Distinct functions of COAR and B3 domains of maize VP1 in induction of ectopic gene expression and plant developmental phenotypes in Arabidopsis

Embryonic reactivation of FLOWERING LOCUS C by ABSCISIC ACID-INSENSITIVE 3 establishes the vernalization requirement in each Arabidopsis generation

Many over-wintering plants grown in temperate climate acquire competence to flower upon prolonged cold exposure in winter, through vernalization. In Arabidopsis thaliana, prolonged cold exposure induces the silencing of the potent floral repressor FLOWERING LOCUS C (FLC) through repressive chromatin modifications by Polycomb proteins. This repression is maintained to enable flowering after return to warmth, but is reset during seed development. Here, we show that embryonic FLC reactivation occurs in two phases: resetting of cold-induced FLC silencing during embryogenesis and further FLC activation during embryo maturation. We found that the B3 transcription factor (TF) ABSCISIC ACID-INSENSITIVE 3 (ABI3) mediates both FLC resetting in embryogenesis and further activation of FLC expression in embryo maturation. ABI3 binds to the cis-acting cold memory element at FLC and recruits a scaffold protein with active chromatin modifiers to reset FLC chromatin into an active state in late embryogenesis. Moreover, in response to abscisic acid (ABA) accumulation during embryo maturation, ABI3, together with the basic leucine zipper TF ABI5, binds to an ABA-responsive cis-element to further activate FLC expression to high level. Therefore, we have uncovered the molecular circuitries underlying embryonic FLC reactivation following parental vernalization, which ensures that each generation must experience winter cold prior to flowering.

ABA-INSENSITIVE 3 with or without FUSCA3 highly up-regulates lipid droplet proteins and activates oil accumulation

ABA-INSENSITIVE 3 (ABI3) has long been known for activation of storage protein accumulation. A role of ABI3 on oil accumulation was previously suggested based on a decrease of oil content in seeds of abi3 mutant. However, this conclusion could not exclude possibilities of indirect or pleiotropic effects, such as through mutual regulatory interactions with FUSCA3 (FUS3), an activator of oil accumulation. To identify that ABI3 functions independent of the effects of related seed transcription factors, we expressed ABI3 under the control of an inducible promoter in tobacco BY2 cells and Arabidopsis rosette leaves. Inducible expression of ABI3 activated oil accumulation in these non-seed cells, demonstrating a general role of ABI3 in regulation of oil biosynthesis. Further expressing ABI3 in rosette leaves of fus3 knockout mutant still caused up to 3-fold greater triacylglycerol accumulation, indicating ABI3 can activate lipid accumulation independently of FUS3. Transcriptome analysis revealed that LIPID DROPLET PROTEIN (LDP) genes, including OLEOSINs and CALEOSINs, were up-regulated up to 1000-fold by ABI3 in the absence of FUS3, while the expression of WRINKLED1 was doubled. Taken together, our results provide genetic evidence that ABI3 activates oil accumulation with or without FUS3, most likely through up-regulating LDPs and WRINKLED1.

Structural variation affecting DNA backbone interactions underlies adaptation of B3 DNA binding domains to constraints imposed by protein architecture

Functional and architectural diversification of transcription factor families has played a central role in the independent evolution of complex development in plants and animals. Here, we investigate the role of architectural constraints on evolution of B3 DNA binding domains that regulate plant embryogenesis. B3 domains of ABI3, FUS3, LEC2 and VAL1 proteins recognize the same cis-element. Complex architectures of ABI3 and VAL1 integrate cis-element recognition with other signals, whereas LEC2 and FUS3 have reduced architectures conducive to roles as pioneer activators. In yeast and plant in vivo assays, B3 domain functions correlate with architectural complexity of the parent transcription factor rather than phylogenetic relatedness. In a complex architecture, attenuated ABI3-B3 and VAL1-B3 activities enable integration of cis-element recognition with hormone signaling, whereas hyper-active LEC2-B3 and FUS3-B3 over-ride hormonal control. Three clade-specific amino acid substitutions (β4-triad) implicated in interactions with the DNA backbone account for divergence of LEC2-B3 and ABI3-B3. We find a striking correlation between differences in in vitro DNA binding affinity and in vivo activities of B3 domains in plants and yeast. Our results highlight the role of DNA backbone interactions that preserve DNA sequence specificity in adaptation of B3 domains to functional constraints associated with domain architecture.

Vegetative desiccation tolerance in the resurrection plant Xerophyta humilis has not evolved through reactivation of the seed canonical LAFL regulatory network

It has been hypothesised that vegetative desiccation tolerance in resurrection plants evolved via reactivation of the canonical LAFL (i.e. LEC1, ABI3, FUS3 and LEC2) transcription factor (TF) network that activates the expression of genes during the maturation of orthodox seeds leading to desiccation tolerance of the plant embryo in most angiosperms. There is little direct evidence to support this, however, and the transcriptional changes that occur during seed maturation in resurrection plants have not previously been studied. Here we performed de novo transcriptome assembly for Xerophyta humilis, and analysed gene expression during seed maturation and vegetative desiccation. Our results indicate that differential expression of a set of 4205 genes is common to maturing seeds and desiccating leaves. This shared set of genes is enriched for gene ontology terms related to abiotic stress, including water stress and abscisic acid signalling, and includes many genes that are seed-specific in Arabidopsis thaliana and targets of ABI3. However, while we observed upregulation of orthologues of the canonical LAFL TFs and ABI5 during seed maturation, similar to what is seen in A. thaliana, this did not occur during desiccation of leaf tissue. Thus, reactivation of components of the seed desiccation program in X. humilis vegetative tissues likely involves alternative transcriptional regulators.

TaABI5, a wheat homolog of Arabidopsis thaliana ABA insensitive 5, controls seed germination

Abscisic acid (ABA) response element (ABRE)-binding factors (ABFs) are basic region/leucine zipper motif (bZIP) transcription factors that regulate the expression of ABA-induced genes containing ABRE in their promoters. The amino acid sequence of the wheat bZIP protein, TaABI5, showed high homology to that of Arabidopsis ABA insensitive 5 (ABI5). TaABI5 was classified into the clade of ABI5s in Arabidopsis and rice, unlike TRAB1 of rice, Wabi5 of wheat, and HvABI5 of barley in the bZIP Group A family, by a phylogenetic analysis. TaABI5 was strongly expressed in seeds during the late ripening and maturing stages; however, its expression level markedly decreased after germination. An in situ hybridization analysis showed that TaABI5 mRNA accumulated in seed embryos, particularly the scutellum. In a transient assay using wheat aleurone cells, TaABI5 activated the promoter of Em containing ABRE, which is an embryogenesis abundant protein gene, indicating that TaABI5 acts as a transcription factor in wheat seeds. Furthermore, the seeds of transgenic Arabidopsis lines introduced with 35S:TaABI5 exhibited high sensitivity to ABA and the inhibition of germination. The seed dormancy of the transgenic Arabidopsis lines was stronger than that of Col. These results support TaABI5 playing an important role in mature seeds, particularly before seed germination, and acting as a functional ortholog to Arabidopsis ABI5.

LEC1 (NF-YB9) directly interacts with LEC2 to control gene expression in seed

The LAFL transcription factors LEC2, ABI3, FUS3 and LEC1 are master regulators of seed development. LEC2, ABI3 and FUS3 are closely related proteins that contain a B3-type DNA binding domain. We have previously shown that LEC1 (a NF-YB type protein) can increase LEC2 and ABI3 but not FUS3 activity. Interestingly, FUS3, LEC2 and ABI3 contain a B2 domain, the function of which remains elusive. We showed that LEC1 and LEC2 partially co-localised in the nucleus of developing embryos. By comparing protein sequences from various species, we identified within the B2 domains a set of highly conserved residues (i.e. TKxxARxxRxxAxxR). This domain directly interacts with LEC1 in yeast. Mutations of the conserved amino acids of the motif in the B2 domain abolished this interaction both in yeast and in moss protoplasts and did not alter the nuclear localisation of LEC2 in planta. Conversely, the mutations of key amino acids for the function of LEC1 in planta (D86K) prevented the interaction with LEC2. These results provide molecular evidences for the binding of LEC1 to B2-domain containing transcription factors, to form heteromers, involved in the control of gene expression.

Characterization and functional analysis of a B3 domain factor from Zea mays

In this study, we isolated a full-length cDNA and named ZmBDF from zea mays. ZmBDF encoded a protein of 356 amino acids and phylogenetic analysis showed that it belongs to a closely related subgroup with B3 domain factors in plants. The transcript level of ZmBDF could be induced by ABA, MeJA, salt or drought treatments. To further investigated the function of ZmBDF, ZmBDF over-expression transgenic lines were got by transforming it into Arabidopsis thaliana. ZmBDF over-expression transgenic plants in Arabidopsis could increase drought and salt tolerant in germination assay. Under drought condition, net photosynthetic rates (PN), stomatal conductance (gs), and internal leaf CO2 concentration (Ci) were less affected in transgenic plants compared with wild type. Besides, the chlorophyll a and chlorophyll b (chl a/chl b) ratio decreased in WT plants than the transgenic plants and total carotenoid content show opposite trends. Moreover, transgenic plants could also reduce the stomatal density and changed the stomatal shape. Taken together, our data suggested that ZmBDF could improve stress tolerance to drought and salt in maize.