GID2, an F-box subunit of the SCF E3 complex, specifically interacts with phosphorylated SLR1 protein and regulates the gibberellin-dependent degradation of SLR1 in rice

The Toxoplasma gondii F-Box Protein L2 Functions as a Repressor of Stage Specific Gene Expression

Toxoplasma gondii is a foodborne pathogen that can cause severe and life-threatening infections in fetuses and immunocompromised patients. Felids are its only definitive hosts, and a wide range of animals, including humans, serve as intermediate hosts. When the transmissible bradyzoite stage is orally ingested by felids, they transform into merozoites that expand asexually, ultimately generating millions of gametes for the parasite sexual cycle. However, bradyzoites in intermediate hosts differentiate exclusively to disease-causing tachyzoites, which rapidly disseminate throughout the host. Though tachyzoites are well-studied, the molecular mechanisms governing transitioning between developmental stages are poorly understood. Each parasite stage can be distinguished by a characteristic transcriptional signature, with one signature being repressed during the other stages. Switching between stages require substantial changes in the proteome, which is achieved in part by ubiquitination. F-box proteins mediate protein poly-ubiquitination by recruiting substrates to SKP1, Cullin-1, F-Box protein E3 ubiquitin ligase (SCF-E3) complexes. We have identified an F-box protein named Toxoplasma gondii F-Box Protein L2 (TgFBXL2), which localizes to distinct perinucleolar sites. TgFBXL2 is stably engaged in an SCF-E3 complex that is surprisingly also associated with a COP9 signalosome complex that negatively regulates SCF-E3 function. At the cellular level, TgFBXL2-depleted parasites are severely defective in centrosome replication and daughter cell development. Most remarkable, RNAseq data show that TgFBXL2 conditional depletion induces the expression of stage-specific genes including a large cohort of genes necessary for sexual commitment. Together, these data suggest that TgFBXL2 is a latent guardian of stage specific gene expression in Toxoplasma and poised to remove conflicting proteins in response to an unknown trigger of development.

Regulatory mechanism of GA3 application on grape (Vitis vinifera L.) berry size

Gibberellin A3 (GA3) is often used as a principal growth regulator to increase plant size. Here, we applied Tween-20 (2%)-formulated GA3 (T1:40 mg/L; T2:70 mg/L) by dipping the clusters at the initial expansion phase of 'Red Globe' grape (Vitis vinifera L.) in 2018 and 2019. Tween-20 (2%) was used as a control. The results showed that GA3 significantly increased fruit cell length, cell size, diameter, and volume. The hormone levels of auxin (IAA) and zeatin (ZT) were significantly increased at 2 h (0 d) -1 d after application (DAA0-1) and remained significantly higher at DAA1 until maturity. Conversely, ABA exhibited an opposite trend. The mRNA and non-coding sequencing results yielded 436 differentially expressed mRNA (DE_mRNAs), 79 DE_lncRNAs and 17 DE_miRNAs. These genes are linked to hormone pathways like cysteine and methionine metabolism (ko00270), glutathione metabolism (ko00480) and plant hormone signal transduction (ko04075). GA3 application reduced expression of insensitive dwarf 2 (GID2, VIT_07s0129g01000), small auxin-upregulated RNA (SAUR, VIT_08s0007g03120) and 1-aminocyclopropane-1-carboxylate synthase (ACS, VIT_18s0001g08520), but increased SAUR (VIT_04s0023g00560) expression. These four genes were predicted to be negatively regulated by vvi-miR156, vvi-miR172, vvi-miR396, and vvi-miR159, corresponding to specific lncRNAs. Therefore, miRNAs could affect grape size by regulating key genes GID2, ACS and SAUR. The R2R3 MYB family member VvRAX2 (VIT_08s0007g05030) was upregulated in response to GA3 application. Overexpression of VvRAX2 in tomato transgenic lines increased fruit size in contrast to the wild type. This study provides a basis and genetic resources for elucidating the novel role of ncRNAs in fruit development.

OsCSN2 orchestrates Oryza sativa L. growth and development through modulation of the GA and BR pathways

The COP9 signalosome (CSN) is a conserved protein complex found in higher eukaryotes, consisting of eight subunits, and it plays a crucial role in regulating various processes of plant growth and development. Among these subunits, CSN2 is one of the most conserved components within the COP9 signalosome complex. Despite its prior identification in other species, its specific function in Oryza sativa L. (Rice) has remained poorly understood. In this study, we investigated the role of CSN2 in rice using gene editing CRISPR/Cas9 technology and overexpression techniques. We created two types of mutants: the oscsn2 mutant and the OsCSN2-OE mutant, both in the background of rice, and also generated point mutants of OsCSN2 (OsCSN2K64E, OsCSN2K67E, OsCSN2K71E and OsCSN2K104E) to further explore the regulatory function of OsCSN2. Phenotypic observation and gene expression analysis were conducted on plants from the generated mutants, tracking their growth from the seedling to the heading stages. The results showed that the loss and modification of OsCSN2 had limited effects on plant growth and development during the early stages of both the wild-type and mutant plants. However, as the plants grew to 60 days, significant differences emerged. The OsCSN2 point mutants exhibited increased tillering compared to the OsCSN2-OE mutant plants, which were already at the tillering stage. On the other hand, the OsCSN2 point mutant had already progressed to the heading and flowering stages, with the shorter plants. These results, along with functional predictions of the OsCSN2 protein, indicated that changes in the 64th, 67th, 71st, and 104th amino acids of OsCSN2 affected its ubiquitination site, influencing the ubiquitination function of CSN and consequently impacting the degradation of the DELLA protein SLR1. Taken together, it can be speculated that OsCSN2 plays a key role in GA and BR pathways by influencing the functional regulation of the transcription factor SLR1 in CSN, thereby affecting the growth and development of rice and the number of tillers.

Genetics and metabolic responses of Artemisia annua L to the lake of phosphorus under the sparingly soluble phosphorus fertilizer: evidence from transcriptomics analysis

The medicinal herb Artemisia annua L. is prized for its capacity to generate artemisinin, which is used to cure malaria. Potentially influencing the biomass and secondary metabolite synthesis of A. annua is plant nutrition, particularly phosphorus (P). However, most soil P exist as insoluble inorganic and organic phosphates, which results to low P availability limiting plant growth and development. Although plants have developed several adaptation strategies to low P levels, genetics and metabolic responses to P status remain largely unknown. In a controlled greenhouse experiment, the sparingly soluble P form, hydroxyapatite (Ca5OH(PO4)3/CaP) was used to simulate calcareous soils with low P availability. In contrast, the soluble P form KH2PO4/KP was used as a control. A. annua's morphological traits, growth, and artemisinin concentration were determined, and RNA sequencing was used to identify the differentially expressed genes (DEGs) under two different P forms. Total biomass, plant height, leaf number, and stem diameter, as well as leaf area, decreased by 64.83%, 27.49%, 30.47%, 38.70%, and 54.64% in CaP compared to KP; however, LC-MS tests showed an outstanding 37.97% rise in artemisinin content per unit biomass in CaP contrary to KP. Transcriptome analysis showed 2015 DEGs (1084 up-regulated and 931 down-regulated) between two P forms, including 39 transcription factor (TF) families. Further analysis showed that DEGs were mainly enriched in carbohydrate metabolism, secondary metabolites biosynthesis, enzyme catalytic activity, signal transduction, and so on, such as tricarboxylic acid (TCA) cycle, glycolysis, starch and sucrose metabolism, flavonoid biosynthesis, P metabolism, and plant hormone signal transduction. Meanwhile, several artemisinin biosynthesis genes were up-regulated, including DXS, GPPS, GGPS, MVD, and ALDH, potentially increasing artemisinin accumulation. Furthermore, 21 TF families, including WRKY, MYB, bHLH, and ERF, were up-regulated in reaction to CaP, confirming their importance in P absorption, internal P cycling, and artemisinin biosynthesis regulation. Our results will enable us to comprehend how low P availability impacts the parallel transcriptional control of plant development, growth, and artemisinin production in A. annua. This study could lay the groundwork for future research into the molecular mechanisms underlying A. annua's low P adaptation.

Genome-Wide Identification and Expression Analysis of DWARF53 Gene in Response to GA and SL Related to Plant Height in Banana

Dwarfing is one of the common phenotypic variations in asexually reproduced progeny of banana, and dwarfed banana is not only windproof and anti-fallout but also effective in increasing acreage yield. As a key gene in the strigolactone signalling pathway, DWARF53 (D53) plays an important role in the regulation of the height of plants. In order to gain insight into the function of the banana D53 gene, this study conducted genome-wide identification of banana D53 gene based on the M. acuminata, M. balbisiana and M. itinerans genome database. Analysis of MaD53 gene expression under high temperature, low temperature and osmotic stress based on transcriptome data and RT-qPCR was used to analyse MaD53 gene expression in different tissues as well as in different concentrations of GA and SL treatments. In this study, we identified three MaD53, three MbD53 and two MiD53 genes in banana. Phylogenetic tree analysis showed that D53 Musa are equally related to D53 Asparagales and Poales. Both high and low-temperature stresses substantially reduced the expression of the MaD53 gene, but osmotic stress treatments had less effect on the expression of the MaD53 gene. GR24 treatment did not significantly promote the height of the banana, but the expression of the MaD53 gene was significantly reduced in roots and leaves. GA treatment at 100 mg/L significantly promoted the expression of the MaD53 gene in roots, but the expression of this gene was significantly reduced in leaves. In this study, we concluded that MaD53 responds to GA and SL treatments, but "Yinniaijiao" dwarf banana may not be sensitive to GA and SL.

The transcription factor MYB110 regulates plant height, lodging resistance, and grain yield in rice

The high-yielding Green Revolution varieties of cereal crops are characterized by a semidwarf architecture and lodging resistance. Plant height is tightly regulated by the availability of phosphate (Pi), yet the underlying mechanism remains obscure. Here, we report that rice (Oryza sativa) R2R3-type Myeloblastosis (MYB) transcription factor MYB110 is a Pi-dependent negative regulator of plant height. MYB110 is a direct target of PHOSPHATE STARVATION RESPONSE 2 (OsPHR2) and regulates OsPHR2-mediated inhibition of rice height. Inactivation of MYB110 increased culm diameter and bending resistance, leading to enhanced lodging resistance despite increased plant height. Strikingly, the grain yield of myb110 mutants was elevated under both high- and low-Pi regimes. Two divergent haplotypes based on single nucleotide polymorphisms in the putative promoter of MYB110 corresponded with its transcript levels and plant height in response to Pi availability. Thus, fine-tuning MYB110 expression may be a potent strategy for further increasing the yield of Green Revolution cereal crop varieties.

Toxoplasma gondii F-Box Protein L2 Silences Feline-Restricted Genes Necessary for Sexual Commitment

Toxoplasma gondii is a foodborne pathogen that can cause severe and life-threatening infections in fetuses and immunocompromised patients. Felids are its only definitive hosts, and a wide range of animals, including humans, serve as intermediate hosts. When the transmissible bradyzoite stage is orally ingested by felids, they transform into merozoites that expand asexually, ultimately generating millions of gametes for the parasite sexual cycle. However, bradyzoites in intermediate hosts differentiate exclusively to disease-causing tachyzoites, which rapidly disseminate throughout the host. Though tachyzoites are well-studied, the molecular mechanisms governing transitioning between developmental stages are poorly understood. Each parasite stage can be distinguished by a characteristic transcriptional signature, with one signature being repressed during the other stages. Switching between stages requires substantial changes in the proteome, which is achieved in part by ubiquitination. F-box proteins mediate protein poly-ubiquitination by recruiting substrates to SKP1, Cullin-1, F-Box protein E3 ubiquitin ligase (SCF-E3) complexes. We have identified an F-box protein named Toxoplasma gondii F-Box Protein L2 (TgFBXL2), which localizes to distinct nuclear sites. TgFBXL2 is stably engaged in an SCF-E3 complex that is surprisingly also associated with a COP9 signalosome complex that negatively regulates SCF-E3 function. At the cellular level, TgFBXL2-depleted parasites are severely defective in centrosome replication and daughter cell development. Most remarkable, RNA seq data show that TgFBXL2 conditional depletion induces the expression of genes necessary for sexual commitment. We suggest that TgFBXL2 is a latent guardian of sexual stage development in Toxoplasma and poised to remove conflicting proteins in response to an unknown trigger of sexual development.

DELLA-mediated gene repression is maintained by chromatin modification in rice

DELLA proteins are master regulators of gibberellic acid (GA) signaling through their effects on gene expression. Enhanced DELLA accumulation in rice and wheat varieties has greatly contributed to grain yield increases during the green revolution. However, the molecular basis of DELLA-mediated gene repression remains elusive. In this work, we show that the rice DELLA protein SLENDER RICE1 (SLR1) forms a tripartite complex with Polycomb-repressive complex 2 (PRC2) and the histone deacetylase HDA702 to repress downstream genes by establishing a silent chromatin state. The slr1 mutation and GA signaling resulted in dissociation of PRC2 and HDA702 from GA-inducible genes. Loss-of-function or downregulation of the chromatin regulators impaired SLR1-dependent histone modification and gene repression. Time-resolved analysis of GA signaling revealed that GA-induced transcriptional activation was associated with a rapid increase of H3K9ac followed by H3K27me3 removal. Collectively, these results establish a general epigenetic mechanism for DELLA-mediated gene repression and reveal details of the chromatin dynamics during transcriptional activation stimulated by GA signaling.

Coordination of growth and drought responses by GA-ABA signaling in rice

The drought caused by global warming seriously affects the crop growth and agricultural production. Plants have evolved distinct strategies to cope with the drought environment. Under drought stress, energy and resources should be diverted from growth toward stress management. However, the molecular mechanism underlying coordination of growth and drought response remains largely elusive. Here, we discovered that most of the gibberellin (GA) metabolic genes were regulated by water scarcity in rice, leading to the lower GA contents and hence inhibited plant growth. Low GA contents resulted in the accumulation of more GA signaling negative regulator SLENDER RICE 1, which inhibited the degradation of abscisic acid (ABA) receptor PYL10 by competitively binding to the co-activator of anaphase-promoting complex TAD1, resulting in the enhanced ABA response and drought tolerance. These results elucidate the synergistic regulation of crop growth inhibition and promotion of drought tolerance and survival, and provide useful genetic resource in breeding improvement of crop drought resistance.

GID2 Interacts With CDKN3 and Regulates Pancreatic Cancer Growth and Apoptosis

Dysregulation of deubiquitinase or ubiquitinase-mediated protein expression contributes to various diseases, including cancer. In the present study, we identified GID2, a subunit of the glucose-induced degradation-deficient (GID) complex that functions as an E3 ubiquitin ligase, as a potential key candidate gene in pancreatic cancer (PC) progression. The functional role and potential mechanism of GID2 in PC progression were investigated. Integrated bioinformatics analysis was performed to identify differentially expressed genes in PC based on the Gene Expression Profiling Interactive Analysis data sets. We found that GID2 was upregulated in PC tissues and that a high level of GID2 expression in clinical PC samples was positively associated with tumor stage and poor survival. Functional assays elucidated that GID2 expression promoted cell growth in vitro and accelerated tumor growth in vivo. GID2 knockdown effectively attenuated the malignant behaviors of PC cells and tumor formation. Furthermore, the protein network that interacted with the GID2 protein was constructed based on the GeneMANIA website. Cyclin-dependent kinase inhibitor 3 (CDKN3), a cell cycle regulator, was identified as a potential target of the GID2 protein. We revealed that GID2 positively regulated CDKN3 expression and inhibited CDKN3 ubiquitination. Furthermore, CDKN3 downregulation reversed the promoting effects of GID2 on PC progression. Therefore, the present study demonstrated that GID2 might regulate PC progression by maintaining the stability of the CDKN3 protein. These findings highlight the potential roles of the GID2/CDKN3 axis as a potential therapeutic target in PC.

The E3 ubiquitin ligases SINA1 and SINA2 integrate with the protein kinase CIPK20 to regulate the stability of RGL2a, a positive regulator of anthocyanin biosynthesis

Although DELLA protein destabilization mediated by post-translational modifications is essential for gibberellin (GA) signal transduction and GA-regulated anthocyanin biosynthesis, the related mechanisms remain largely unknown. In this study, we report the ubiquitination and phosphorylation of an apple DELLA protein MdRGL2a in response to GA signaling and its regulatory role in anthocyanin biosynthesis. MdRGL2a could interact with MdWRKY75 to enhance the MdWRKY75-activated transcription of anthocyanin activator MdMYB1 and interfere with the interaction between anthocyanin repressor MdMYB308 and MdbHLH3 or MdbHLH33, thereby promoting anthocyanin accumulation. A protein kinase MdCIPK20 was found to phosphorylate and protect MdRGL2a from degradation, and it was essential for MdRGL2a-promoting anthocyanin accumulation. However, MdRGL2a and MdCIPK20 were ubiquitinated and degraded by E3 ubiquitin ligases MdSINA1 and MdSINA2, respectively, both of which were activated in the presence of GA. Our results display the integration of SINA1/2 with CIPK20 to dynamically regulate GA signaling and will be helpful toward understanding the mechanism of GA signal transduction and GA-inhibited anthocyanin biosynthesis. The discovery of extensive interactions between DELLA and SINA and CIPK proteins in apple will provide reference for the study of ubiquitination and phosphorylation of DELLA proteins in other species.

PsRGL1 negatively regulates chilling- and gibberellin-induced dormancy release by PsF-box1-mediated targeting for proteolytic degradation in tree peony

Tree peony bud endodormancy is a common survival strategy similar to many perennial woody plants in winter, and the activation of the GA signaling pathway is the key to breaking endodormancy. GA signal transduction is involved in many physiological processes. Although the GA-GID1-DELLA regulatory module is conserved in many plants, it has a set of specific components that add complexity to the GA response mechanism. DELLA proteins are key switches in GA signaling. Therefore, there is an urgent need to identify the key DELLA proteins involved in tree peony bud dormancy release. In this study, the prolonged chilling increased the content of endogenously active gibberellins. PsRGL1 among three DELLA proteins was significantly downregulated during chilling- and exogenous GA3-induced bud dormancy release by cell-free degradation assay, and a high level of polyubiquitination was detected. Silencing PsRGL1 accelerated bud dormancy release by increasing the expression of the genes associated with dormancy release, including PsCYCD, PsEBB1, PsEBB3, PsBG6, and PsBG9. Three F-box protein family members responded to chilling and GA3 treatments, resulting in PsF-box1 induction. Yeast two-hybrid and BiFC assays indicated that only PsF-box1 could bind to PsRGL1, and the binding site was in the C-terminal domain. PsF-box1 overexpression promoted dormancy release and upregulated the expression of the dormancy-related genes. In addition, yeast two-hybrid and pull-down assays showed that PsF-box1 also interacted with PsSKP1 to form an E3 ubiquitin ligase. These findings enriched the molecular mechanism of the GA signaling pathway during dormancy release, and enhanced the understanding of tree peony bud endodormancy.

Peach DELLA Protein PpeDGYLA Is Not Degraded in the Presence of Active GA and Causes Dwarfism When Overexpressed in Poplar and Arabidopsis

Controlling the tree size of fruit species such as peach can reduce the amount of labor and input needed for orchard management. The phytohormone gibberellin (GA) positively regulates tree size by inducing degradation of the GA signaling repressor DELLA. The N-terminal DELLA domain in this protein is critical for its GA-dependent interaction with the GA receptor GID1 and the resulting degradation of the DELLA protein, which allows for growth-promoting GA signaling. In this study, a DELLA family member, PpeDGYLA, contains a DELLA domain but has amino acid changes in three conserved motifs (DELLA into DGYLA, LEQLE into LERLE, and TVHYNP into AVLYNP). In the absence or presence of GA₃, the PpeDGYLA protein did not interact with PpeGID1c and was stable in 35S-PpeDGYLA peach transgenic callus. The overexpression of PpeDGYLA in both polar and Arabidopsis showed an extremely dwarfed phenotype, and these transgenic plants were insensitive to GA₃ treatment. PpeDGYLA could interact with PpeARF6-1 and -2, supposed growth-promoting factors. It is suggested that the changes in the DELLA domain of PpeDGYLA may, to some extent, account for the severe dwarf phenotype of poplar and Arabidopsis transgenic plants. In addition, our study showed that the DELLA family contained three clades (DELLA-like, DELLA, and DGLLA). PpeDGYLA clustered into the DGLLA clade and was expressed in all of the analyzed tissues. These results lay the foundation for the further study of the repression of tree size by PpeDGYLA.

A rice seed-specific glycine-rich protein OsDOR1 interacts with GID1 to repress GA signaling and regulates seed dormancy

Seed dormancy is an important agronomic trait under the control of complex genetic and environmental interactions, which have not been yet comprehensively understood. From the field screening of rice mutant library generated by a Ds transposable element, we identified a pre-harvest sprouting (PHS) mutant dor1. This mutant has a single insertion of Ds element at the second exon of OsDOR1 (LOC_Os03g20770), which encodes a novel seed-specific glycine-rich protein. This gene successfully complemented the PHS phenotype of dor1 mutant and its ectopic expression enhanced seed dormancy. Here, we demonstrated that OsDOR1 protein binds to the GA receptor protein, OsGID1 in rice protoplasts, and interrupts with the formation OsGID1-OsSLR1 complex in yeast cells. Co-expression of OsDOR1 with OsGID1 in rice protoplasts attenuated the GA-dependent degradation of OsSLR1, the key repressor of GA signaling. We showed the endogenous OsSLR1 protein level in the dor1 mutant seeds is significantly lower than that of wild type. The dor1 mutant featured a hypersensitive GA-response of α-amylase gene expression during seed germination. Based on these findings, we suggest that OsDOR1 is a novel negative player of GA signaling operated in the maintenance of seed dormancy. Our findings provide a novel source of PHS resistance.

The DnaJ domain-containing heat-shock protein NAL11 determines plant architecture by mediating gibberellin homeostasis in rice (Oryza sativa)

Ideal Plant Architecture 1 (IPA1) is a key regulator of plant architecture. However, knowledge of downstream genes applicable for improving rice plant architecture is very limited. We identified the plant architecture regulatory gene NARROW LEAF 11 (NAL11), which encodes a heat-shock protein (HSP) containing a DnaJ domain. A promising rare allele of NAL11 (NAL11^-923del-1552 ) positively selected in Aus cultivars was identified; this allele exhibited increased expression and generated relatively few tillers, thick stems, and large panicles, components of the ideal plant architecture (IPA). NAL11 is involved in regulating the cell cycle and cell proliferation. NAL11 loss-of-function mutants present impaired chloroplast development and gibberellin (GA) defects. Biochemical analyses show that IPA1 directly binds to elements in the missing fragment of the NAL11^-923del-1552 promoter and negatively regulates NAL11 expression. Genetic analyses support the hypothesis that NAL11 acts downstream of IPA1 to regulate IPA by modulating GA homeostasis, and NAL11 may be an essential complement for IPA1. Our work revealed that avoidance of the inhibition of NAL11^-923del-1552 caused by IPA1 represents a positive strategy for rescuing GA defects accompanied by the upregulation of IPA1 in breeding high-yield rice.

OsHLS1 regulates plant height and development by controlling active gibberellin accumulation in rice (Oryza sativa L.)

In this study, we identified a gene related to plant height, leaf, and premature senescence in rice, and named it OsHLS1. Through bioinformatics analysis, it was found that this gene belongs to a new gene family-HLS family, and this gene family exists widely in higher plants. Expression of OsHLS1 was significantly brought about by gibberellin (GA). Subcellular localization showed that OsHLS1 was located in the nucleus. oshls1-3 displayed a GA-deficient phenotype, with dwarf plants. In addition, oshls1-3 also showed premature senescence, shorter and narrower leaves, and pollen abortion. Exogenous GA₃ can restore the plant height of oshls1-3. Histomorphological analysis showed that the gene affected the progress of internode cells in the first and third nodes under the rice panicle. Through the verification of the homologous gene AT4G25690 in Arabidopsis, it was found that the mutant at4g25690 lines also showed plant dwarfing, premature senescence, and shortening and narrowing of leaves and pollen abortion. OsHLS1 affected the expression levels of genes involved in the GA metabolic pathway and affected the content of active GA, thereby regulating plant height development in rice. In conclusion, we suggest that OsHLS1 regulates plant height and development by controlling the accumulation of active gibberellins in rice.

Potentially Useful Dwarfing or Semi-dwarfing Genes in Rice Breeding in Addition to the sd1 Gene

The "Green revolution" gene sd1 has been used widely in the breeding of modern rice varieties for over half a century. The application of this gene has increased rice yields and thereby supported a significant proportion of the global population. The use of a single gene, however, has raised concerns in the scientific community regarding its durability, especially given the bottleneck in genetic background and the need for large input of fertilizer. New dwarfing or semi-dwarfing genes are needed to alleviate our dependence on the sole "Green revolution" gene. In the past few years, several new dwarfing and semi-dwarfing genes as well as their mutants have been reported. Here, we provide an extensive review of the recent discoveries concerning newly identified genes that are potentially useful in rice breeding, including methods employed to create and effectively screen new rice mutants, the phenotypic characteristics of the new dwarfing and semi-dwarfing mutants, potential values of the new dwarfing and semi-dwarfing genes in rice breeding, and potential molecular mechanisms associated with the newly identified genes.

Genome-Wide Analysis and Characterization of Eggplant F-Box Gene Superfamily: Gene Evolution and Expression Analysis under Stress

F-box genes play an important role in plant growth and resistance to abiotic and biotic stresses. To date, systematic analysis of F-box genes and functional annotation in eggplant (Solanum melongena) is still limited. Here, we identified 389 F-box candidate genes in eggplant. The domain study of F-box candidate genes showed that the F-box domain is conserved, whereas the C-terminal domain is diverse. There are 376 SmFBX candidate genes distributed on 12 chromosomes. A collinearity analysis within the eggplant genome suggested that tandem duplication is the dominant form of F-box gene replication in eggplant. The collinearity analysis between eggplant and the three other species (Arabidopsis thaliana, rice and tomato) provides insight into the evolutionary characteristics of F-box candidate genes. In addition, we analyzed the expression of SmFBX candidate genes in different tissues under high temperature and bacterial wilt stress. The results identified several F-box candidate genes that potentially participate in eggplant heat tolerance and bacterial wilt resistance. Moreover, the yeast two-hybrid assay showed that several representative F-box candidate proteins interacted with representative Skp1 proteins. Overexpression of SmFBX131 and SmFBX230 in tobacco increased resistance to bacterial wilt. Overall, these results provide critical insights into the functional analysis of the F-box gene superfamily in eggplant and provide potentially valuable targets for heat and bacterial resistance.

The Role of Exogenous Gibberellic Acid and Methyl Jasmonate against White-Backed Planthopper (Sogatella furcifera) Stress in Rice (Oryza sativa L.)

Rice (Oryza sativa L.) is one of the essential staple foods for more than half of the world's population, and its production is affected by different environmental abiotic and biotic stress conditions. The white-backed planthopper (WBPH, Sogatella furcifera) causes significant damage to rice plants, leading to substantial economic losses due to reduced production. In this experiment, we applied exogenous hormones (gibberellic acid and methyl jasmonate) to WBPH-infested rice plants and examined the relative expression of related genes, antioxidant accumulation, the recovery rate of affected plants, endogenous hormones, the accumulation of H₂O₂, and the rate of cell death using DAB and trypan staining, respectively. The expression of the transcriptional regulator (OsGAI) and gibberellic-acid-mediated signaling regulator (OsGID2) was upregulated significantly in GA 50 µM + WBPH after 36 h. OsGAI was upregulated in the control, GA 50 µM + WBPH, GA 100 µM + WBPH, and MeJA 100 µM + WBPH. However, after 48 h, the OsGID2 was significantly highly expressed in all groups of plants. The glutathione (GSH) values were significantly enhanced by GA 100 µM and MeJA 50 µM treatment. Unlike glutathione (GSH), the catalase (CAT) and peroxidase (POD) values were significantly reduced in control + WBPH plants. However, a slight increase in CAT and POD values was observed in GA 50 + WBPH plants and a reduction in the POD value was observed in GA 100 µM + WBPH and MeJA 50 µM + WBPH plants. GA highly recovered the WBPH-affected rice plants, while no recovery was seen in MeJA-treated plants. MeJA was highly accumulated in control + WBPH, MeJA 50 µM + WBPH, and GA 100 µM + WBPH plants. The H₂O₂ accumulation was highly decreased in GA-treated plants, while extensive cell death was observed in MeJA-treated plants compared with GA-treated plants. From this study, we can conclude that the exogenous application of GA can overcome the effects of the WBPH and enhance resistance in rice.

OsDREB2B, an AP2/ERF transcription factor, negatively regulates plant height by conferring GA metabolism in rice

The AP2/ERF family is a large group of plant-specific transcription factors that play an important role in many biological processes, such as growth, development, and abiotic stress responses. OsDREB2B, a dehydration responsive factor (DRE/CRT) in the DREB subgroup of the AP2/ERF family, is associated with abiotic stress responses, such as cold, drought, salt, and heat stress, in Arabidopsis or rice. However, its role in regulating plant growth and development in rice is unclear. In this study, we reported a new function of OsDREB2B, which negatively regulates plant height in rice. Compared with wild type (WT), OsDREB2B-overexpressing (OE) rice exhibited dwarf phenotypes, such as reduction in plant height, internode length, and seed length, as well as grain yield, while the knockout mutants developed by CRISPR/Cas9 technology exhibited similar phenotypes. Spatial expression analysis revealed that OsDREB2B was highly expressed in the leaf sheaths. Under exogenous GA₃ application, OsDREB2B expression was induced, and the length of the second leaf sheath of the OsDREB2B-OE lines recovered to that of the WT. OsDREB2B localized to the nucleus of the rice protoplast acted as a transcription activator and upregulated OsAP2-39 by directly binding to its promoter. OsDREB2B-OE lines reduced endogenous bioactive GA levels by downregulating seven GA biosynthesis genes and upregulating eight GA deactivation genes but not GA signaling genes. The yeast two-hybrid assay and bimolecular fluorescence complementation assay showed that OsDREB2B interacted with OsWRKY21. In summary, our study suggests that OsDREB2B plays a negative role in rice growth and development by regulating GA metabolic gene expression, which is mediated by OsAP2-39 and OsWRKY21, thereby reducing GA content and rice plant height.

Gibberellin-related genes regulate dwarfing mechanism in wintersweet

Chimonanthus praecox (wintersweet) is an important cut flower and pot plant with a high ornamental and economic value in China. The development of dwarf wintersweet varieties has become an important research topic for the wintersweet industry. The lack of natural dwarf germplasm has hindered research into the molecular mechanisms of developing dwarf wintersweet, limiting its cultivation. After a long-term investigation and collection of germplasm resources of C. praecox, we obtained the germplasm of a dwarf C. praecox (dw). Here, the dwarf and normal C. praecox (NH) were used to identify the types of hormones regulating dw formation using phenotypic identification and endogenous hormone determination. Differentially expressed genes in the dw and NH groups were screened using transcriptome analysis. The functions of key genes in the dwarf trait were verified by heterologous expression. It was found that the internode length and cell number were significantly reduced in dw than in NH, and the thickness of the xylem and pith was significantly decreased. The dwarfness of dw could be recovered by exogenous gibberellic acid (GA) application, and endogenous GA levels showed that the GA4 content of dw was substantially lower than that of NH. Transcriptome differential gene analysis showed that the elevated expression of the CpGA2ox gene in the GA synthesis pathway and that of CpGAI gene in the signal transduction pathway might be the key mechanisms leading to dwarfing. Combined with the results of weighted gene co-expression network analysis, we selected the CpGAI gene for analysis and functional verification. These results showed that CpGAI is a nuclear transcriptional activator. Overexpression of CpGAI in Populus tomentosa Carr. showed that CpGAI could lead to the dwarfing in poplar. We analyzed the dwarfing mechanism of C. praecox, and the results provided a reference for dwarf breeding of wintersweet.

An engineered platform for reconstituting functional multisubunit SCF E3 ligase in vitro

Multisubunit SKP1/Cullin1/F-box (SCF) E3 ligases play essential roles in regulating the stability of crucial regulatory factors and controlling growth and development in eukaryotes. Detecting E3 ligase activity in vitro is important for exploring the molecular mechanism of protein ubiquitination. However, in vitro ubiquitination assay systems for multisubunit E3 ligases remain difficult to achieve, especially in plants, mainly owing to difficulties in achieving active components of multisubunit E3 ligases with high purity and characterizing specific E2 and E3 pairs. In this study, we characterized components of the rice SCF^DWARF3 (SCF^D3) E3 ligase, screened the coordinated E2, and reconstituted active SCF^D3 E3 ligase in vitro. We further engineered SCF^D3 E3 ligase using a fused SKP1-Cullin1-RBX1 (eSCR) protein and found that both the wild-type SCF^D3 E3 ligase and the engineered SCF^D3 E3 ligase catalyzed ubiquitination of the substrate D53, which is the key transcriptional repressor in strigolactone signaling. Finally, we replaced D3 with other F-box proteins from rice and humans and reconstituted active eSCF E3 ligases, including eSCF^GID2, eSCF^FBXL18, and eSCF^CDC4 E3 ligases. Our work reconstitutes functional SCF E3 ligases in vitro and generates an engineered system with interchangeable F-box proteins, providing a powerful platform for studying the mechanisms of multisubunit SCF E3 ligases in eukaryotes.

An F-box protein from wheat, TaFBA-2A, negatively regulates JA biosynthesis and confers improved salt tolerance and increased JA responsiveness to transgenic rice plants

Soil salinity is a serious problem encountered by agriculture worldwide, which will lead to many harmful effects on plant growth, development, and even crop yield. F-box protein is the core subunit of the Skp1-Cullin-F-box (SCF) complex E3 ligase and plays crucial roles in regulating the growth, development, biotic & abiotic stresses, as well as hormone signaling pathway in plants. In this study, an FBA type F-box gene TaFBA-2A was isolated from wheat (Triticum aestivum L.). This study showed that TaFBA-2A could interact with TaSKP1, and TaOPR2, the crucial enzyme involving in jasmonic acid (JA) biosynthesis. TaFBA-2A negatively regulates JA biosynthesis, probably by mediating the degradation of TaOPR2 via the ubiquitin-26S proteasome pathway. Ectopic expression of TaFBA-2A improved the salt tolerance and increased the JA responsiveness of the transgenic rice lines. In addition, some agronomic traits closely related to crop yield were significantly enhanced in the rice lines ectopic expressing TaFBA-2A. The data obtained in this study shed light on the function and mechanisms of TaFBA-2A in JA biosynthesis and the responses to salt stress and JA treatment; this study also suggested that TaFBA-2A has the potential in improving the salt tolerance and crop yield of transgenic rice plants.

Combining Proteomics and Metabolomics to Analyze the Effects of Spaceflight on Rice Progeny

Spaceflight is a special abiotic stress, the biological effect mechanism of which on contemporary rice has been clarified, However, its effect on offspring rice was still unclear. In order to understand the response mechanism of F2 generation plants to space flight, this study used SJ-10 recoverable satellite to carry DN423 rice seeds for 12.5 days in orbit flight. After returning to the ground, the plants were then planted to F2 generation to explore the biological effect mechanism. Our research showed that in the F2 generation of TLS, the rice plant height of the space flight group increased by 33.8%, the ear length and thousand-grain weight decreased by 9.7 and 4.6%, respectively, and the grain number per panicle increased by 6.5%. Moreover, related proteins that control changes in agronomic traits have been identified. The changes of MDA, H2O2, soluble sugar, electron leakage and antioxidant enzyme activity confirmed the stress response in F2 generation plants. ITRAQ and LC-MS technology were used to reveal the change pattern of protein levels and metabolite levels in F2 generation plants, 389 and 405 proteins were identified as differentially abundant proteins in TLS and TS, respectively. In addition, there were 124 and 125 metabolites that changed during these two periods. The proteome and metabolome result further confirmed that the F2 generation plants still retained the memory of space flight stress, and retained the memory of space flight stress through genome instability. Oxidative stress signals activated sugar signals to rebuild metabolic networks to adapt to space flight stress. The reconstruction of energy metabolism, amino acid metabolism, phenylalanine metabolism, and flavonoid metabolism played an important role in the process of adapting to space flight stress. The results of this study broaden the perspective of space biological effects and provide a basis for studying the effects of abiotic stress on plant progeny.

Importance of Tyrosine Phosphorylation in Hormone-Regulated Plant Growth and Development

Protein phosphorylation is the most frequent post-translational modification (PTM) that plays important regulatory roles in a wide range of biological processes. Phosphorylation mainly occurs on serine (Ser), threonine (Thr), and tyrosine (Tyr) residues, with the phosphorylated Tyr sites accounting for ~1–2% of all phosphorylated residues. Tyr phosphorylation was initially believed to be less common in plants compared to animals; however, recent investigation indicates otherwise. Although they lack typical protein Tyr kinases, plants possess many dual-specificity protein kinases that were implicated in diverse cellular processes by phosphorylating Ser, Thr, and Tyr residues. Analyses of sequenced plant genomes also identified protein Tyr phosphatases and dual-specificity protein phosphatases. Recent studies have revealed important regulatory roles of Tyr phosphorylation in many different aspects of plant growth and development and plant interactions with the environment. This short review summarizes studies that implicated the Tyr phosphorylation in biosynthesis and signaling of plant hormones.

Genome-Wide Analysis of Genes Involved in the GA Signal Transduction Pathway in 'duli' Pear (Pyrus betulifolia Bunge)

Gibberellic acid (GA) is an important phytohormone that regulates every aspect of plant growth and development. While elements involved in GA signaling have been identified and, hence, their functions have been well studied in model plants, such as Arabidopsis and rice, very little is known in pear. We, therefore, analyzed the genes related to GA signaling from the recently sequenced genome of the wildtype ‘duli’ pear (Pyrus betulifolia Bunge), a widely used rootstock for grafting in pear cultivation in China due to its vigorous growth and resistance to abiotic and biotic stress. In total, 15 genes were identified, including five GA receptors PbGID1s (GA-INSENSTIVE DWARF 1), six GA negative regulators, PbDELLAs, and four GA positive regulators, PbSLYs. Exogenous application of GA could promote the expression of PbGID1s but inhibit that of PbDELLAs and PbSLYs in tissue culture ‘duli’ pear seedlings. The expression profiles of these genes in field-grown trees under normal growth conditions, as well as in tissue-cultured seedlings treated with auxin (IAA), GA, paclobutrazol (PAC), abscisic acid (ABA), and sodium chloride (NaCl), were also studied, providing further evidence of the involvement of these genes in GA signaling in ‘duli’ pear plants. The preliminary results obtained in this report lay a good foundation for future research into GA signaling pathways in pear. Importantly, the identification and preliminary functional verification of these genes could guide molecular breeding in order to obtain the highly desired dwarf pear rootstocks for high-density plantation to aid easy orchard management and high yielding of pear fruits.

Geminivirus C4 proteins inhibit GA signaling via prevention of NbGAI degradation, to promote viral infection and symptom development in N. benthamiana

The phytohormone gibberellin (GA) is a vital plant signaling molecule that regulates plant growth and defense against abiotic and biotic stresses. To date, the molecular mechanism of the plant responses to viral infection mediated by GA is still undetermined. DELLA is a repressor of GA signaling and is recognized by the F-box protein, a component of the SCF^SLY1/GID2 complex. The recognized DELLA is degraded by the ubiquitin-26S proteasome, leading to the activation of GA signaling. Here, we report that ageratum leaf curl Sichuan virus (ALCScV)-infected N. benthamiana plants showed dwarfing symptoms and abnormal flower development. The infection by ALCScV significantly altered the expression of GA pathway-related genes and decreased the content of endogenous GA in N. benthamiana. Furthermore, ALCScV-encoded C4 protein interacts with the DELLA protein NbGAI and interferes with the interaction between NbGAI and NbGID2 to prevent the degradation of NbGAI, leading to inhibition of the GA signaling pathway. Silencing of NbGAI or exogenous GA₃ treatment significantly reduces viral accumulation and disease symptoms in N. benthamiana plants. The same results were obtained from experiments with the C4 protein encoded by tobacco curly shoot virus (TbCSV). Therefore, we propose a novel mechanism by which geminivirus C4 proteins control viral infection and disease symptom development by interfering with the GA signaling pathway.

Gibberellins (GAs) are plant hormones essential for many developmental processes in plants. Plant virus infection can induce abnormal flower development and influence the GA pathway, resulting in plant dwarfing symptoms, but the underlying mechanisms are still not well described. Here, we demonstrate that the geminivirus-encoded C4 protein regulates the GA signaling pathway to promote viral accumulation and disease symptom development. By directly interacting with NbGAI, the C4 protein interferes with the interaction between NbGAI and NbGID2, which inhibits the degradation of NbGAI. As a result, the GA signaling pathway is blocked, and the infected plants display symptoms of typical dwarfing and delayed flowering. Our results reveal a novel mechanism by which geminivirus C4 proteins influence viral pathogenicity by interfering with the GA signaling pathway and provide new insights into the interaction between the virus and host.

Genome-wide identification and characterization of F-box family proteins in sweet potato and its expression analysis under abiotic stress

In this study, genome-wide characterization of F-box proteins in sweet potato yielded 243 IbFBX genes, unevenly distributed on the 15 chromosomes of sweet potato. Gene duplication analysis suggested segmental duplication as the principal factor influencing the expansive evolution of IbFBX genes in sweet potato. Phylogenetic analysis clustered F-box proteins in sweet potato, Arabidopsis, and rice into six clades (I-VI). Gene structure analysis of the IbFBX genes revealed that most of the genes within the same clade were highly conserved. Expression profiles of IbFBX family genes in 9 different tissues and under stress conditions revealed that the IbFBXs were highly upregulated or downregulated in response to salt and drought stress, suggesting their significant roles in abiotic stress response and adaptation. Knowledge of the diverse functions and expression patterns of IbFBXs presents a solid theoretical basis for annotating the functions of IbFBXs and further facilitate the molecular breeding of sweet potato.

Chromatin remodeling factors OsYAF9 and OsSWC4 interact to promote internode elongation in rice

Deposition of H2A.Z and H4 acetylation by SWI2/SNF2-Related 1 Chromatin Remodeling (SWR1) and Nucleosome Acetyltransferase of H4 (NuA4) complexes in specific regulatory regions modulates transcription and development. However, little is known about these complexes in Oryza sativa (rice) development. Here, we reported that OsYAF9 and OsSWC4, two subunits of SWR1 and NuA4 complexes, are involved in rice vegetative and reproductive development. Loss of OsYAF9 resulted in reduced height, fewer tillers, fewer pollen grains, and defects in embryogenesis and seed filling. OsYAF9 directly interacted with OsSWC4 in vitro and in vivo. Loss of OsSWC4 function exhibited defects in pollen germination and failure to generate seeds, whereas knockdown of OsSWC4 resulted in reduced height and fewer tillers. The reduced height caused by OsYAF9 mutation and OsSWC4 knockdown was due to shorter internodes and defects in cell elongation, and this phenotype was rescued with gibberellin (GA) treatment, suggesting that both OsYAF9 and OsSWC4 are involved in the GA biosynthesis pathway. OsSWC4 was directly bound to the AT-rich region of GA biosynthesis genes, which in turn accomplished H2A.Z deposition and H4 acetylation at the GA biosynthesis genes with OsYAF9. Together, our study provides insights into the mechanisms involving OsSWC4 and OsYAF9 forming a protein complex to promote rice internode elongation with H2A.Z deposition and H4 acetylation.

Interactions of Gibberellins with Phytohormones and Their Role in Stress Responses

Gibberellins are amongst the main plant growth regulators. Discovered over a century ago, the interest in gibberellins research is growing due to their current and potential applications in crop production and their role in the responses to environmental stresses. In the present review, the current knowledge on gibberellins’ homeostasis and modes of action is outlined. Besides this, the complex interrelations between gibberellins and other plant growth regulators are also described, providing an intricate network of interactions that ultimately drives towards precise and specific gene expression. Thus, genes and proteins identified as being involved in gibberellin responses in model and non-model species are highlighted. Furthermore, the molecular mechanisms governing the gibberellins’ relation to stress responses are also depicted. This review aims to provide a comprehensive picture of the state-of-the-art of the current perceptions of the interactions of gibberellins with other phytohormones, and their responses to plant stresses, thus allowing for the identification of the specific mechanisms involved. This knowledge will help us to improve our understanding of gibberellins’ biology, and might help increase the biotechnological toolbox needed to refine plant resilience, particularly under a climate change scenario.

Morphological Characterization and Transcriptome Analysis of New Dwarf and Narrow-Leaf (dnl2) Mutant in Maize

Lodging is the primary factor limiting high yield under a high plant density. However, an optimal plant height and leaf shape can effectively decrease the lodging risk. Here we studied an ethyl methanesulfonate (EMS)-induced dwarf and a narrow-leaf mutant, dnl2. Gene mapping indicated that the mutant was controlled by a gene located on chromosome nine. Phenotypic and cytological observations revealed that dnl2 showed inhibited cell growth, altered vascular bundle patterning, and disrupted secondary cell wall structure when compared with the wild-type, which could be the direct cause of the dwarf and narrow-leaf phenotype. The phytohormone levels, especially auxin and gibberellin, were significantly decreased in dnl2 compared to the wild-type plants. Transcriptome profiling of the internodes of the dnl2 mutant and wild-type revealed a large number of differentially expressed genes enriched in the cell wall biosynthesis, remodeling, and hormone biosynthesis and signaling pathways. Therefore, we suggest that crosstalk between hormones (the altered vascular bundle and secondary cell wall structure) may contribute to the dwarf and narrow-leaf phenotype by influencing cell growth. These results provide a foundation for DNL2 gene cloning and further elucidation of the molecular mechanism of the regulation of plant height and leaf shape in maize.

Genome and transcriptome-based characterization of high energy carbon-ion beam irradiation induced delayed flower senescence mutant in Lotus japonicus

BACKGROUND

Flower longevity is closely related to pollen dispersal and reproductive success in all plants, as well as the commercial value of ornamental plants. Mutants that display variation in flower longevity are useful tools for understanding the mechanisms underlying this trait. Heavy-ion beam irradiation has great potential to improve flower shapes and colors; however, few studies are available on the mutation of flower senescence in leguminous plants.

RESULTS

A mutant (C416) exhibiting blossom duration eight times longer than that of the wild type (WT) was isolated in Lotus japonicus derived from carbon ion beam irradiation. Genetic assays supported that the delayed flower senescence of C416 was a dominant trait controlled by a single gene, which was located between 4,616,611 Mb and 5,331,876 Mb on chromosome III. By using a sorting strategy of multi-sample parallel genome sequencing, candidate genes were narrowed to the gene CUFF.40834, which exhibited high identity to ethylene receptor 1 in other model plants. A physiological assay demonstrated that C416 was insensitive to ethylene precursor. Furthermore, the dynamic changes of phytohormone regulatory network in petals at different developmental stages was compared by using RNA-seq. In brief, the ethylene, jasmonic acid (JA), and salicylic acid (SA) signaling pathways were negatively regulated in C416, whereas the brassinosteroid (BR) and cytokinin signaling pathways were positively regulated, and auxin exhibited dual effects on flower senescence in Lotus japonicus. The abscisic acid (ABA) signaling pathway is positively regulated in C416.

CONCLUSION

So far, C416 might be the first reported mutant carrying a mutation in an endogenous ethylene-related gene in Lotus japonicus, rather than through the introduction of exogenous genes by transgenic techniques. A schematic of the flower senescence of Lotus japonicus from the perspective of the phytohormone regulatory network was provided based on transcriptome profiling of petals at different developmental stages. This study is informative for elucidating the molecular mechanism of delayed flower senescence in C416, and lays a foundation for candidate flower senescence gene identification in Lotus japonicus. It also provides another perspective for the improvement of flower longevity in legume plants by heavy-ion beam.

Gibberellins orchestrate panicle architecture mediated by DELLA-KNOX signalling in rice

Panicle architecture is a key determinant of grain yield in cereals, but the mechanisms governing panicle morphogenesis and organ development remain elusive. Here, we have identified a quantitative trait locus (qPA1) associated with panicle architecture using chromosome segment substitution lines from parents Nipponbare and 9311. The panicle length, branch number and grain number of Nipponbare were significantly higher than CSSL-9. Through map-based cloning and complementation tests, we confirmed that qPA1 was identical to SD1 (Semi Dwarf1), which encodes a gibberellin 20-oxidase enzyme participating in gibberellic acid (GA) biosynthesis. Transcript analysis revealed that SD1 was widely expressed during early panicle development. Analysis of sd1/osga20ox2 and gnp1/ osga20ox1 single and double mutants revealed that the two paralogous enzymes have non-redundant functions during panicle development, likely due to differences in spatiotemporal expression; GNP1 expression under control of the SD1 promoter could rescue the sd1 phenotype. The DELLA protein SLR1, a component of the GA signalling pathway, accumulated more highly in sd1 plants. We have demonstrated that SLR1 physically interacts with the meristem identity class I KNOTTED1-LIKE HOMEOBOX (KNOX) protein OSH1 to repress OSH1-mediated activation of downstream genes related to panicle development, providing a mechanistic link between gibberellin and panicle architecture morphogenesis.

From Green Revolution to Green Balance: The Nitrogen and Gibberellin Mediated Rice Tiller Growth

Rice tillering is an important characteristic that responds to both GA (gibberellin) and nitrogen-based fertilizers. How plants balance these two responses? A newly identified NGR5 (NITROGEN-MEDIATED TILLER GROWTH RESPONSE 5) protein reveals its important role in controlling the balance between GA-regulated dwarfism and nitrogen-regulated tillering. NGR5 directly interacts with PRC2 (Polycomb Repressive Complex 2) to form a repressive complex at the shoot branching inhibitory genes in nitrogen-dependent way, thereby repressing branching inhibitors and promoting tillering in response to nitrogen fertilizers. The GA receptor GID1 (GIBBERELLIN INSENSITIVE DWARF1) targets NGR5 for proteolysis by the 26S proteasome. The rice DELLA proteins of GA signaling way competitively inhibit GID1-NGR5 interaction, thereby protecting NGR5 from degradation and enhancing nitrogen-induced tiller number.

Germinating seed can sense low temperature for the floral transition and vernalization of winter rapeseed (Brassica rapa)

The hybrid production of winter rapeseed is limited by the difficult vernalization processes. Thus, floral regulation of winter rapeseed parental lines cannot be executed through selection of sowing time during hybrid production. Therefore, in this study, strong winter rapeseed was used as the material to analyse the floral transition mechanism of germinating seed vernalization. Results demonstrated that germinating seeds could sense low temperatures and complete vernalization following a low temperature treatment for 56.5 d with a 100 % vernalization rate. The regression equation between vernalization rate (y) and vernalization treatment days (x) was determined as y = 0.019x - 0.0765 (R² = 0.8529). When the vernalization treatment time was prolonged, the vernalization rate and fruiting ability increased rapidly, and variations were observed in the membrane lipid oxidation and physiological characteristics. Furthermore, at the prolonged treatment time of 10-50 d, the salicylic acid (SA) content continued to decrease, with values significantly lower than those of the control. SA content is significantly positively correlated with the level of BrFLC transcription and a significantly negatively correlated with the vernalization rate of germinating seeds. Moreover, the expressions of genes associated with SA biosynthesis, SA signal transduction, the flowering key negative regulators were suppressed and that of positive regulators were promoted during vernalization. These results suggest that SA as a floral repressor is involved in the regulation of the vernalization process of winter rapeseed germination seeds. In addition, SA may be related to the counting dosage of vernalization.

OsGRF6 interacts with SLR1 to regulate OsGA2ox1 expression for coordinating chilling tolerance and growth in rice

Low temperature is one of the abiotic stressors that affect growth and productivity of rice. The plant hormone gibberellin not only regulates growth and development but is also involved in stress defense. Our rice seedling experiments demonstrated that overexpression of SLR1, a gene that encodes the rice DELLA protein, enhanced chilling tolerance. In contrast, overexpression of the active GA synthesis gene OsGA20ox1 reduced chilling tolerance, indicating that weakening GA signaling promoted plant defense against cold stress. CoIP-MS and BiFC assays showed that SLR1 physically interacted with OsGRF6. After cold treatment and recovery, the survival rates of OsGRF6-overexpression lines and an osgrf6 mutant and its complementary lines indicated that OsGRF6 is a negative regulator of chilling tolerance in rice. The yeast one-hybrid, qRT-PCR, and transactivation assays showed that both SLR1 and OsGRF6 can bind to the promoter of the active GA catabolic gene OsGA2ox1, where SLR1 promoted and OsGRF6 suppressed OsGA2ox1 expression. At normal temperature, OsGRF6 was responsible for maintaining active GA levels by inhibiting OsGA2ox1. When rice seedlings were subjected to chilling stress, the repressive effect of OsGRF6 on OsGA2ox1 was released by cold-induced SLR1, which activated OsGA2ox1 expression to decrease the active GA levels, enhancing chilling tolerance. These results suggest that OsGRF6 is an important regulator in the balance between growth and chilling tolerance in rice.

A Cys2/His2 Zinc Finger Protein Acts as a Repressor of the Green Revolution Gene SD1/OsGA20ox2 in Rice (Oryza sativa L.)

Gibberellins (GAs) play important roles in the regulation of plant growth and development. The green revolution gene SD1 encoding gibberellin 20-oxidase 2 (GA20ox2) has been widely used in modern rice breeding. However, the molecular mechanism of how SD1/OsGA20ox2 expression is regulated remains unclear. Here, we report a Cys2/His2 zinc finger protein ZFP207 acting as a transcriptional repressor of OsGA20ox2. ZFP207 was mainly accumulated in young tissues and more specifically in culm nodes. ZFP207-overexpression (ZFP207OE) plants displayed semidwarfism phenotype and small grains by modulating cell length. RNA interference of ZFP207 caused increased plant height and grain length. The application of exogenous GA3 could rescue the semidwarf phenotype of ZFP207OE rice seedlings. Moreover, ZFP207 repressed the expression of OsGA20ox2 via binding to its promoter region. Taken together, ZFP207 acts as a transcriptional repressor of SD1/OsGA20ox2 and it may play a critical role in plant growth and development in rice through the fine-tuning of GA biosynthesis .

Functional characterization of a gibberellin F-box protein, PslSLY1, during plum fruit development

Fruit development is orchestrated by a complex network of interactions between hormone signaling pathways. The phytohormone gibberellin (GA) is known to regulate a diverse range of developmental processes; however, the mechanisms of GA action in perennial fruit species are yet to be elucidated. In the current study, a GA signaling gene PslSLY1, encoding a putative F-box protein that belongs to the SLY1 (SLEEPY1)/GID2 (gibberellin-insensitive dwarf2) gene family, was isolated from Japanese plum (Prunus salicina). PslSLY1 transcript abundance declined as fruit development progressed, along with potential negative feedback regulation of PslSLY1 by GA. Subcellular localization and protein-protein interaction assays suggested that PslSLY1 functions as an active GA signaling component that interacts with the ASK1 (Arabidopsis SKP1) subunit of an SCF-ubiquitin ligase complex and with PslDELLA repressors, in a GA-independent manner. By using a domain omission strategy, we illustrated that the F-box and C-terminal domains of PslSLY1 are essential for its interactions with the downstream GA signaling components. PslSLY1 overexpression in wild-type and Arabidopsissly1.10 mutant backgrounds resulted in a dramatic enhancement in overall plant growth, presumably due to triggered GA signaling. This includes germination characteristics, stem elongation, flower structure, and fertility. Overall, our findings shed new light on the GA strategy and signaling network in commercially important perennial crops.

Regulation of DELLA Proteins by Post-translational Modifications

DELLA proteins are the negative regulators of the gibberellin (GA) signaling pathway. GAs have a pervasive effect on plant physiology, influencing processes that span the entire life cycle of the plant. All the information encoded by GAs, either environmental or developmental in origin, is canalized through DELLAs, which modulate the activity of many transcription factors and transcriptional regulators. GAs unlock the signaling pathway by triggering DELLA polyubiquitination and degradation by the 26S proteasome. Recent reports indicate, however, that there are other pathways that trigger DELLA polyubiquitination and degradation independently of GAs. Moreover, results gathered during recent years indicate that other post-translational modifications (PTMs), namely phosphorylation, SUMOylation and glycosylation, modulate DELLA function. The convergence of several PTMs in DELLA therefore highlights the strict regulation to which these proteins are subject. In this review, we summarize these discoveries and discuss DELLA PTMs from an evolutionary perspective and examine the possibilities these and other post-translational regulations offer to improve DELLA-dependent agronomic traits.

Gibberellin Metabolism and Signaling: Targets for Improving Agronomic Performance of Crops

Gibberellins (GAs) are a class of tetracyclic diterpenoid phytohormones that regulate many aspects of plant development, including seed germination, stem elongation, leaf expansion, pollen maturation, and the development of flowers, fruits and seeds. During the past decades, the primary objective of crop breeding programs has been to increase productivity or yields. 'Green Revolution' genes that can produce semidwarf, high-yielding crops were identified as GA synthesis or response genes, confirming the value of research on GAs in improving crop productivity. The manipulation of GA status either by genetic alteration or by exogenous application of GA or GA biosynthesis inhibitors is often used to optimize plant growth and yields. In this review, we summarize the roles of GAs in major aspects of crop growth and development and present the possible targets for the fine-tuning of GA metabolism and signaling as a promising strategy for crop improvement.

Wheat Germination Is Dependent on Plant Target of Rapamycin Signaling

Germination is a process of seed sprouting that facilitates embryo growth. The breakdown of reserved starch in the endosperm into simple sugars is essential for seed germination and subsequent seedling growth. At the early stage of germination, gibberellic acid (GA) activates transcription factor GAMYB to promote de novo synthesis of isoforms of α-amylase in the aleurone layer and scutellar epithelium of the embryo. Here, we demonstrate that wheat germination is regulated by plant target of rapamycin (TOR) signaling. TOR is a central component of the essential-nutrient–dependent pathway controlling cell growth in all eukaryotes. It is known that rapamycin, a highly specific allosteric inhibitor of TOR, is effective in yeast and animal cells but ineffective in most of higher plants likely owing to structural differences in ubiquitous rapamycin receptor FKBP12. The action of rapamycin on wheat growth has not been studied. Our data show that rapamycin inhibits germination of wheat seeds and of their isolated embryos in a dose-dependent manner. The involvement of Triticum aestivum TOR (TaTOR) in wheat germination was consistent with the suppression of wheat embryo growth by specific inhibitors of the TOR kinase: pp242 or torin1. Rapamycin or torin1 interfered with GA function in germination because of a potent inhibitory effect on α-amylase and GAMYB gene expression. The TOR inhibitors selectively targeted the GA-dependent gene expression, whereas expression of the abscisic acid-dependent ABI5 gene was not affected by either rapamycin or torin1. To determine whether the TaTOR kinase activation takes place during wheat germination, we examined phosphorylation of a ribosomal protein, T. aestivum S6 kinase 1 (TaS6K1; a substrate of TOR). The phosphorylation of serine 467 (S467) in a hydrophobic motif on TaS6K1 was induced in a process of germination triggered by GA. Moreover, the germination-induced phosphorylation of TaS6K1 on S467 was dependent on TaTOR and was inhibited by rapamycin or torin1. Besides, a gibberellin biosynthesis inhibitor (paclobutrazol; PBZ) blocked not only α-amylase gene expression but also TaS6K1 phosphorylation in wheat embryos. Thus, a hormonal action of GA turns on the synthesis of α-amylase in wheat germination via activation of the TaTOR–S6K1 signaling pathway.

Systematic Analysis of Gibberellin Pathway Components in Medicago truncatula Reveals the Potential Application of Gibberellin in Biomass Improvement

Gibberellins (GAs), a class of phytohormones, act as an essential natural regulator of plant growth and development. Many studies have shown that GA is related to rhizobial infection and nodule organogenesis in legume species. However, thus far, GA metabolism and signaling components are largely unknown in the model legume Medicago truncatula. In this study, a genome-wide analysis of GA metabolism and signaling genes was carried out. In total 29 components, including 8 MtGA20ox genes, 2 MtGA3ox genes, 13 MtGA2ox genes, 3 MtGID1 genes, and 3 MtDELLA genes were identified in M. truncatula genome. Expression profiles revealed that most members of MtGAox, MtGID1, and MtDELLA showed tissue-specific expression patterns. In addition, the GA biosynthesis and deactivation genes displayed a feedback regulation on GA treatment, respectively. Yeast two-hybrid assays showed that all the three MtGID1s interacted with MtDELLA1 and MtDELLA2, suggesting that the MtGID1s are functional GA receptors. More importantly, M. truncatula exhibited increased plant height and biomass by ectopic expression of the MtGA20ox1, suggesting that enhanced GA response has the potential for forage improvement.

Transcriptome Analysis in Male Strobilus Induction by Gibberellin Treatment in Cryptomeria japonica D. Don

The plant hormone gibberellin (GA) is known to regulate elongating growth, seed germination, and the initiation of flower bud formation, and it has been postulated that GAs originally had functions in reproductive processes. Studies on the mechanism of induction of flowering by GA have been performed in Arabidopsis and other model plants. In coniferous trees, reproductive organ induction by GAs is known to occur, but there are few reports on the molecular mechanism in this system. To clarify the gene expression dynamics of the GA induction of the male strobilus in Cryptomeria japonica, we performed comprehensive gene expression analysis using a microarray. A GA-treated group and a nontreated group were allowed to set, and individual trees were sampled over a 6-week time course. A total of 881 genes exhibiting changed expression was identified. In the GA-treated group, genes related to ‘stress response’ and to ‘cell wall’ were initially enriched, and genes related to ‘transcription’ and ‘transcription factor activity’ were enriched at later stages. This analysis also clarified the dynamics of the expression of genes related to GA signaling transduction following GA treatment, permitting us to compare and contrast with the expression dynamics of genes implicated in signal transduction responses to other plant hormones. These results suggested that various plant hormones have complex influences on the male strobilus induction. Additionally, principal component analysis (PCA) using expression patterns of the genes that exhibited sequence similarity with flower bud or floral organ formation-related genes of Arabidopsis was performed. PCA suggested that gene expression leading to male strobilus formation in C. japonica became conspicuous within one week of GA treatment. Together, these findings help to clarify the evolution of the mechanism of induction of reproductive organs by GA.

A Novel AP2/ERF Transcription Factor, OsRPH1, Negatively Regulates Plant Height in Rice

The APETALA 2/ethylene response factors (AP2/ERF) are widespread in the plant kingdom and play essential roles in regulating plant growth and development as well as defense responses. In this study, a novel rice AP2/ERF transcription factor gene, OsRPH1, was isolated and functionally characterized. OsRPH1 falls into group-IVa of the AP2/ERF family. OsRPH1 protein was found to be localized in the nucleus and possessed transcriptional activity. Overexpression of OsRPH1 resulted in a decrease in plant height and length of internode and leaf sheath as well as other abnormal characters in rice. The length of the second leaf sheath of OsRPH1-overexpressing (OE) plants recovered to that of Kitaake (non-transgenic recipient) in response to exogenous gibberellin A₃ (GA₃) application. The expression of GA biosynthesis genes (OsGA20ox1-OsGA20ox4, OsGA3ox1, and OsGA3ox2) was significantly downregulated, whereas that of GA inactivation genes (OsGA2ox7, OsGA2ox9, and OsGA2ox10) was significantly upregulated in OsRPH1-OE plants. Endogenous bioactive GA contents significantly decreased in OsRPH1-OE plants. OsRPH1 interacted with a blue light receptor, OsCRY1b, in a blue light-dependent manner. Taken together, our results demonstrate that OsRPH1 negatively regulates plant height and bioactive GA content by controlling the expression of GA metabolism genes in rice. OsRPH1 is involved in blue light inhibition of leaf sheath elongation by interacting with OsCRY1b.

Origin and evolution of gibberellin signaling and metabolism in plants

Gibberellins modulate multiple aspects of plant behavior. The molecular mechanism by which these hormones are perceived and how this information is translated into transcriptional changes has been elucidated in vascular plants: gibberellins are perceived by the nuclear receptor GID1, which then interacts with the DELLA nuclear proteins and promote their degradation, resulting in the modification of the activity of transcription factors with which DELLAs interact physically. However, several important questions are still pending: how does a single molecule perform such a vast array of functions along plant development? What property do gibberellins add to plant behavior? A closer look at gibberellin action from an evolutionary perspective can help answer these questions. DELLA proteins are conserved in all land plants, and predate the emergence of a full gibberellin metabolic pathway and the GID1 receptor in the ancestor of vascular plants. The origin of gibberellin signaling is linked to the exaptation by GID1 of the N-terminal domain in DELLA, which already acted as a transcriptional coactivator domain in the ancestral DELLA proteins. At least the ability to control plant growth seems to be encoded already in the ancestral DELLA protein too, suggesting that gibberellins' functional diversity is the direct consequence of DELLA protein activity. Finally, comparative network analysis suggests that gibberellin signaling increases the coordination of transcriptional responses, providing a theoretical framework for the role of gibberellins in plant adaptation at the evolutionary scale, which further needs experimental testing.

Cyclophilin OsCYP20-2 with a novel variant integrates defense and cell elongation for chilling response in rice

Coordinating stress defense and plant growth is a survival strategy for adaptation to different environments that contains a series of processes, such as, cell growth, division and differentiation. However, little is known about the coordination mechanism for protein conformation change. A cyclophilin OsCYP20-2 with a variant interacts with SLENDER RICE1 (SLR1) and OsFSD2 in the nucleus and chloroplasts, respectively, to integrate chilling tolerance and cell elongation in rice (Oryza sativa) (FSD2, Fe-superoxide dismutase 2). Mass spectrum assay showed that OsNuCYP20-2 localized at the nucleus (nuclear located OsCYP20-2) was a new variant of OsCYP20-2 that truncated 71 amino-acid residues in N-terminal. The loss-of function OsCYP20-2 mutant showed sensitivity to chilling stress with accumulation of extra reactive oxygen species (ROS). In chloroplasts, the full-length OsCYP20-2 promotes OsFSD2 forming homodimers which enhance its activity, eliminating the accumulation of ROS under chilling stress. However, the mutant had shorter epidermal cells in comparison with wild-type Hwayoung (HY). In the nucleus, OsCYP20-2 caused conformation change of SLR1 to promote its degradation for cell elongation. Our data reveal a cyclophilin with a variant with dual-localization in chloroplasts and the nucleus, which mediate chilling tolerance and cell elongation.

Diverse and dynamic roles of F-box proteins in plant biology

The SCF complex is a widely studied multi-subunit ring E3 ubiquitin ligase that tags targeted proteins with ubiquitin for protein degradation by the ubiquitin 26S-proteasome system (UPS). The UPS is an important system that generally keeps cellular events tightly regulated by purging misfolded or damaged proteins and selectively degrading important regulatory proteins. The specificity of this post-translational regulation is controlled by F-box proteins (FBPs) via selective recognition of a protein-protein interaction motif at the C-terminal domain. Hence, FBPs are pivotal proteins in determining the plant response in multiple scenarios. It is not surprising that the FBP family is one of the largest protein families in the plant kingdom. In this review, the roles of FBPs, specifically in plants, are compiled to provide insights into their involvement in secondary metabolites, plant stresses, phytohormone signalling, plant developmental processes and miRNA biogenesis.

Illumina-based transcriptomic analysis on recalcitrant seeds of Panax notoginseng for the dormancy release during the after-ripening process

Panax notoginseng (Burk) F.H. Chen is an economically and medicinally important plant of the family Araliacease, with seed dormancy being a key factor limiting the extended cultivation of P. notoginseng. The seeds belong to the morphophysiological dormancy (MPD) group, and it has also been described as the recalcitrant seed. To date, the molecular mechanism of dormancy release in the recalcitrant seed of P. notoginseng is unknown. In the present study, the transcript profiles of seeds from different after-ripening stages (0, 20, 40 and 60 days) were investigated using Illumina Hiseq 2500 technology. 91 979 946 clean reads were generated, and 81 575 unigenes were annotated in at least one database. In addition, the differentially expressed genes (DEGs) were identified by the pairwise comparisons. We screened out 2483 DEGs by the three key groups of 20 days vs 0 d, 40 d vs 0 d and 60 d vs 0 d. The DEGs were analyzed by gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway annotation. Meanwhile, we obtained 78 DEGs related to seeds dormancy release at different after-ripening stages of P. notoginseng, of which 15 DEGs were associated with abscisic acid and gibberellin. 26 DEGs that encode late embryogenesis abundant protein and antioxidant enzyme were correlated with desiccation tolerance in seeds. In summary, the results obtained here showed that PECTINESTERASE-2-LIKE, GA-INSENSITIVE, ENT-KAURENE SYNTHASE, PROTEIN PHOSPHATASE 2C, GIBBERELLIN 2-BETA-DIOXYGENASE, SUPEROXIDE DISMUTASE, L-ASCORBATE PEROXIDASE, CATALASE, LATE EMBRYOGENESIS ABUNDANT PROTEIN DC3 and DEHYDRIN 9 were potentially involved in dormancy release and desiccation sensitivity of P. notoginseng seeds. The data might provide a basis for researches on MPD.

Comparative gene expression profile analysis of ovules provides insights into Jatropha curcas L. ovule development

Jatropha curcas, an economically important biofuel feedstock with oil-rich seeds, has attracted considerable attention among researchers in recent years. Nevertheless, valuable information on the yield component of this plant, particularly regarding ovule development, remains scarce. In this study, transcriptome profiles of anther and ovule development were established to investigate the ovule development mechanism of J. curcas. In total, 64,325 unigenes with annotation were obtained, and 1723 differentially expressed genes (DEGs) were identified between different stages. The DEG analysis showed the participation of five transcription factor families (bHLH, WRKY, MYB, NAC and ERF), five hormone signaling pathways (auxin, gibberellic acid (GA), cytokinin, brassinosteroids (BR) and jasmonic acid (JA)), five MADS-box genes (AGAMOUS-2, AGAMOUS-1, AGL1, AGL11, and AGL14), SUP and SLK3 in ovule development. The role of GA and JA in ovule development was evident with increases in flower buds during ovule development: GA was increased approximately twofold, and JA was increased approximately sevenfold. In addition, the expression pattern analysis using qRT-PCR revealed that CRABS CLAW and AGAMOUS-2 were also involved in ovule development. The upregulation of BR signaling genes during ovule development might have been regulated by other phytohormone signaling pathways through crosstalk. This study provides a valuable framework for investigating the regulatory networks of ovule development in J. curcas.