossypium hirsutum (cotton), while mutants (loss-of-function) of both AGL15 and AGL18 (closely related to AGL15) significantly reduce SE in Arabidopsis (Harding et al, 2003 ; Thakare et al, 2008 ; Zheng and Perry, 2014 ). Like AGL15, AGL18 is able to promote SE when ectopically expressed in soybean and Arabidopsis (Zheng and Perry, 2014 ; Paul et al, 2021 ).…”