Genome-wide analysis of genes targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during seed germination in Arabidopsis

Phytochrome-interacting factor 4 (PIF4) inhibits expression of SHORT HYPOCOTYL 2 (SHY2) to promote hypocotyl growth during shade avoidance in Arabidopsis

Plants sense the presence of competing neighboring vegetation as a change in light quality. These changes initiate shade avoidance syndrome (SAS) responses. PHYTOCHROME INTERACTING FACTORS (PIFs) are crucial factors in the SAS response. In particular, they mediate the expression of multiple phytohormones and cell expansion genes. Many positive regulatory factors in the SAS response have been identified, but the negative regulation of SAS transcription factors remains poorly understood. The functions of the short hypocotyl 2 (SHY2) transcription factor during the SAS response have not been established, although its roles in the participating hormone and stress responses are well documented. Here, the SHY2 loss-of-function (shy2-31) mutant had a longer hypocotyl, but the gain-of-function (shy2-2) hypocotyl was shorter than that of the wild type under white and shade conditions. We showed that the SHY2 expression level and its associated protein significantly accumulated under shade conditions. Furthermore, SHY2 transcript levels significantly increased in mutant pifQ, but decreased in PIF4OX compared to the wild type, which indicated that PIF4 is a transcriptional repressor of SHY2. ChIP assays have consistently shown that PIF4 directly binds to the promoters of SHY2. We further show that PIF4OX partially rescued the short hypocotyl characteristic of shy2-2 under white and shade conditions. Our results provide new insights into the regulatory mechanisms controlling SAS mediated elongation of the hypocotyl by PIF4-SHY2 modules in Arabidopsis.

Genome-wide analysis of PmTCP4 transcription factor binding sites by ChIP-Seq during pistil abortion in Japanese apricot

The TCP4 transcription factor plays an important role in plant growth and development, especially in flower development. PmTCP4 is involved in the process of pistil abortion in Japanese apricot, but its molecular mechanism, particularly the DNA binding sites and co-regulatory genes, are quite unknown. Therefore, to identify the genome-wide binding sites of PmTCP4 transcription factors and their co-regulatory genes, chromatin immunoprecipitation sequencing (ChIP-Seq) was carried out. ChIP-Seq data produced the maximum enriched peaks in two Japanese apricot cultivars 'Daqiandi' (DQD) and 'Longyan' (LY), which showed that the majority of DNA-protein interactions are relevant and have a significant function in binding sites. Moreover, 720 and 251 peak-associated genes regulated by PmTCP4 were identified in DQD and LY, respectively, and most of them were involved in the flower and pistil development process. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that photosynthesis and oxidative phosphorylation were the most enriched pathways in both cultivars and all identified genes related to these pathways were down-regulated. This study will provide a reference for a better understanding of the PmTCP4 regulatory mechanism during pistil abortion in Japanese apricot.

The PIFs Redundantly Control Plant Defense Response against Botrytis cinerea in Arabidopsis

Endogenous and exogenous signals are perceived and integrated by plants to precisely control defense responses. As a crucial environmental cue, light reportedly plays vital roles in plant defenses against necrotrophic pathogens. Phytochrome-interacting factor (PIF) is one of the important transcription factors which plays essential roles in photoreceptor-mediated light response. In this study, we revealed that PIFs negatively regulate plant defenses against Botrytis cinerea. Gene expression analyses showed that the expression level of a subset of defense-response genes was higher in pifq (pif1/3/4/5) mutants than in the wild-type control, but was lower in PIF-overexpressing plants. Chromatin immunoprecipitation assays proved that PIF4/5 binds directly to the ETHYLENE RESPONSE FACTOR1 (ERF1) promoter. Moreover, genetic analyses indicated that the overexpression of ERF1 dramatically rescues the susceptibility of PIF4-HA and PIF5-GFP transgenic plants, and that PIF controls the resistance to B. cinerea in a COI1- and EIN2-dependent manner. Our results provide compelling evidence that PIF, together with the jasmonate/ethylene pathway, is important for plant resistance to B. cinerea.

Comparative sequence analysis across Brassicaceae, regulatory diversity in KCS5 and KCS6 homologs from Arabidopsis thaliana and Brassica juncea, and intronic fragment as a negative transcriptional regulator

Intra- and epicuticular-waxes primarily comprising of very long chain aliphatic lipid (VLCFA), terpenoids and secondary metabolites such as sterol and flavonoids played a major role in successful colonization of terrestrial ecosystem by aquatic plants and are thus considered as a key evolutionary innovation. The key rate limiting step of Fatty Acid (FA) biosynthesis of condensation/elongation are catalyzed by the enzyme, β-ketoacyl coenzyme A synthase (KCS), part of FAE (Fatty Acid Elongase) complex. KCS6 has been shown to be responsible for elongation using C22 fatty acid as substrate and is considered essential for synthesis of VLCFA for cuticular waxes. Earlier studies have established KCS5 as a close paralog of KCS6 in Arabidopsis thaliana, albeit with non-redundant function. We subsequently established segmental duplication responsible for origin of KCS6-KCS5 paralogy which is exclusive to Brassicaceae. In the present study, we aim to understand impact of duplication on regulatory diversification and evolution, through sequence and functional analysis of cis-regulatory element of KCS5 and KCS6. High level of sequence variation leading to conservation of only the proximal end of the promoter corresponding to the core promoter was observed among Brassicaceae members; such high diversity was also revealed when sliding window analysis revealed only two to three phylogenetic footprints. Profiling of transcription factor binding sites (TFBS) across Brassicaceae shows presence of light, hormone and stress responsive motifs; a few motifs involved in tissue specific expression (Skn-1; endosperm) were also detected. Functional characterization using transcriptional fusion constructs revealed regulatory diversification when promoter activity of homologs from A. thaliana and Brassica juncea were compared. When subjected to 5-Azacytidine, altered promoter activity was observed, implying role of DNA methylation in transcriptional regulation. Finally, investigation of the role of an 87 bp fragment from first intron that is retained in a splice variant, revealed it to be a transcriptional repressor. This is a first report on comparative sequence and functional analysis of transcriptional regulation of KCS5 and KCS6; further studies are required before manipulation of cuticular waxes as a strategy for mitigating stress.

PIF1 and RVE1 form a transcriptional feedback loop to control light-mediated seed germination in Arabidopsis

The phytochrome B (phyB) photoreceptor plays a major role that inputs light signals to regulate seed dormancy and germination. PHYTOCHROME-INTERACTING FACTOR1 (PIF1) is a key transcription factor repressing phyB-mediated seed germination, while REVEILLE1 (RVE1) factor functions as a curial regulator in controlling both seed dormancy and germination. However, the relationship between the PIF1- and RVE1-modulated signaling pathways remains mostly unknown. Here, we find that PIF1 physically interacts with RVE1. Genetic analysis indicates that RVE1 inhibition on seed germination requires PIF1; reciprocally, the repressive effect of PIF1 is partially dependent on RVE1. Strikingly, PIF1 and RVE1 directly bind to the promoter and activate the expression of each other. Furthermore, PIF1 and RVE1 coordinately regulate the transcription of many downstream genes involved in abscisic acid and gibberellin pathways. Moreover, PIF1 enhances the DNA-binding ability and transcriptional repression activity of RVE1 in regulating GIBBERELLIN 3-OXIDASE2, and RVE1 promotes PIF1's DNA-binding ability in modulating ABSCISIC ACID-INSENSITIVE3 expression. Thus, this study demonstrates that PIF1 and RVE1 form a transcriptional feedback loop that coordinately inhibits seed germination, providing a mechanistic understanding of how phyB-mediated light signal is transduced to the seeds.

MYB5-like and bHLH influence flavonoid composition in pomegranate

The fruit of the pomegranate (Punica granatum L.) is an important nutraceutical food rich in polyphenolic compounds, including hydrolysable tannins, anthocyanins and flavonols. Their composition varies according to cultivar, tissue and fruit development stage and is probably regulated by a combination of MYB and bHLH type transcription factors (TFs). In this study, metabolomics analysis during fruit developmental stages in the main pomegranate cultivars, Wonderful and Valenciana with contrasting colour of their ripe fruits, showed that flavonols were mostly present in flowers while catechins were highest in unripe fruits and anthocyanins in late fruit maturation stages. A novel MYB TF, PgMYB5-like, was identified, which differs from previously isolated pomegranate TFs by unique C-terminal protein motifs and lack of the amino-acid residues conserved among anthocyanins promoting MYBs. In both pomegranate cultivars the expression of PgMYB5-like was high at flowering stage, while it decreased during fruit ripening. A previously identified bHLH-type TF, PgbHLH, also showed high transcript levels at flowering stage in both cultivars, while it showed a decrease in expression during fruit ripening in cv. Valenciana, but not in cv. Wonderful. Functional analysis of both TFs was performed by agro-infiltration into Nicotiana benthamiana leaves. Plants infiltrated with the PgMYB5-like+PgbHLH combined construct showed a specific and significant accumulation of intermediates of the flavonoid pathway, especially dihydroflavonols, while anthocyanins were not produced. Thus, we propose a role for PgMYB5-like and PgbHLH in the first steps of flavonoid production in flowers and in unripe fruits. The expression patterns of these two TFs may be key in determining the differential flavonoid composition in both flowers and fruits of the pomegranate varieties Wonderful and Valenciana.

The role of light in regulating seed dormancy and germination

Seed dormancy is an adaptive trait in plants. Breaking seed dormancy determines the timing of germination and is, thereby essential for ensuring plant survival and agricultural production. Seed dormancy and the subsequent germination are controlled by both internal cues (mainly hormones) and environmental signals. In the past few years, the roles of plant hormones in regulating seed dormancy and germination have been uncovered. However, we are only beginning to understand how light signaling pathways modulate seed dormancy and interaction with endogenous hormones. In this review, we summarize current views of the molecular mechanisms by which light controls the induction, maintenance and release of seed dormancy, as well as seed germination, by regulating hormone metabolism and signaling pathways.

Combined metabolome and transcriptome analyses of photosynthetic pigments in red maple

Leaf color is affected primarily by the content and proportion of various pigments. Not only do photosynthetic pigments display various colors, they are also key to the physiological activities of plants. To precisely elucidate the mechanisms of chlorophyll and carotenoid biosynthesis and their interactions in red maple, transcriptomic and metabolomic profiling were performed on green, red and yellow leaves from a selected red maple mutant. In the chlorophyll pathway, ArPOR1, ArCLH2, and ArCLH4 positively regulated chlorophyll a, and made it the dominant pigment in green leaves, whereas ArNOL8 and ArNOL14 negatively regulated chlorophyll synthesis. In the carotenoid pathway, under the positive regulation of ArLUT5-1 and ArLUT5-4, the synthesis of carotenoids changed from α-branch to β-branch during the gradual senescence of leaves. Through integrated data analysis, we obtained genes that directly coordinated between carotenoid and chlorophyll biosynthesis. Ultimately, the results of this paper will be a valuable resource for future research on gene-to-metabolite correlations in red maple, and provide basic information toward facilitating the improvement of color in foliage plants.

A Molecular Signal Integration Network Underpinning Arabidopsis Seed Germination

Seed dormancy is an adaptive trait defining where and when plants are established. Diverse signals from the environment are used to decide when to initiate seed germination, a process driven by the expansion of cells within the embryo. How these signals are integrated and transduced into the biomechanical changes that drive embryo growth remains poorly understood. Using Arabidopsis seeds, we demonstrate that cell-wall-loosening EXPANSIN (EXPA) genes promote gibberellic acid (GA)-mediated germination, identifying EXPAs as downstream molecular targets of this developmental phase transition. Molecular interaction screening identified transcription factors (TFs) that bind to both EXPA promoter fragments and DELLA GA-response regulators. A subset of these TFs is targeted each by nitric oxide (NO) and the phytochrome-interacting TF PIL5. This molecular interaction network therefore directly links the perception of an external environmental signal (light) and internal hormonal signals (GA and NO) with downstream germination-driving EXPA gene expression. Experimental validation of this network established that many of these TFs mediate GA-regulated germination, including TCP14/15, RAP2.2/2.3/2.12, and ZML1. The reduced germination phenotype of the tcp14 tcp15 mutant seed was partially rescued through ectopic expression of their direct target EXPA9. The GA-mediated control of germination by TCP14/15 is regulated through EXPA-mediated control of cell wall loosening, providing a mechanistic explanation for this phenotype and a previously undescribed role for TCPs in the control of cell expansion. This network reveals the paths of signal integration that culminate in seed germination and provides a resource to uncover links between the genetic and biomechanical bases of plant growth.

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The network linking integration of environmental signals to seed growth is mapped

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EXPANSIN gene expression is redundantly regulated and promotes GA-mediated germination

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The TCP14 transcription factor directly regulates EXPANSIN9 expression

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The tcp14/15 germination phenotype is complemented by EXPANSIN9 expression

Transcriptional regulatory network of the light signaling pathways

The developmental program by which plants respond is tightly controlled by a complex cascade in which photoreceptors perceive and transduce the light signals that drive signaling processes and direct the transcriptional reprogramming, yielding specific cellular responses. The molecular mechanisms involved in the transcriptional regulation include light-regulated nuclear localization (the phytochromes and UVR8) and nuclear accumulation (the cryptochrome, cry2) of photoreceptors. This regulatory cascade also includes master regulatory transcription factors (TFs) that bridge photoreceptor activation with chromatin remodeling and regulate the expression of numerous light-responsive genes. Light signaling-related TFs often function as signal convergence points in concert with TFs in other signaling pathways to integrate complex endogenous and environmental cues that help the plant adapt to the surrounding environment. Increasing evidence suggests that chromatin modifications play a critical role in regulating light-responsive gene expression and provide an additional layer of light signaling regulation. Here, we provide an overview of our current knowledge of the transcriptional regulatory network involved in the light response, particularly the roles of TFs and chromatin in regulating light-responsive gene expression.

Direct and indirect targets of the arabidopsis seed transcription factor ABSCISIC ACID INSENSITIVE3

Arabidopsis thaliana ABSCISIC ACID INSENSITIVE3 (ABI3) is a transcription factor in the B3 domain family. ABI3, along with B3 domain transcription factors LEAFY COTYLEDON2 (LEC2) and FUSCA3 (FUS3), and LEC1, a subunit of the CCAAT box-binding complex, form the so-called LAFL network to control various aspects of seed development and maturation. ABI3 also contributes to the abscisic acid (ABA) response. We report on chromatin immunoprecipitation-tiling array experiments to map binding sites for ABI3 globally. We also assessed transcriptomes in response to ABI3 by comparing developing abi3-5 and wild-type seeds and combined this information to ascertain direct and indirect responsive ABI3 target genes. ABI3 can induce and repress its transcription of target genes directly and some intriguing differences exist in cis motifs between these groups of genes. Directly regulated targets reflect the role of ABI3 in seed maturation, desiccation tolerance, entry into a quiescent state and longevity. Interestingly, ABI3 directly represses a gene encoding a microRNA (MIR160B) that targets AUXIN RESPONSE FACTOR (ARF)10 and ARF16 that are involved in establishment of dormancy. In addition, ABI3, like FUS3, regulates genes encoding MIR156 but while FUS3 only induces genes encoding this product, ABI3 induces these genes during the early stages of seed development, but represses these genes during late development. The interplay between ABI3, the other LAFL genes, and the VP1/ABI3-LIKE (VAL) genes, which are involved in the transition to seedling development are examined and reveal complex interactions controlling development.

Vascular plant one-zinc finger 1 (VOZ1) and VOZ2 negatively regulate phytochrome B-mediated seed germination in Arabidopsis

Seed germination is regulated by light. Phytochromes (Phys) act as red and far-red light photoreceptors to mediate seed germination. However, the mechanism of this process is not well understood. In this study, we found that the Arabidopsis thaliana mutants vascular plant one-zinc finger 1 (voz1) and voz2 showed higher seed germination percentage than wild type when PhyB was inactivated by far-red light. In wild type, VOZ1 and VOZ2 expression were downregulated after seed imbibition, repressed by PhyB, and upregulated by Phytochrome-interacting factor 1 (PIF1), a key negative regulator of seed germination. Red light irradiation and the voz1voz2 mutation caused increased expression of Gibberellin 3-oxidase 1 (GA3ox1), a gibberellin (GA) biosynthetic gene. We also found that VOZ2 is bound directly to the promoter of GA3ox1 in vitro and in vivo. Our findings suggest that VOZs play a negative role in PhyB-mediated seed germination, possibly by directly regulating GA3ox1 expression.

CONSTITUTIVELY PHOTOMORPHOGENIC1 promotes ABA-mediated inhibition of post-germination seedling establishment

Under acute stress conditions, precocious seedling development may result in the premature death of young seedlings, before they switch to autotrophic growth. The phytohormone abscisic acid (ABA) inhibits seed germination and post-germination seedling establishment under unfavorable conditions. Various environmental signals interact with the ABA pathway to optimize these early developmental events under stress. Here, we show that light availability critically influences ABA sensitivity during early seedling development. In dark conditions, the ABA-mediated inhibition of post-germination seedling establishment is strongly enhanced. COP1, a central regulator of seedling development in the dark, is necessary for this enhanced post-germination ABA sensitivity in darkness. Despite their slower germination, cop1 seedlings establish faster than wild type in the presence of ABA in both light and dark. PHY and CRY photoreceptors that inhibit COP1 activity in light modulate ABA-mediated inhibition of seedling establishment in light. Genetically, COP1 acts downstream to ABI5, a key transcriptional regulator of ABA signaling, and does not influence the transcriptional and protein levels of ABI5 during the early post-germination stages. COP1 promotes post-germination growth arrest independent of the antagonistic interaction between ABA and cytokinin signaling pathways. COP1 facilitates the binding of ABI5 on its target promoters and the ABA-mediated upregulation of these target genes is reduced in cop1-4. Together, our results suggest that COP1 positively regulates ABA signaling to inhibit post-germination seedling establishment under stress.

PHYTOCHROME INTERACTING FACTORs in the moss Physcomitrella patens regulate light-controlled gene expression

Phytochromes are red and far-red light receptors in plants that control growth and development in response to changes in the environment. Light-activated phytochromes enter the nucleus and act on a set of downstream signalling components to regulate gene expression. PHYTOCHROME INTERACTING FACTORs (PIFs) belong to the basic helix-loop-helix family of transcription factors and directly bind to light-activated phytochromes. Potential homologues of PIFs have been identified in ferns, bryophytes and streptophyte algae, and it has been shown that the potential PIF homologues from Physcomitrella patens, PIF1 to PIF4, have PIF function when expressed in Arabidopsis. However, their function in Physcomitrella is still unknown. Seed plant PIFs bind to G-box-containing promoters and, therefore, we searched the Physcomitrella genome for genes that contain G-boxes in their promoter. Here, we show that Physcomitrella PIFs activate these promoters in a G-box-dependent manner, suggesting that they could be direct PIF targets. Furthermore, we generated Physcomitrella pif1, pif2, pif3 and pif4 knock out mutant lines and quantified the expression of potential PIF direct target genes. The expression of these genes was generally reduced in pif mutants compared to the wildtype, but for several genes, the relative induction upon a short light treatment was higher in pif mutants than the wildtype. In contrast, expression of these genes was strongly repressed in continuous light, and pif mutants showed partial downregulation of these genes in the dark. Thus, the overall function of PIFs in light-regulated gene expression might be an ancient property of PIFs.

DRT111/SFPS Splicing Factor Controls Abscisic Acid Sensitivity during Seed Development and Germination

RNA splicing is a fundamental mechanism contributing to the definition of the cellular protein population in any given environmental condition. DNA-DAMAGE REPAIR/TOLERATION PROTEIN111 (DRT111)/SPLICING FACTOR FOR PHYTOCHROME SIGNALING is a splicing factor previously shown to interact with phytochrome B and characterized for its role in splicing of pre-mRNAs involved in photomorphogenesis. Here, we show that DRT111 interacts with Arabidopsis (Arabidopsis thaliana) Splicing Factor1, involved in 3' splicing site recognition. Double- and triple-mutant analysis shows that DRT111 controls splicing of ABI3 and acts upstream of the splicing factor SUPPRESSOR OF ABI3-ABI5. DRT111 is highly expressed in seeds and stomata of Arabidopsis and is induced by long-term treatments of polyethylene glycol and abscisic acid (ABA). DRT111 knock-out mutants are defective in ABA-induced stomatal closure and are hypersensitive to ABA during seed germination. Conversely, DRT111 overexpressing plants show ABA-hyposensitive seed germination. RNA-sequencing experiments show that in dry seeds, DRT111 controls expression and splicing of genes involved in osmotic-stress and ABA responses, light signaling, and mRNA splicing, including targets of ABSCISIC ACID INSENSITIVE3 (ABI3) and PHYTOCHROME INTERACTING FACTORs (PIFs). Consistently, expression of the germination inhibitor SOMNUS, induced by ABI3 and PIF1, is upregulated in imbibed seeds of drt111-2 mutants. Together, these results indicate that DRT111 controls sensitivity to ABA during seed development, germination, and stomatal movements, and integrates ABA- and light-regulated pathways to control seed germination.

Coordinated Transcriptional Regulation by the UV-B Photoreceptor and Multiple Transcription Factors for Plant UV-B Responses

Non-damaging ultraviolet B (UV-B) light promotes photomorphogenic development and stress acclimation through UV-B-specific signal transduction in Arabidopsis. UV-B irradiation induces monomerization and nuclear translocation of the UV-B photoreceptor UV RESISTANCE LOCUS 8 (UVR8). However, it is not clear how the nuclear localization of UVR8 leads to changes in global gene expression. Here, we reveal that nuclear UVR8 governs UV-B-responsive transcriptional networks in concert with several previously known transcription factors, including ELONGATED HYPOCOTYL 5 (HY5) and PHYTOCHROME INTERACTING FACTOR 4 (PIF4). Based on the transcriptomic analysis, we identify MYB13 as a novel positive regulator in UV-B-induced cotyledon expansion and stress acclimation. MYB13 is UV-B inducible and is predominantly expressed in the cotyledons. Our results demonstrate that MYB13 protein functions as a transcription factor to regulate the expression of genes involved in auxin response and flavonoid biosynthesis through direct binding with their promoters. In addition, photoactivated UVR8 interacts with MYB13 in a UV-B-dependent manner and differentially modulates the affinity of MYB13 with its targets. Taken together, our results elucidate the cooperative function of the UV-B photoreceptor UVR8 with various transcription factors in the nucleus to orchestrate the expression of specific sets of downstream genes and, ultimately, mediate plant responses to UV-B light.

MfPIF1 of Resurrection Plant Myrothamnus flabellifolia Plays a Positive Regulatory Role in Responding to Drought and Salinity Stresses in Arabidopsis

Phytochrome-interacting factors (PIFs), a subfamily of basic helix-loop-helix (bHLH) transcription factors (TFs), play critical roles in regulating plant growth and development. The resurrection plant Myrothamnus flabellifolia possesses a noteworthy tolerance to desiccation, but no PIFs related to the response to abiotic stress have been functionally studied. In this study, a dehydration-inducible PIF gene, MfPIF1, was cloned and characterized. Subcellular localization assay revealed that MfPIF1 is localized predominantly in the nucleus. Overexpression of MfPIF1 in Arabidopsis thaliana led to enhanced drought and salinity tolerance, which was attributed to higher contents of chlorophyll, proline (Pro), soluble protein, and soluble sugar, activities of antioxidant enzymes as well as lower water loss rate, malondialdehyde (MDA) content, and reactive oxygen species (ROS) accumulation in transgenic lines compared with control plants. Moreover, MfPIF1 decreased stomatal aperture after drought and abscisic acid (ABA) treatment, and increased expression of both ABA biosynthesis and ABA-responsive genes including NCED3, P5CS, and RD29A. Overall, these results indicated that MfPIF1 may act as a positive regulator to drought and salinity responses, and therefore could be considered as a potential gene for plant genetic improvement of drought and salinity tolerance.

OsbHLH073 Negatively Regulates Internode Elongation and Plant Height by Modulating GA Homeostasis in Rice

Internode elongation is one of the key agronomic traits determining a plant’s height and biomass. However, our understanding of the molecular mechanisms controlling internode elongation is still limited in crop plant species. Here, we report the functional identification of an atypical basic helix-loop-helix transcription factor (OsbHLH073) through gain-of-function studies using overexpression (OsbHLH073-OX) and activation tagging (osbhlh073-D) lines of rice. The expression of OsbHLH073 was significantly increased in the osbhlh073-D line. The phenotype of osbhlh073-D showed semi-dwarfism due to deficient elongation of the first internode and poor panicle exsertion. Transgenic lines overexpressing OsbHLH073 confirmed the phenotype of the osbhlh073-D line. Exogenous gibberellic acid (GA₃) treatment recovered the semi-dwarf phenotype of osbhlh073-D plants at the seedling stage. In addition, quantitative expression analysis of genes involving in GA biosynthetic and signaling pathway revealed that the transcripts of rice ent-kaurene oxidases 1 and 2 (OsKO1 and OsKO2) encoding the GA biosynthetic enzyme were significantly downregulated in osbhlh073-D and OsbHLH073-OX lines. Yeast two-hybrid and localization assays showed that the OsbHLH073 protein is a nuclear localized-transcriptional activator. We report that OsbHLH073 participates in regulating plant height, internode elongation, and panicle exsertion by regulating GA biosynthesis associated with the OsKO1 and OsKO2 genes.

PHYTOCHROME-INTERACTING FACTORS Interact with the ABA Receptors PYL8 and PYL9 to Orchestrate ABA Signaling in Darkness

PHYTOCHROME-INTERACTING FACTORS (PIFs) are a group of basic helix-loop-helix transcription factors that can physically interact with photoreceptors, including phytochromes and cryptochromes. It was previously demonstrated that PIFs accumulated in darkness and repressed seedling photomorphogenesis, and that PIFs linked different photosensory and hormonal pathways to control plant growth and development. In this study, we show that PIFs positively regulate the ABA signaling pathway during the seedling stage specifically in darkness. We found that PIFs positively regulate ABI5 transcript and protein levels in darkness in response to exogenous ABA treatment by binding directly to the G-box motifs in the ABI5 promoter. Consistently, PIFs and the G-box motifs in the ABI5 promoter determine ABI5 expression in darkness, and overexpression of ABI5 could rescue the ABA-insensitive phenotypes of pifq mutants in the dark. Moreover, we discovered that PIFs can physically interact with the ABA receptors PYL8 and PYL9, and that this interaction is not regulated by ABA. Further analyses showed that PYL8 and PYL9 promote PIF4 protein accumulation in the dark and enhance PIF4 binding to the ABI5 promoter, but negatively regulate PIF4-mediated ABI5 activation. Taken together, our data demonstrate that PIFs interact with ABA receptors to orchestrate ABA signaling in darkness by controlling ABI5 expression, providing new insights into the pivotal roles of PIFs as signal integrators in regulating plant growth and development.

Interplay between REVEILLE1 and RGA-LIKE2 regulates seed dormancy and germination in Arabidopsis

Environmental light signal and GAs synergistically regulate seed dormancy and germination. The phytochrome B (phyB) photoreceptor regulates expression of the REVEILLE1 (RVE1) transcription factor, which directly inhibits GIBBERELLIN 3-OXIDASE2 transcription, suppressing GA biosynthesis. However, whether phyB-RVE1 coordinates with GA signaling in controlling seed dormancy and germination remains unknown. Here, we demonstrate that RVE1 regulation of seed dormancy and germination requires a DELLA repressor, REPRESSOR OF GA-LIKE2 (RGL2), in Arabidopsis thaliana. RVE1 interacts with both RGL2 and its E3 ubiquitin ligase SLEEPY1 (SLY1) and promotes RGL2 stability by restraining the RGL2-SLY1 interaction. Furthermore, RVE1 and RGL2 synergistically regulate global transcriptome changes; RGL2 enhances the DNA-binding capacity and transcriptional activity of RVE1 in regulating downstream gene expression. Moreover, RGL2 expression is repressed by phyB. Our study reveals a novel regulatory mechanism in which the RVE1-RGL2 module coordinately controls seed dormancy and germination by integrating light perception, GA metabolism and GA signaling pathways.

PHYTOCHROME INTERACTING FACTOR8 Inhibits Phytochrome A-Mediated Far-Red Light Responses in Arabidopsis

PHYTOCHROME INTERACTING FACTORs (PIFs) are a group of basic helix-loop-helix (bHLH) transcription factors that repress plant light responses. PIF8 is one of the less-characterized Arabidopsis (Arabidopsis thaliana) PIFs, whose putative orthologs are conserved in other plant species. PIF8 possesses a bHLH motif and an active phytochrome B motif but not an active phytochrome A motif. Consistent with this motif composition, PIF8 binds to G-box elements and interacts with the Pfr form of phyB but only very weakly, if at all, with that of phyA. PIF8 differs, however, from other PIFs in its protein accumulation pattern and functional roles in different light conditions. First, PIF8 inhibits phyA-induced seed germination, suppression of hypocotyl elongation, and randomization of hypocotyl growth orientation in far-red light, but it does not inhibit phyB-induced red light responses. Second, PIF8 protein accumulates more in far-red light than in darkness or red light. This is distinct from the pattern observed with PIF3, which accumulates more in darkness. This PIF8 accumulation pattern requires degradation of PIF8 by CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1) in darkness, inhibition of COP1 by phyA in far-red light, and promotion of PIF8 degradation by phyB in red light. Together, our results indicate that PIF8 is a genuine PIF that represses phyA-mediated light responses.

ARABIDOPSIS NITRATE REGULATED 1 acts as a negative modulator of seed germination by activating ABI3 expression

Seed germination is a crucial transition point in plant life and is tightly regulated by environmental conditions through the coordination of two phytohormones, gibberellin and abscisic acid (ABA). To avoid unfavorable conditions, plants have evolved safeguard mechanisms for seed germination. The present contribution reports a novel function of the Arabidopsis MCM1/AGAMOUS/DEFICIENS/SRF(MADS)-box transcription factor ARABIDOPSIS NITRATE REGULATED 1 (ANR1) in seed germination. ANR1 knockout mutant is insensitive to ABA, salt and osmotic stress during the seed germination and early seedling development stages, whereas ANR1-overexpressing lines are hypersensitive. ANR1 is responsive to ABA and abiotic stresses and upregulates the expression of ABA Intolerant (ABI)3 to suppress seed germination. ANR1 and ABI3 have similar expression pattern during seed germination. Genetically, ABI3 acts downstream of ANR1. Chromatin immunoprecipitation and yeast-one-hybrid assays showed that ANR1 could bind to the ABI3 promoter to regulate its expression. In addition, ANR1 acts synergistically with AGL21 to suppress seed germination in response to ABA as evidenced by anr1 agl21 double mutant. Taken together, the results herein demonstrate that the ANR1 plays an important role in regulating seed germination and early postgermination growth. ANR1 and AGL21 together constitutes a safeguard mechanism for seed germination to avoid unfavorable conditions.

Integration of Abscisic Acid Signaling with Other Signaling Pathways in Plant Stress Responses and Development

Plants are immobile and, to overcome harsh environmental conditions such as drought, salt, and cold, they have evolved complex signaling pathways. Abscisic acid (ABA), an isoprenoid phytohormone, is a critical signaling mediator that regulates diverse biological processes in various organisms. Significant progress has been made in the determination and characterization of key ABA-mediated molecular factors involved in different stress responses, including stomatal closure and developmental processes, such as seed germination and bud dormancy. Since ABA signaling is a complex signaling network that integrates with other signaling pathways, the dissection of its intricate regulatory network is necessary to understand the function of essential regulatory genes involved in ABA signaling. In the present review, we focus on two aspects of ABA signaling. First, we examine the perception of the stress signal (abiotic and biotic) and the response network of ABA signaling components that transduce the signal to the downstream pathway to respond to stress tolerance, regulation of stomata, and ABA signaling component ubiquitination. Second, ABA signaling in plant development processes, such as lateral root growth regulation, seed germination, and flowering time regulation is investigated. Examining such diverse signal integration dynamics could enhance our understanding of the underlying genetic, biochemical, and molecular mechanisms of ABA signaling networks in plants.

An Integrative Approach to Analyze Seed Germination in Brassica napus

Seed germination is a complex trait determined by the interaction of hormonal, metabolic, genetic, and environmental components. Variability of this trait in crops has a big impact on seedling establishment and yield in the field. Classical studies of this trait in crops have focused mainly on the analyses of one level of regulation in the cascade of events leading to seed germination. We have carried out an integrative and extensive approach to deepen our understanding of seed germination in Brassica napus by generating transcriptomic, metabolic, and hormonal data at different stages upon seed imbibition. Deep phenotyping of different seed germination-associated traits in six winter-type B. napus accessions has revealed that seed germination kinetics, in particular seed germination speed, are major contributors to the variability of this trait. Metabolic profiling of these accessions has allowed us to describe a common pattern of metabolic change and to identify the levels of malate and aspartate metabolites as putative metabolic markers to estimate germination performance. Additionally, analysis of seed content of different hormones suggests that hormonal balance between ABA, GA, and IAA at crucial time points during this process might underlie seed germination differences in these accessions. In this study, we have also defined the major transcriptome changes accompanying the germination process in B. napus. Furthermore, we have observed that earlier activation of key germination regulatory genes seems to generate the differences in germination speed observed between accessions in B. napus. Finally, we have found that protein-protein interactions between some of these key regulator are conserved in B. napus, suggesting a shared regulatory network with other plant species. Altogether, our results provide a comprehensive and detailed picture of seed germination dynamics in oilseed rape. This new framework will be extremely valuable not only to evaluate germination performance of B. napus accessions but also to identify key targets for crop improvement in this important process.

DELAY OF GERMINATION 1-LIKE 4 acts as an inducer of seed reserve accumulation

More than 70% of global food supply depends on seeds. The major seed reserves, such as proteins, lipids, and polysaccharides, are produced during seed maturation. Here, we report that DELAY OF GERMINATION 1-LIKE 4 (DOGL4) is a major inducer of reserve accumulation during seed maturation. The DOGL family proteins are plant-specific proteins of largely unknown biochemical function. DOGL4 shares only limited homology in amino acid sequence with DOG1, a major regulator of seed dormancy. DOGL4 was identified as one of the outstanding abscisic acid (ABA)-induced genes in our RNA sequencing analysis, whereas DOG1 was not induced by ABA. Induction of DOGL4 caused the expression of 70 seed maturation-specific genes, even in germinating seeds, including the major seed reserves ALBUMIN, CRUCIFERIN and OLEOSIN. Although DOG1 affects the expression of many seed maturation genes, the major seed reserve genes induced by DOGL4 are not altered by the dog1 mutation. Furthermore, the reduced dormancy and longevity phenotypes observed in the dog1 seeds were not observed in the dogl4 mutants, suggesting that these two genes have limited functional overlap. Taken together, these results suggest that DOGL4 is a central factor mediating reserve accumulation in seeds, and that the two DOG1 family proteins have diverged over the course of evolution into independent regulators of seed maturation, but retain some overlapping function.

Transcriptional Regulation of Carotenoid Biosynthesis in Plants: So Many Regulators, So Little Consensus

In plants, the carotenoid biosynthesis pathway (CBP) is essential for the production of photosynthetic and protective pigments, plant hormones, and visual/olfactory attractants for animal pollinators and seed dispersers. The regulation of carotenoid biosynthesis at the transcriptional level is vitally important for all of these functions and has been the subject of intensive research. Many putative transcriptional regulators, both direct and indirect, have been identified through conventional mutant analysis, transcriptome profiling, yeast one-hybrid screening, and candidate gene approaches. Despite this progress, our understanding of the transcriptional regulation of carotenoid biosynthesis remains fragmented and incomplete. Frequently, a stimulus or regulator is known, but the mechanism by which it affects transcription has not been elucidated. In other cases, mechanisms have been proposed (such as direct binding of a CBP gene promoter by a transcription factor), but function was tested only in vitro or in heterologous systems, making it unclear whether these proteins actually play a role in carotenoid regulation in their endogenous environments. Even in cases where the mechanism is relatively well understood, regulators are often studied in isolation, either in a single plant species or outside the context of other known regulators. This presents a conundrum: why so many candidate regulators but so little consensus? Here we summarize current knowledge on transcriptional regulation of the CBP, lay out the challenges contributing to this conundrum, identify remaining knowledge gaps, and suggest future research directions to address these challenges and knowledge gaps.

The basic helix-loop-helix transcription factor, OsPIL15, regulates grain size via directly targeting a purine permease gene OsPUP7 in rice

As members of the basic helix-loop-helix transcription factor families, phytochrome-interacting factors regulate an array of developmental responses ranging from seed germination to plant growth. However, little is known about their roles in modulating grain development. Here, we firstly analyzed the expression pattern of rice OsPIL genes in grains and found that OsPIL15 may play an important role in grain development. We then generated knockout (KO) OsPIL15 lines in rice using CRISPR/Cas9 technology, the silencing expression of OsPIL15 led to increased numbers of cells, which thus enhanced grain size and weight. Moreover, overexpression and suppression of OsPIL15 in the rice endosperm resulted in brown rice showing grain sizes and weights that were decreased and increased respectively. Further studies indicated that OsPIL15 binds to N1-box (CACGCG) motifs of the purine permease gene OsPUP7 promoter. Measurement of isopentenyl adenosine, a bioactive form of cytokinin (CTK), revealed increased contents in the OsPIL15-KO spikelets compared with the wild-type. Overall, our results demonstrate a possible pathway whereby OsPIL15 directly targets OsPUP7, affecting CTK transport and thereby influencing cell division and subsequent grain size. These findings provide a valuable insight into the molecular functions of OsPIL15 in rice grains, highlighting a useful genetic improvement leading to increased rice yield.

polyamine uptake transporter 2 (put2) and decaying seeds enhance phyA-mediated germination by overcoming PIF1 repression of germination

Red light promotes germination after activating phytochrome phyB, which destabilizes the germination repressor PIF1. Early upon seed imbibition, canopy light, unfavorable for photosynthesis, represses germination by stabilizing PIF1 after inactivating phyB. Paradoxically, later upon imbibition, canopy light stimulates germination after activating phytochrome phyA. phyA-mediated germination is poorly understood and, intriguingly, is inefficient, compared to phyB-mediated germination, raising the question of its physiological significance. A genetic screen identified polyamine uptake transporter 2 (put2) mutants that overaccumulate polyamines, a class of antioxidant polycations implicated in numerous cellular functions, which we found promote phyA-mediated germination. In WT seeds, our data suggest that canopy light represses polyamines accumulation through PIF1 while red light promotes polyamines accumulation. We show that canopy light also downregulates PIF1 levels, through phyA; however, PIF1 reaccumulates rapidly, which limits phyA-mediated germination. High polyamines levels in decaying seeds bypass PIF1 repression of germination and stimulate phyA-mediated germination, suggesting an adaptive mechanism promoting survival when viability is compromised.

The Transcription Factor INDUCER OF CBF EXPRESSION1 Interacts with ABSCISIC ACID INSENSITIVE5 and DELLA Proteins to Fine-Tune Abscisic Acid Signaling during Seed Germination in Arabidopsis

ABSCISIC ACID INSENSITIVE5 (ABI5) is a crucial regulator of abscisic acid (ABA) signaling pathways involved in repressing seed germination and postgerminative growth in Arabidopsis (Arabidopsis thaliana). ABI5 is precisely modulated at the posttranslational level; however, the transcriptional regulatory mechanisms underlying ABI5 and its interacting transcription factors remain largely unknown. Here, we found that INDUCER OF CBF EXPRESSION1 (ICE1) physically associates with ABI5. ICE1 negatively regulates ABA responses during seed germination and directly suppresses ABA-responsive LATE EMBRYOGENESIS ABUNDANT6 (EM6) and EM1 expression. Genetic analysis demonstrated that the ABA-hypersensitive phenotype of the ice1 mutant requires ABI5. ICE1 interferes with the transcriptional activity of ABI5 to mediate downstream regulons. Importantly, ICE1 also interacts with DELLA proteins, which stimulate ABI5 during ABA signaling. Disruption of ICE1 partially restored the ABA-hyposensitive phenotype of the della mutant, gai-t6 rga-t2 rgl1-1 rgl2-1, indicating that ICE1 functions antagonistically with DELLA in ABA signaling. Consistently, DELLA proteins repress ICE1's transcriptional function and the antagonistic effect of ICE1 on ABI5. Collectively, our study demonstrates that ICE1 antagonizes ABI5 and DELLA activity to maintain the appropriate level of ABA signaling during seed germination, providing a mechanistic understanding of how ABA signaling is fine-tuned by a transcriptional complex involving ABI5 and its interacting partners.

Phytochrome-interacting factor-like protein OsPIL15 integrates light and gravitropism to regulate tiller angle in rice

Rice phytochrome-interacting factor-like protein OsPIL15 regulates tiller angle through light and gravity signals in rice. Tiller angle of cereal crops is a key agronomic trait that contributes to grain production. An understanding of how tiller angle is controlled is helpful for achieving ideal plant architecture to improve grain yield. Phytochrome-interacting factors (PIFs) are known to regulate seed germination, seedling skotomorphogenesis, shade avoidance, and flowering in Arabidopsis thaliana. Here, we report that OsPIL15 is, indeed, a rice PIF that negatively regulates tiller angle. Dominant-negative OsPIL15 plants displayed a larger tiller angle, which was associated with reduced shoot gravitropism. Phytochrome B (phyB) is the main photoreceptor perceiving the low red:far-red ratio of shade light. Compared with wild-type rice plants, loss-of-function phyB plants and OsPIL15-overexpressing plants showed smaller tiller angles and enhanced shoot gravitropism. In addition, more OsPIL15 protein accumulated in phyB plants than in wild-type plants. Light regulates the level of the OsPIL15 protein negatively, depending on phyB partially. We propose that OsPIL15 integrates light and gravity signals to regulate tiller angle in rice.

Aethionema arabicum: a novel model plant to study the light control of seed germination

The timing of seed germination is crucial for seed plants and is coordinated by internal and external cues, reflecting adaptations to different habitats. Physiological and molecular studies with lettuce and Arabidopsis thaliana have documented a strict requirement for light to initiate germination and identified many receptors, signaling cascades, and hormonal control elements. In contrast, seed germination in several other plants is inhibited by light, but the molecular basis of this alternative response is unknown. We describe Aethionema arabicum (Brassicaceae) as a suitable model plant to investigate the mechanism of germination inhibition by light, as this species has accessions with natural variation between light-sensitive and light-neutral responses. Inhibition of germination occurs in red, blue, or far-red light and increases with light intensity and duration. Gibberellins and abscisic acid are involved in the control of germination, as in Arabidopsis, but transcriptome comparisons of light- and dark-exposed A. arabicum seeds revealed that, upon light exposure, the expression of genes for key regulators undergo converse changes, resulting in antipodal hormone regulation. These findings illustrate that similar modular components of a pathway in light-inhibited, light-neutral, and light-requiring germination among the Brassicaceae have been assembled in the course of evolution to produce divergent pathways, likely as adaptive traits.

Transcriptional Regulatory Network of GA Floral Induction Pathway in LA Hybrid Lily

BACKGROUND

The LA hybrid lily 'Aladdin' has both excellent traits of Longiflorum hybrids and Asiatic hybrids-such as big and vivid flower, strong stem, high self-propagation coefficient, and shorter low temperature time required to release bulb dormancy in contrast to Oriental hybrids. A genome-wide transcriptional analysis using transcriptome RNA-Seq was performed in order to explore whether there is a gibberellin floral induction pathway in the LA hybrid lily. Subsequently, gene co-expression network analysis was used to analyze the possible interactions of key candidate genes screened from transcriptome data. At the same time, a series of physiological, biochemical, and cultivation tests were carried out.

RESULTS

The content of five endogenous hormones changed sharply in the shoot apex during the treatment of 200 mg/L exogenous gibberellin and the ratio of ABA/GA3 dropped and stayed at a lower level after 4 hours' treatment from the higher levels initially, reaching a dynamic balance. In addition, the metabolism of carbohydrates in the bulbs increase during exogenous gibberellin treatment. A total of 124,041 unigenes were obtained by RNA-seq. With the transcriptome analysis, 48,927 unigenes and 48,725 unigenes respectively aligned to the NR database and the Uniprot database. 114,138 unigenes, 25,369 unigenes, and 19,704 unigenes respectively aligned to the COG, GO, and KEGG databases. 2148 differentially expression genes (DEGs) were selected with the indicators RPKM ≥ 0, FDR ≤ 0.05 and |log2(ratio)| ≥ 2. The number of the upregulated unigenes was significantly more than the number of the downregulated unigenes. Some MADS-box genes related to flowering transformation-such as AGL20, SOC1, and CO-were found to be upregulated. A large number of gibberellin biosynthesis related genes such as GA2ox, GA3ox, GA20ox, Cytochrome P450, CYP81, and gibberellin signal transduction genes such as DELLA, GASA, and GID1 were significantly differentially expressed. The plant hormones related genes such as NCED3 and sugar metabolism related genes such as α-amylase, sucrose synthase hexokinase, and so on were also found expressing differentially. In addition, stress resistance related genes such as LEA1, LEA2, LEA4, serine/threonine protein kinase, LRR receptor-like serine/threonine protein kinase, P34 kinase, histidine kinase 3 and epigenetic related genes in DNA methylation, histone methylation, acetylation, ubiquitination of ribose were also found. Particularly, a large number of transcription factors responsive to the exogenous gibberellin signal including WRKY40, WRKY33, WRKY27, WRKY21, WRKY7, MYB, AP2/EREBP, bHLH, NAC1, NAC2, and NAC11 were found to be specially expressing. 30 gene sequences were selected from a large number of differentially expressed candidate genes for qRT-PCR expression verification (0, 2, 4, 8, and 16 h) and compared with the transcriptome expression levels.

CONCLUSIONS

200mg/L exogenous GA3 can successfully break the bulb's dormancy of the LA hybrid lily and significantly accelerated the flowering process, indicating that gibberellin floral induction pathway is present in the LA lily 'Aladdin'. With the GCNs analysis, two second messenger G protein-coupled receptor related genes that respond to gibberellin signals in the cell were discovered. The downstream transport proteins such as AMT, calcium transport ATPase, and plasma membrane ATPase were also discovered participating in GA signal transduction. Transcription factors including WRKY7, NAC2, NAC11, and CBF specially regulated phosphorylation and glycosylation during the ubiquitination degradation process of DELLA proteins. These transcription factors also activated in abscisic acid metabolism. A large number of transcription factors such as WRKY21, WRKY22, NAC1, AP2, EREB1, P450, and CYP81 that both regulate gibberellin signaling and low-temperature signals have also been found. Finally, the molecular mechanism of GA floral induction pathway in the LA hybrid lily 'Aladdin' was constructed.

Response of the Circadian Clock and Diel Starch Turnover to One Day of Low Light or Low CO2

Diel starch turnover responds rapidly to changes in the light regime. We investigated if these responses require changes in the temporal dynamics of the circadian clock. Arabidopsis (Arabidopsis thaliana) was grown in a 12-h photoperiod for 19 d, shifted to three different reduced light levels or to low CO₂ for one light period, and returned to growth conditions. The treatments produced widespread changes in clock transcript abundance. However, almost all of the changes were restricted to extreme treatments that led to carbon starvation and were small compared to the magnitude of the circadian oscillation. Changes included repression of EARLY FLOWERNG 4, slower decay of dusk components, and a slight phase delay at the next dawn, possibly due to abrogated Evening Complex function and sustained expression of PHYTOCHROME INTERACTING FACTORs and REVEILLEs during the night. Mobilization of starch in the night occurred in a linear manner and was paced to dawn, both in moderate treatments that did not alter clock transcripts and in extreme treatments that led to severe carbon starvation. We conclude that pacing of starch mobilization to dawn does not require retrograde carbon signaling to the transcriptional clock. On the following day, growth decreased, sugars rose, and starch accumulation was stimulated in low-light-treated plants compared to controls. This adaptive response was marked after moderate treatments and occurred independently of changes in the transcriptional clock. It is probably a time-delayed response to low-C signaling in the preceding 24-h cycle, possibly including changes in PHYTOCHROME INTERACTING FACTOR and REVEILLE expression.

Comparative transcriptomic analysis reveals genes regulating the germination of morphophysiologically dormant Paris polyphylla seeds during a warm stratification

We previously analyzed the expression of genes associated with Paris polyphylla var. yunnanensis seed maturation and dormancy release; however, we were unable to clarify the relationship between gene expression levels and these processes. To reveal the molecular mechanisms underlying P. polyphylla var. yunnanensis seed dormancy release during a warm stratification, the transcriptomes of dormant and germinating P. polyphylla var. yunnanensis seeds were separately analyzed by RNA sequencing and were also compared with the transcriptomes of stem-leaf and root tissues harvested during the seed maturation stage. The RNA sequencing of five tissues generated 234,331 unigenes, of which 10,137 (4.33%) were differentially expressed among the analyzed tissues. The 6,619 unigenes whose expression varied among mature dormant, sprouted, and germinated seeds included 95 metabolic and 62 signaling genes related to abscisic acid, gibberellin, auxin, brassinosteroid, cytokinin, ethylene, jasmonic acid and salicylic acid. Additionally, 243 differentially expressed genes were annotated as known seed dormancy/germination-related genes. Among these genes, 109 were regulated by hormones or involved in hormone signal transduction. Finally, 310 transcription factor unigenes, including 71 homologs of known seed dormancy/ germination-related genes, were observed to be differentially expressed during a warm stratification. These results confirm that multiple hormones and transcription factors influence P. polyphylla var. yunnanensis seed dormancy release and germination during a warm stratification. This study identified candidate genes (e.g., ABI5) that should be cloned and functionally characterized regarding their effects on the release of P. polyphylla var. yunnanensis seed morphophysiological dormancy.

Alternative Splicing Regulation During Light-Induced Germination of Arabidopsis thaliana Seeds

Seed dormancy and germination are relevant processes for a successful seedling establishment in the field. Light is one of the most important environmental factors involved in the relief of dormancy to promote seed germination. In Arabidopsis thaliana seeds, phytochrome photoreceptors tightly regulate gene expression at different levels. The contribution of alternative splicing (AS) regulation in the photocontrol of seed germination is still unknown. The aim of this work is to study gene expression modulated by light during germination of A. thaliana seeds, with focus on AS changes. Hence, we evaluated transcriptome-wide changes in stratified seeds irradiated with a pulse of red (Rp) or far-red (FRp) by RNA sequencing (RNA-seq). Our results show that the Rp changes the expression of ∼20% of the transcriptome and modifies the AS pattern of 226 genes associated with mRNA processing, RNA splicing, and mRNA metabolic processes. We further confirmed these effects for some of the affected AS events. Interestingly, the reverse transcriptase-polymerase chain reaction (RT-PCR) analyses show that the Rp modulates the AS of splicing-related factors (At-SR30, At-RS31a, At-RS31, and At-U2AF65A), a light-signaling component (At-PIF6), and a dormancy-related gene (At-DRM1). Furthermore, while the phytochrome B (phyB) is responsible for the AS pattern changes of At-U2AF65A and At-PIF6, the regulation of the other AS events is independent of this photoreceptor. We conclude that (i) Rp triggers AS changes in some splicing factors, light-signaling components, and dormancy/germination regulators; (ii) phyB modulates only some of these AS events; and (iii) AS events are regulated by R and FR light, but this regulation is not directly associated with the intensity of germination response. These data will help in boosting research in the splicing field and our understanding about the role of this mechanism during the photocontrol of seed germination.

Papaya CpbHLH1/2 regulate carotenoid biosynthesis-related genes during papaya fruit ripening

The ripening of papaya is a physiological and metabolic process associated with accumulation of carotenoids, alternation of flesh color and flavor, which depending on genotype and external factors such as light and hormone. Transcription factors regulating carotenoid biosynthesis have not been analyzed during papaya fruit ripening. RNA-Seq experiments were implemented using different ripening stages of papaya fruit from two papaya varieties. Cis-elements in lycopene β-cyclase genes (CpCYC-B and CpLCY-B) were identified, and followed by genome-wide analysis to identify transcription factors binding to these cis-elements, resulting in the identification of CpbHLH1 and CpbHLH2, two bHLH genes. The expressions of CpbHLH1/2 were changed during fruit development, coupled with transcript increase of carotenoid biosynthesis-related genes including CpCYC-B, CpLCY-B, CpPDS2, CpZDS, CpLCY-E, and CpCHY-B. Yeast one-hybrid (Y1H) and transient expression assay revealed that CpbHLH1/2 could bind to the promoters of CpCYC-B and CpLCY-B, and regulate their transcriptions. In response to strong light, the results of elevated expression of carotenoid biosynthesis-related genes and the changed expression of CpbHLH1/2 indicated that CpbHLH1/2 were involved in light-mediated mechanisms of regulating critical genes in the carotenoid biosynthesis pathway. Collectively, our findings demonstrated several TF family members participating in the regulation of carotenoid genes and proved that CpbHLH1 and CpbHLH2 individually regulated the transcription of lycopene β-cyclase genes (CpCYC-B and CpLCY-B). This study yielded novel findings on regulatory mechanism of carotenoid biosynthesis during papaya fruit ripening.

The B-box bridge between light and hormones in plants

Plant development is meticulously modulated by interactions between the surrounding environment and the endogenous phytohormones. Light, as an external signal coordinates with the extensive networks of hormones inside the plant to execute its effects on growth and development. Several proteins in plants have been identified for their crucial roles in mediating light regulated development. Among these are the B-box (BBX) family of transcription factors characterized by the presence of zinc-finger B-box domain in their N-terminal region. In Arabidopsis there are 32 BBX proteins that are divided into five structural groups on the basis of the domains present. Several BBX proteins play important roles in seedling photomorphogenesis, neighbourhood detection and photoperiodic regulation of flowering. There is increasing evidence that besides light signaling BBX proteins also play integral roles in several hormone signaling pathways in plants. Here we attempt to comprehensively integrate the roles of multiple BBX proteins in various light and hormone signaling pathways. We further discuss the role of the BBX proteins in mediating crosstalk between the two signaling pathways to harmonize plant growth and development. Finally, we try to analyse the conservation of BBX genes across species and discuss the role of BBX proteins in regulating economically important traits in crop plants.

Overexpression of OsPIL1 enhanced biomass yield and saccharification efficiency in switchgrass

Switchgrass (Panicum virgatum L.) is a herbaceous cellulosic biofuel plant with broad adaptability. However, the intrinsic recalcitrance of biomass and limited land for switchgrass planting hinder its utilization as feedstock for biofuel ethanol production. The OsPIL1 (PHYTOCHROME INTERACTING FACTOR 3-LIKE 1) gene encodes a basic helix-loop-helix transcription factor. Its expression is induced by light, which facilitated the expression of cell wall-related genes, promoted cell elongation and resulted in longer internode in rice. Here, we introduced the OsPIL1 gene into switchgrass by Agrobacterium-mediated transformation with the aim of improving biomass yield of transgenic switchgrass plants. The transgenic plants were verified by PCR, Southern-blotting, RT-PCR and qRT-PCR tests, respectively. The transgenic plants overexpression of OsPIL1 showed increased plant height and biomass yield. Microscopy analysis showed that the length of epidermal cells of transgenic plants was longer than that of wild type. OsPIL1 overexpressed transgenic switchgrass plants also released more soluble sugar after enzymatic hydrolysis, indicating improved saccharification efficiency. The results suggest OsPIL1 can be used as a useful molecular tool in improving plant biomass and saccharification efficiency with the purpose of plant fiber biofuel ethanol production.

Shedding light on the methylerythritol phosphate (MEP)-pathway: long hypocotyl 5 (HY5)/phytochrome-interacting factors (PIFs) transcription factors modulating key limiting steps

The plastidial methylerythritol phosphate (MEP) pathway is an essential route for plants as the source of precursors for all plastidial isoprenoids, many of which are of medical and biotechnological importance. The MEP pathway is highly sensitive to environmental cues as many of these compounds are linked to photosynthesis and growth and light is one of the main regulatory factors. However, the mechanisms coordinating the MEP pathway with light cues are not fully understood. Here we demonstrate that by a differential direct transcriptional modulation, via the key-master integrators of light signal transduction HY5 and PIFs which target the genes that encode the rate-controlling DXS1, DXR and HDR enzymes, light imposes a direct, rapid and potentially multi-faceted response that leads to unique protein dynamics of this pathway, resulting in a significant difference in the protein levels. For DXS1, PIF1/HY5 act as a direct activation/suppression module. In contrast, DXR accumulation in response to light results from HY5 induction with minor contribution of de-repression by PIF1. Finally, HDR transcription increases in the light exclusively by suppression of the PIFs repression. This is an example of how light signaling components can differentially multi-target the initial steps of a pathway whose products branch downstream to all chloroplastic isoprenoids. These findings demonstrate the diversity and flexibility of light signaling components that optimize key biochemical pathways essential for plant growth.

PHYTOCHROME INTERACTING FACTOR1 interactions leading to the completion or prolongation of seed germination

In Arabidopsis thaliana, the basic Helix Loop Helix transcription factor, PHYTOCHROME INTERACTING FACTOR1 (PIF1) is known to orchestrate the seed transcriptome such that, ultimately, proteins repressing the completion of germination are produced in darkness. While PIF1-mediated control of abscisic acid (ABA) and gibberellic acid (GA) anabolism/catabolism is indirect, PIF1 action favors ABA while discriminating against GA, firmly establishing ABA's repressive influence on the completion of germination. The result is tissue that is more sensitive to and producing more ABA; and is less responsive to and deficient in GA. Illumination of the appropriate wavelength activates phytochrome which enters the nucleus, and binds to PIF1, initiating PIF1's phosphorylation by diverse kinases, subsequent polyubiquitination, and hydrolysis. One mechanism by which phosphorylated PIF1 is eliminated from the cells of the seed upon illumination involves an F-BOX protein, COLD TEMPERATURE GERMINATING10 (CTG10). Discovered in an unbiased screen of activation tagged lines hastening the completion of seed germination at 10°C, one indirect consequence of CTG10 action in reducing PIF1 titer, should be to enhance the transcription of genes whose products work to increase bioactive GA titer, shifting the intracellular milieu from one that is repressive to, toward one conducive to, the completion of seed germination. We have tested this hypothesis using a variety of Arabidopsis lines altered in CTG10 amounts. Here we demonstrate using bimolecular fluorescence complementation that PIF1 interacts with CTG10 and show that, in light exposed seeds, PIF1 is more persistent in ctg10 relative to WT seeds while it is less stable in seeds over-expressing CTG10. These results are congruent with the relative transcript abundance from three genes whose products are involved in bioactive GA accumulation. We put forth a model of how PIF1 interactions in imbibed seeds change during germination and how a permissive light signal influences these changes, leading to the completion of germination of these positively photoblastic propagules.

The tomato IQD gene SUN24 regulates seed germination through ABA signaling pathway

Gene expression and functional analysis of the tomato IQD gene SUN24 revealed that it regulates seed germination through ABA signaling pathway. Ca²⁺ signaling plays crucial roles in diverse biological processes including ABA-mediated seed germination. The plant-specific IQ67-Domain (IQD) proteins are hypothesized to regulate Ca²⁺ signaling and plant development through interactions with calmodulins (CaMs). Despite a few IQD genes have been identified to regulate herbivore resistance and plant growth and development, the molecular functions of most members in this gene family are not known. In this study, we characterized the role of the tomato IQD gene SUN24 in seed germination. Using pSUN24::GUS reporter lines and by quantitative reverse transcription PCR analysis, we show that SUN24 is mainly expressed in the roots, flowers, young fruits, seeds, and other young developing tissues, and its expression is repressed by ABA treatments. Functional analysis shows that knockdown of SUN24 expression by RNA interference delays seed germination, whereas overexpression of this IQD gene promotes germination. Further gene expression analysis reveals that SUN24 negatively regulates expression of two key ABA signaling genes Solanum lycopersicum ABA-insensitive 3 (SlABI3) and SlABI5 in germinating seeds. Moreover, SUN24, targeting to microtubule and nuclear bodies, can interact with four tomato CaMs (SlCaM1, 2, 3, and 6) in yeast cells. Our results demonstrate that SUN24 regulates seed germination through ABA signaling pathway, expanding our understanding of the roles of the IQD protein family members in plant physiological processes.

Arabidopsis small ubiquitin-related modifier protease ASP1 positively regulates abscisic acid signaling during early seedling development

The small ubiquitin-related modifier (SUMO) modification plays an important role in the regulation of abscisic acid (ABA) signaling, but the function of the SUMO protease, in ABA signaling, remains largely unknown. Here, we show that the SUMO protease, ASP1 positively regulates ABA signaling. Mutations in ASP1 resulted in an ABA-insensitive phenotype, during early seedling development. Wild-type ASP1 successfully rescued, whereas an ASP1 mutant (C577S), defective in SUMO protease activity, failed to rescue, the ABA-insensitive phenotype of asp1-1. Expression of ABI5 and MYB30 target genes was attenuated in asp1-1 and our genetic analyses revealed that ASP1 may function upstream of ABI5 and MYB30. Interestingly, ASP1 accumulated upon ABA treatment, and ABA-induced accumulation of ABI5 (a positive regulator of ABA signaling) was abolished, whereas ABA-induced accumulation of MYB30 (a negative regulator of ABA signaling) was increased in asp1-1. These findings support the hypothesis that increased levels of ASP1, upon ABA treatment, tilt the balance between ABI5 and MYB30 towards ABI5-mediated ABA signaling.

Integrated Regulation of Apical Hook Development by Transcriptional Coupling of EIN3/EIL1 and PIFs in Arabidopsis

The apical hook protects the meristems of dicot seedlings as they protrude through the soil; multiple factors, including phytohormones and light, mediate apical hook development. HOOKLESS1 (HLS1) plays an indispensable role, as HLS1 mutations cause a hookless phenotype. The ETHYLENE INSENSITIVE3 (EIN3) and EIN3-LIKE1 (EIL1) transcription factors integrate multiple signals (ethylene, gibberellins, and jasmonate) and activate HLS1 expression to enhance hook development. Here, we found that Arabidopsis thaliana PHYTOCHROME INTERACTING FACTOR (PIF) transcription factors act in parallel with EIN3/EIL1 and promote hook curvature by activating HLS1 transcription at a distinct binding motif. EIN3/EIL1 and PIFs can promote hook formation in the absence of the other. Jasmonate represses PIF function to inhibit hook development. Like EIN3 and EIL1, MYC2 interacts with PIF4 and hampers its activity. Acting together, EIN3/EIL1 and PIFs alleviate the negative effects of jasmonate/light and facilitate the positive effects of ethylene/gibberellins. Mutating EIN3/EIL1 and PIFs causes a complete hookless phenotype, marginal HLS1 expression, and insensitivity to upstream signals. Transcriptome profiling revealed that EIN3/EIL1 and PIFs additively and distinctly regulate a wide array of processes, including apical hook development. Together, our findings identify an integrated framework underlying the regulation of apical hook development and show that EIN3/EIL1 and PIFs fine-tune adaptive growth in response to hormone and light signals.

The interplay between cytokinins and light during senescence in detached Arabidopsis leaves

Light and cytokinins are known to be the key players in the regulation of plant senescence. In detached leaves, the retarding effect of light on senescence is well described; however, it is not clear to what extent is this effect connected with changes in endogenous cytokinin levels. We have performed a detailed analysis of changes in endogenous content of 29 cytokinin forms in detached leaves of Arabidopsis thaliana (wild-type and 3 cytokinin receptor double mutants). Leaves were kept under different light conditions, and changes in cytokinin content were correlated with changes in chlorophyll content, efficiency of photosystem II photochemistry, and lipid peroxidation. In leaves kept in darkness, we have observed decreased content of the most abundant cytokinin free bases and ribosides, but the content of cis-zeatin increased, which indicates the role of this cytokinin in the maintenance of basal leaf viability. Our findings underscore the importance of light conditions on the content of specific cytokinins, especially N⁶ -(Δ² -isopentenyl)adenine. On the basis of our results, we present a scheme summarizing the contribution of the main active forms of cytokinins, cytokinin receptors, and light to senescence regulation. We conclude that light can compensate the disrupted cytokinin signalling in detached leaves.

HRB2 and BBX21 interaction modulates Arabidopsis ABI5 locus and stomatal aperture

Blue light triggers the opening of stomata in the morning to allow CO₂ uptake and water loss through transpiration. During the day, plants may experience periodic drought and accumulate abscisic acid (ABA). ABA antagonizes blue light signalling through phosphatidic acid and reduces stomatal aperture. This study reveals a molecular mechanism by which two light signalling proteins interact to repress ABA signalling in the control of stomatal aperture. A hypersensitive to red and blue 2 (hrb2) mutant has a defective ATP-dependent chromatin-remodelling factor, PKL, in the chromodomain/helicase/DNA binding family. HRB2 enhances the light-induced expression of a B-box transcription factor gene, BBX21. BBX21 binds a T/G box in the ABI5 promoter and recruits HRB2 to modulate the chromatin structure at the ABI5 locus. Mutation in either HRB2 or BBX21 led to reduced water loss and ABA hypersensitivity. This hypersensitivity to ABA was well explained by the enhanced expression of the ABA signalling gene ABI5 in both mutants. Indeed, stomatal aperture was significantly reduced by ABI5 overexpression in the absence or presence of ABA under monochromatic light conditions. Overall, we present a regulatory loop in which two light signalling proteins repress ABA signalling to sustain gas exchange when plants experience periodic drought.

MOTHER-OF-FT-AND-TFL1 represses seed germination under far-red light by modulating phytohormone responses in Arabidopsis thaliana

Seed germination in many plant species is triggered by sunlight, which is rich in the red (R) wavelength and repressed by under-the-canopy light rich in far red (FR). R:FR ratios are sensed by phytochromes to regulate levels of gibberellins (GAs) and abscisic acid (ABA), which induce and inhibit germination respectively. In this study we have discovered that, under FR light conditions, germination is repressed by MOTHER-OF-FT-AND-TFL1 (MFT) through the regulation of the ABA and GA signaling pathways. We also show that MFT gene expression is tightly regulated by light quality. Previous work has shown that under FR light conditions the transcription factor PHYOCHROME-INTERACTING-FACTOR1 (PIF1) accumulates and promotes expression of SOMNUS (SOM) that, in turn, leads to increased ABA and decreased GA levels. PIF1 also promotes expression of genes encoding ABA-INSENSITIVE5 (ABI5) and DELLA growth-repressor proteins, which act in the ABA and GA signaling pathways, respectively. Here we show that MFT gene expression is promoted by FR light through the PIF1/SOM/ABI5/DELLA pathway and is repressed by R light via the transcription factor SPATULA (SPT). Consistent with this, we also show that SPT gene expression is repressed under FR light in a PIF1-dependent manner. Furthermore, transcriptomic analyses presented in this study indicate that MFT exerts its function by promoting expression of known ABA-induced genes and repressing cell wall expansion-related genes.

Phytochrome and Phytohormones: Working in Tandem for Plant Growth and Development

Being sessile organisms, plants need to continually adapt and modulate their rate of growth and development in accordance with the changing environmental conditions, a phenomenon referred to as plasticity. Plasticity in plants is a highly complex process that involves a well-coordinated interaction between different signaling pathways, the spatiotemporal involvement of phytohormones and cues from the environment. Though research studies are being carried out over the years to understand how plants perceive the signals from changing environmental conditions and activate plasticity, such remain a mystery to be resolved. Among all environmental cues, the light seems to be the stand out factor influencing plant growth and development. During the course of evolution, plants have developed well-equipped signaling system that enables regulation of both quantitative and qualitative differences in the amount of perceived light. Light influences essential developmental switches in plants ranging from germination or transition to flowering, photomorphogenesis, as well as switches in response to shade avoidances and architectural changes occurring during phototropism. Abscisic acid (ABA) is controlling seed germination and is regulated by light. Furthermore, circadian clock adds another level of regulation to plant growth by integrating light signals with different hormonal pathways. MYB96 has been identified as a regulator of circadian gating of ABA-mediated responses in plants by binding to the TIMING OF CAB EXPRESSION 1(TOC1) promoter. This review will present a representative regulatory model, highlight the successes achieved in employing novel strategies to dissect the levels of interaction and provide perspective for future research on phytochrome-phytohormones relationships toward facilitating plant growth, development, and function under abiotic-biotic stresses.

Arabidopsis ANGUSTIFOLIA3 (AN3) is associated with the promoter of CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1) to regulate light-mediated stomatal development

Light signals are perceived by multiple photoreceptors that converge to suppress the RING E3 ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1) for the regulation of stomatal development. Thus, COP1 is a point of integration between light signaling and stomatal patterning. However, how light signaling is collected into COP1 for the production and spacing of stomata is still unknown. Here, we report that the loss-of-function mutant of ANGUSTIFOLIA3 (AN3) delays asymmetric cell division, which leads to decreased stomatal index. Furthermore, overexpression of AN3 accelerates asymmetric cell division, which results in clusters of stomata. In addition, the stomatal development through AN3 regulation is mediated by light signaling. Finally, we find that an3 is a light-signaling mutant, and that AN3 protein is light regulated. Self-activation by AN3 contributes to the control of AN3 expression. Thus, AN3 is a point of collection between light signaling and stomatal patterning. Target-gene analysis indicates that AN3 is associated with COP1 promoter for the regulation of light-controlling stomatal development. Together, these components for regulating stomatal development form an AN3-COP1-E3 ubiquitin ligase complex, allowing the integration of light signaling into the production and spacing of stomata.