CYP72B1 inactivates brassinosteroid hormones: an intersection between photomorphogenesis and plant steroid signal transduction

Unravelling the biostimulant activity of a protein hydrolysate in lettuce plants under optimal and low N availability: a multi-omics approach

The application of protein hydrolysates (PH) biostimulants is considered a promising approach to promote crop growth and resilience against abiotic stresses. Nevertheless, PHs bioactivity depends on both the raw material used for their preparation and the molecular fraction applied. The present research aimed at investigating the molecular mechanisms triggered by applying a PH and its fractions on plants subjected to nitrogen limitations. To this objective, an integrated transcriptomic-metabolomic approach was used to assess lettuce plants grown under different nitrogen levels and treated with either the commercial PH Vegamin® or its molecular fractions PH1(>10 kDa), PH2 (1-10 kDa) and PH3 (<1 kDa). Regardless of nitrogen provision, biostimulant application enhanced lettuce biomass, likely through a hormone-like activity. This was confirmed by the modulation of genes involved in auxin and cytokinin synthesis, mirrored by an increase in the metabolic levels of these hormones. Consistently, PH and PH3 upregulated genes involved in cell wall growth and plasticity. Furthermore, the accumulation of specific metabolites suggested the activation of a multifaceted antioxidant machinery. Notwithstanding, the modulation of stress-response transcription factors and genes involved in detoxification processes was observed. The coordinated action of these molecular entities might underpin the increased resilience of lettuce plants against nitrogen-limiting conditions. In conclusion, integrating omics techniques allowed the elucidation of mechanistic aspects underlying PH bioactivity in crops. Most importantly, the comparison of PH with its fraction PH3 showed that, except for a few peculiarities, the effects induced were equivalent, suggesting that the highest bioactivity was ascribable to the lightest molecular fraction.

Overexpression of a BR inactivating enzyme gene GhPAG1 impacts eggplant fruit development and anthocyanin accumulation mainly by altering hormone homeostasis

Brassinosteroids (BRs) function importantly in plant growth and development, but the roles in regulating fruit development and anthocyanin pigmentation remain unclear. Eggplant (Solanum melongena L.) is an important Solanaceae vegetable crop rich in anthocyanins. The fruit size and coloration are important agronomic traits for eggplant breeding. In this study, transgenic eggplant exhibiting endogenous BRs deficiency was created by overexpressing a heterologous BRs-inactivating enzyme gene GhPAG1 driven by CaMV 35 S promoter. 35 S::GhPAG1 eggplant exhibited severe dwarfism, reduced fruit size, and less anthocyanin accumulation. Microscopic observation showed that the cell size of 35 S::GhPAG1 eggplant was significantly reduced compared to WT. Furthermore, the levels of IAA, ME-IAA, and active JAs (JA, JA-ILE, and H2JA) all decreased in 35 S::GhPAG1 eggplant fruit. RNA-Seq analyses showed a decrease in the expression of genes involved in cell elongation, auxin signaling, and JA signaling. Besides, overexpression of GhPAG1 significantly downregulated anthocyanin biosynthetic genes and associated transcription regulators. Altogether, these results strongly suggest that endogenous brassinosteroid deficiency arising from GhPAG1 overexpression impacts eggplant fruit development and anthocyanin coloration mainly by altering hormone homeostasis.

Brassinosteroid catabolic enzyme CYP734A129 regulates the morphologies of leaves and floral organs in woodland strawberry

Brassinosteroids (BRs) play critical roles in plant growth and development and regulate many important agronomic traits. However, the functions of BRs in strawberry are unclear. This study identified two mutants, named P6 and R87, in woodland strawberry (Fragaria vesca) from EMS mutagenesis populations that exhibit narrow leaves, petals and sepals. Mapping by sequencing and genetic studies revealed that the F. vesca CYP734A129, encoding a putative BR catabolic enzyme, is the causative gene for both P6 and R87. Overexpression of CYP734A129 in both F. vesca and Arabidopsis causes a severe dwarf phenotype, and the BRI1-EMS-SUPPRESSOR 1 (BES1) protein is less abundant in the CYP734A129-overexpressing Arabidopsis seedlings. This suggests that CYP734A129 is functionally conserved with CYP734A1, as a BR-inactivating enzyme. Transcriptome analysis of young leaves revealed that four BR biosynthetic genes were significantly downregulated in P6 (cyp734a129), and photosynthesis-related genes were highly enriched among the up-regulated genes in P6 compared to the wild type. This further supports that CYP734A129 inactivates BRs in F. vesca. Furthermore, we showed that mutations in CYP734A129 do not affect fruit shape and color during ripening in strawberry. Overall, our results suggest that F. vesca CYP734A129 is a BR catabolic enzyme, and provide insights into the roles of CYP734A129 in strawberry.

Genomic evidence supports the genetic convergence of a supergene controlling the distylous floral syndrome

Heterostyly, a plant sexual polymorphism controlled by the S-locus supergene, has evolved numerous times among angiosperm lineages and represents a classic example of convergent evolution in form and function. Determining whether underlying molecular convergence occurs could provide insights on constraints to floral evolution. Here, we investigated S-locus genes in distylous Gelsemium (Gelsemiaceae) to determine whether there is evidence of molecular convergence with unrelated distylous species. We used several approaches, including anatomical measurements of sex-organ development and transcriptome and whole-genome sequencing, to identify components of the S-locus supergene. We also performed evolutionary analysis with candidate S-locus genes and compared them with those reported in Primula and Turnera. The candidate S-locus supergene of Gelsemium contained four genes, of which three appear to have originated from gene duplication events within Gelsemiaceae. The style-length genes GeCYP in Gelsemium and CYP734A50 in Primula likely arose from duplication of the same gene, CYP734A1. Three out of four S-locus genes in Gelsemium elegans were hemizygous, as previously reported in Primula and Turnera. We provide genomic evidence on the genetic convergence of the supergene underlying distyly among distantly related angiosperm lineages and help to illuminate the genetic architecture involved in the evolution of heterostyly.

The fine mapping of dwarf gene Rht5 in bread wheat and its effects on plant height and main agronomic traits

Rht5 was narrowed to an approximately 1 Mb interval and had pleiotropic effects on plant height, spike length and grain size. TraesCS3B02G025600 was predicted as the possible candidate gene. Plant height is an important component related to plant architecture, lodging resistance, and yield performance. The utilization of dwarf genes has made great contributions to wheat breeding and production. In this study, two F₂ populations derived from the crosses of Jinmai47 and Ningchun45 with Marfed M were employed to identify the genetic region of reduce plant height 5 (Rht5), and their derived lines were used to evaluate its effects on plant height and main agronomic traits. Rht5 was fine-mapped between markers Kasp-25 and Kasp-23, in approximately 1 Mb region on chromosome 3BS, which harbored 17 high-confidence annotated genes based on the reference genome of Chinese Spring (IWGSC RefSeq v1.1). TraesCS3B02G025600 were predicted as the possible candidate gene based on its differential expression and sequence variation between dwarf and tall lines and parents. The results of phenotypic evaluation showed that Rht5 had pleiotropic effects on plant height, spike length, culm diameter, grain size and grain yield. The plant height of Rht5 dwarf lines was reduced by an average of 32.67% (32.53 cm) and 27.84% (33.62 cm) in the Jinmai47 and Ningchun45 population, respectively. While Rht5 showed significant and negative pleiotropic effects on culm diameter, aboveground biomass, grain yield, spike length, spikelet number, grain number per spike, grain size, grain weight and filling degree of basal second internode. The culm lodging resistance index (CLRI) of dwarf lines was significantly higher than that of tall lines in the two population. In conclusion, these results lay a foundation for understanding the dwarfing mechanism of Rht5.

Combining Fine Mapping, Whole-Genome Re-Sequencing, and RNA-Seq Unravels Candidate Genes for a Soybean Mutant with Short Petioles and Weakened Pulvini

A short petiole is an important agronomic trait for the development of plant ideotypes with high yields. However, the genetic basis underlying this trait remains unclear. Here, we identified and characterized a novel soybean mutant with short petioles and weakened pulvini, designated as short petioles and weakened pulvini (spwp). Compared with the wild type (WT), the spwp mutant displayed shortened petioles, owing to the longitudinally decreased cell length, and exhibited a smaller pulvinus structure due to a reduction in motor cell proliferation and expansion. Genetic analysis showed that the phenotype of the spwp mutant was controlled by two recessive nuclear genes, named as spwp1 and spwp2. Using a map-based cloning strategy, the spwp1 locus was mapped in a 183 kb genomic region on chromosome 14 between markers S1413 and S1418, containing 15 annotated genes, whereas the spwp2 locus was mapped in a 195 kb genomic region on chromosome 11 between markers S1373 and S1385, containing 18 annotated genes. Based on the whole-genome re-sequencing and RNA-seq data, we identified two homologous genes, Glyma.11g230300 and Glyma.11g230600, as the most promising candidate genes for the spwp2 locus. In addition, the RNA-seq analysis revealed that the expression levels of genes involved in the cytokinin and auxin signaling transduction networks were altered in the spwp mutant compared with the WT. Our findings provide new gene resources for insights into the genetic mechanisms of petiole development and pulvinus establishment, as well as soybean ideotype breeding.

Transcriptomic Changes in Internode Explants of Stinging Nettle during Callogenesis

Callogenesis, the process during which explants derived from differentiated plant tissues are subjected to a trans-differentiation step characterized by the proliferation of a mass of cells, is fundamental to indirect organogenesis and the establishment of cell suspension cultures. Therefore, understanding how callogenesis takes place is helpful to plant tissue culture, as well as to plant biotechnology and bioprocess engineering. The common herbaceous plant stinging nettle (Urtica dioica L.) is a species producing cellulosic fibres (the bast fibres) and a whole array of phytochemicals for pharmacological, nutraceutical and cosmeceutical use. Thus, it is of interest as a potential multi-purpose plant. In this study, callogenesis in internode explants of a nettle fibre clone (clone 13) was studied using RNA-Seq to understand which gene ontologies predominate at different time points. Callogenesis was induced with the plant growth regulators α-napthaleneacetic acid (NAA) and 6-benzyl aminopurine (BAP) after having determined their optimal concentrations. The process was studied over a period of 34 days, a time point at which a well-visible callus mass developed on the explants. The bioinformatic analysis of the transcriptomic dataset revealed specific gene ontologies characterizing each of the four time points investigated (0, 1, 10 and 34 days). The results show that, while the advanced stage of callogenesis is characterized by the iron deficiency response triggered by the high levels of reactive oxygen species accumulated by the proliferating cell mass, the intermediate and early phases are dominated by ontologies related to the immune response and cell wall loosening, respectively.

Cytochrome P450 Enzymes as Key Drivers of Alkaloid Chemical Diversification in Plants

Plants produce more than 20,000 nitrogen-containing heterocyclic metabolites called alkaloids. These chemicals serve numerous eco-physiological functions in the plants as well as medicines and psychedelic drugs for human for thousands of years, with the anti-cancer agent vinblastine and the painkiller morphine as the best-known examples. Cytochrome P450 monooxygenases (P450s) play a key role in generating the structural variety that underlies this functional diversity of alkaloids. Most alkaloid molecules are heavily oxygenated thanks to P450 enzymes' activities. Moreover, the formation and re-arrangement of alkaloid scaffolds such as ring formation, expansion, and breakage that contribute to their structural diversity and bioactivity are mainly catalyzed by P450s. The fast-expanding genomics and transcriptomics databases of plants have accelerated the investigation of alkaloid metabolism and many players behind the complexity and uniqueness of alkaloid biosynthetic pathways. Here we discuss recent discoveries of P450s involved in the chemical diversification of alkaloids and how these inform our approaches in understanding plant evolution and producing plant-derived drugs.

Two ATAF transcription factors ANAC102 and ATAF1 contribute to the suppression of cytochrome P450-mediated brassinosteroid catabolism in Arabidopsis

PHYB ACTIVATION TAGGED SUPPRESSOR 1 (BAS1) and SUPPRESSOR OF PHYB-4 7 (SOB7) are two cytochrome P450 enzymes that inactivate brassinosteroids (BRs) in Arabidopsis. The NAC transcription factor (TF) ATAF2 (ANAC081) and the core circadian clock regulator CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) both suppress the expression of BAS1 and SOB7 via direct promoter binding. Additionally, BRs cause feedback suppression on ATAF2 expression. Here, we report that two ATAF-subgroup TFs, ANAC102 and ATAF1 (ANAC002), also contribute to the transcriptional suppression of BAS1 and SOB7. ANAC102 and ATAF1 gene-knockout mutants exhibit elevated expression of both BAS1 and SOB7, expanded tissue-level accumulation of their protein products and reduced hypocotyl growth in response to exogenous BR treatments. Similar to ATAF2, both ANAC102 and ATAF1 are transcriptionally suppressed by BRs and white light. Neither BAS1 nor SOB7 expression is further elevated in ATAF double or triple mutants, suggesting that the suppression effect of these three ATAFs is not additive. In addition, ATAF single, double, and triple mutants have similar levels of BR responsiveness with regard to hypocotyl elongation. ATAF2, ANAC102, ATAF1, and CCA1 physically interact with itself and each other, suggesting that they may coordinately suppress BAS1 and SOB7 expression via protein-protein interactions. Despite the absence of CCA1-binding elements in their promoters, ANAC102 and ATAF1 have similar transcript circadian oscillation patterns as that of CCA1, suggesting that these two ATAF genes may be indirectly regulated by the circadian clock.

Local brassinosteroid biosynthesis enables optimal root growth

Brassinosteroid (BR) hormones are indispensable for root growth and control both cell division and cell elongation through the establishment of an increasing signalling gradient along the longitudinal root axis. Because of their limited mobility, the importance of BR distribution in achieving a signalling maximum is largely overlooked. Expression pattern analysis of all known BR biosynthetic enzymes revealed that not all cells in the Arabidopsis thaliana root possess full biosynthetic machinery, and that completion of biosynthesis relies on cell-to-cell movement of hormone precursors. We demonstrate that BR biosynthesis is largely restricted to the root elongation zone, where it overlaps with BR signalling maxima. Moreover, optimal root growth requires hormone concentrations to be low in the meristem and high in the root elongation zone, attributable to increased biosynthesis. Our finding that spatiotemporal regulation of hormone synthesis results in local hormone accumulation provides a paradigm for hormone-driven organ growth in the absence of long-distance hormone transport in plants.

Brassinosteroid homeostasis is critical for the functionality of the Medicago truncatula pulvinus

Many plant species open their leaves during the daytime and close them at night as if sleeping. This leaf movement is known as nyctinasty, a unique and intriguing phenomenon that been of great interest to scientists for centuries. Nyctinastic leaf movement occurs widely in leguminous plants, and is generated by a specialized motor organ, the pulvinus. Although a key determinant of pulvinus development, PETIOLULE-LIKE PULVINUS (PLP), has been identified, the molecular genetic basis for pulvinus function is largely unknown. Here, through an analysis of knockout mutants in barrelclover (Medicago truncatula), we showed that neither altering brassinosteroid (BR) content nor blocking BR signal perception affected pulvinus determination. However, BR homeostasis did influence nyctinastic leaf movement. BR activity in the pulvinus is regulated by a BR-inactivating gene PHYB ACTIVATION TAGGED SUPPRESSOR1 (BAS1), which is directly activated by PLP. A comparative analysis between M. truncatula and the non-pulvinus forming species Arabidopsis and tomato (Solanum lycopersicum) revealed that PLP may act as a factor that associates with unknown regulators in pulvinus determination in M. truncatula. Apart from exposing the involvement of BR in the functionality of the pulvinus, these results have provided insights into whether gene functions among species are general or specialized.

The Turnera Style S-Locus Gene TsBAHD Possesses Brassinosteroid-Inactivating Activity When Expressed in Arabidopsis thaliana

Heterostyly distinct hermaphroditic floral morphs enforce outbreeding. Morphs differ structurally, promote cross-pollination, and physiologically block self-fertilization. In Turnera the self-incompatibility (S)-locus controlling heterostyly possesses three genes specific to short-styled morph genomes. Only one gene, TsBAHD, is expressed in pistils and this has been hypothesized to possess brassinosteroid (BR)-inactivating activity. We tested this hypothesis using heterologous expression in Arabidopsis thaliana as a bioassay, thereby assessing growth phenotype, and the impacts on the expression of endogenous genes involved in BR homeostasis and seedling photomorphogenesis. Transgenic A. thaliana expressing TsBAHD displayed phenotypes typical of BR-deficient mutants, with phenotype severity dependent on TsBAHD expression level. BAS1, which encodes an enzyme involved in BR inactivation, was downregulated in TsBAHD-expressing lines. CPD and DWF, which encode enzymes involved in BR biosynthesis, were upregulated. Hypocotyl growth of TsBAHD dwarfs responded to application of brassinolide in light and dark in a manner typical of plants over-expressing genes encoding BR-inactivating activity. These results provide empirical support for the hypothesis that TsBAHD possesses BR-inactivating activity. Further this suggests that style length in Turnera is controlled by the same mechanism (BR inactivation) as that reported for Primula, but using a different class of enzyme. This reveals interesting convergent evolution in a biochemical mechanism to regulate floral form in heterostyly.

Self-transcriptional repression of the Arabidopsis NAC transcription factor ATAF2 and its genetic interaction with phytochrome A in modulating seedling photomorphogenesis

The NAC transcription factor ATAF2 suppresses its own transcription via self-promoter binding. ATAF2 genetically interacts with the circadian regulator CCA1 and phytochrome A to modulate seedling photomorphogenesis in Arabidopsis thaliana. ATAF2 (ANAC081) is a NAC (NAM, ATAF and CUC) transcription factor (TF) that participates in the regulation of disease resistance, stress tolerance and hormone metabolism in Arabidopsis thaliana. We previously reported that ATAF2 promotes Arabidopsis hypocotyl growth in a light-dependent manner via transcriptionally suppressing the brassinosteroid (BR)-inactivating cytochrome P450 genes BAS1 (CYP734A1, formerly CYP72B1) and SOB7 (CYP72C1). Assays using low light intensities suggest that the photoreceptor phytochrome A (PHYA) may play a more critical role in ATAF2-regulated photomorphogenesis than phytochrome B (PHYB) and cryptochrome 1 (CRY1). In addition, ATAF2 is also regulated by the circadian clock. The core circadian TF CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) physically interacts with ATAF2 at the DNA-protein and protein-protein levels, and both differentially suppress BAS1- and SOB7-mediated BR catabolism. In this research, we show that ATAF2 can bind its own promoter as a transcriptional self-repressor. This self-feedback-suppression loop is a typical feature of multiple circadian-regulated genes. Additionally, ATAF2 and CCA1 synergistically suppress seedling photomorphogenesis as reflected by the light-dependent hypocotyl growth analysis of their single and double gene knock-out mutants. Similar fluence-rate response assays using ATAF2 and photoreceptor (PHYB, CRY1 and PHYA) knock-out mutants demonstrate that PHYA is required for ATAF2-regulated photomorphogenesis in a wide range of light intensities. Furthermore, disruption of PHYA can suppress the BR-insensitive hypocotyl-growth phenotype of ATAF2 loss-of-function seedlings in the light, but not in darkness. Collectively, our results provide a genetic interaction synopsis of the circadian-clock-photomorphogenesis-BR integration node involving ATAF2, CCA1 and PHYA.

Discovery and modification of cytochrome P450 for plant natural products biosynthesis

Cytochrome P450s are widespread in nature and play key roles in the diversification and functional modification of plant natural products. Over the last few years, there has been remarkable progress in plant P450s identification with the rapid development of sequencing technology, "omics" analysis and synthetic biology. However, challenges still persist in respect of crystal structure, heterologous expression and enzyme engineering. Here, we reviewed several research hotspots of P450 enzymes involved in the biosynthesis of plant natural products, including P450 databases, gene mining, heterologous expression and protein engineering.

Emerging Molecular Links Between Plant Photomorphogenesis and Virus Resistance

Photomorphogenesis refers to photoreceptor-mediated morphological changes in plant development that are triggered by light. Multiple photoreceptors and transcription factors (TFs) are involved in the molecular regulation of photomorphogenesis. Likewise, light can also modulate the outcome of plant-virus interactions since both photosynthesis and many viral infection events occur in the chloroplast. Despite the apparent association between photosynthesis and virus infection, little is known about whether there are also interplays between photomorphogenesis and plant virus resistance. Recent research suggests that plant-virus interactions are potentially regulated by several photoreceptors and photomorphogenesis regulators, including phytochromes A and B (PHYA and PHYB), cryptochromes 2 (CRY2), phototropin 2 (PHOT2), the photomorphogenesis repressor constitutive photomorphogenesis 1 (COP1), the NAM, ATAF, and CUC (NAC)-family TF ATAF2, the Aux/IAA protein phytochrome-associated protein 1 (PAP1), the homeodomain-leucine zipper (HD-Zip) TF HAT1, and the core circadian clock component circadian clock associated 1 (CCA1). Particularly, the plant growth promoting brassinosteroid (BR) hormones play critical roles in integrating the regulatory pathways of plant photomorphogenesis and viral defense. Here, we summarize the current understanding of molecular mechanisms linking plant photomorphogenesis and defense against viruses, which represents an emerging interdisciplinary research topic in both molecular plant biology and virology.

Auxin treatment of grapevine (Vitis vinifera L.) berries delays ripening onset by inhibiting cell expansion

Auxin treatment of grape (Vitis vinifera L.) berries delays ripening by inducing changes in gene expression and cell wall metabolism and could combat some deleterious climate change effects. Auxins are inhibitors of grape berry ripening and their application may be useful to delay harvest to counter effects of climate change. However, little is known about how this delay occurs. The expression of 1892 genes was significantly changed compared to the control during a 48 h time-course where the auxin 1-naphthaleneacetic acid (NAA) was applied to pre-veraison grape berries. Principal component analysis showed that the control and auxin-treated samples were most different at 3 h post-treatment when approximately three times more genes were induced than repressed by NAA. There was considerable cross-talk between hormone pathways, particularly between those of auxin and ethylene. Decreased expression of genes encoding putative cell wall catabolic enzymes (including those involved with pectin) and increased expression of putative cellulose synthases indicated that auxins may preserve cell wall structure. This was confirmed by immunochemical labelling of berry sections using antibodies that detect homogalacturonan (LM19) and methyl-esterified homogalacturonan (LM20) and by labelling with the CMB3a cellulose-binding module. Comparison of the auxin-induced changes in gene expression with the pattern of these genes during berry ripening showed that the effect on transcription is a mix of changes that may specifically alter the progress of berry development in a targeted manner and others that could be considered as non-specific changes. Several lines of evidence suggest that cell wall changes and associated berry softening are the first steps in ripening and that delaying cell expansion can delay ripening providing a possible mechanism for the observed auxin effects.

PcDWF1, a pear brassinosteroid biosynthetic gene homologous to AtDWARF1, affected the vegetative and reproductive growth of plants

BACKGROUND

The steroidal hormones brassinosteroids (BRs) play important roles in plant growth and development. The pathway and genes involved in BR biosynthesis have been identified primarily in model plants like Arabidopsis, but little is known about BR biosynthesis in woody fruits such as pear.

RESULTS

In this study, we found that applying exogenous brassinolide (BL) could significantly increase the stem growth and rooting ability of Pyrus ussuriensis. PcDWF1, which had a significantly lower level of expression in the dwarf-type pear than in the standard-type pear, was cloned for further analysis. A phylogenetic analysis showed that PcDWF1 was a pear brassinosteroid biosynthetic gene that was homologous to AtDWARF1. The subcellular localization analysis indicated that PcDWF1 was located in the plasma membrane. Overexpression of PcDWF1 in tobacco (Nicotiana tabacum) or pear (Pyrus ussuriensis) plants promoted the growth of the stems, which was caused by a larger cell size and more developed xylem than those in the control plants, and the rooting ability was significantly enhanced. In addition to the change in vegetative growth, the tobacco plants overexpressing PcDWF1 also had a delayed flowering time and larger seed size than did the control tobacco plants. These phenotypes were considered to result from the higher BL contents in the transgenic lines than in the control tobacco and pear plants.

CONCLUSIONS

Taken together, these results reveal that the pear BR biosynthetic gene PcDWF1 affected the vegetative and reproductive growth of Pyrus ussuriensis and Nicotiana tabacum and could be characterized as an important BR biosynthetic gene in perennial woody fruit plants.

Roles of Brassinosteroids in Plant Reproduction

Brassinosteroids (BRs) are a group of steroid hormones, essentially important for plant development and growth. BR signaling functions to promote cell expansion and cell division, and plays a role in etiolation and reproduction. As the phytohormone originally identified in the pollen grains of Brassica napus, BR promotes the elongation of stigma. Recent studies have revealed that BR is also critical for floral transition, inflorescence stem architecture formation and other aspects of plant reproductive processes. In this review, we focus on the current understanding of BRs in plant reproduction, the spatial and temporal control of BR signaling, and the downstream molecular mechanisms in both the model plant Arabidopsis and crops. The crosstalk of BR with environmental factors and other hormones in reproduction will also be discussed.

CIRCADIAN CLOCK ASSOCIATED 1 and ATAF2 differentially suppress cytochrome P450-mediated brassinosteroid inactivation

Brassinosteroids (BRs) are a group of steroid hormones regulating plant growth and development. Since BRs do not undergo transport among plant tissues, their metabolism is tightly regulated by transcription factors (TFs) and feedback loops. BAS1 (CYP734A1, formerly CYP72B1) and SOB7 (CYP72C1) are two BR-inactivating cytochrome P450s identified in Arabidopsis thaliana. We previously found that a TF ATAF2 (ANAC081) suppresses BAS1 and SOB7 expression by binding to the Evening Element (EE) and CIRCADIAN CLOCK ASSOCIATED 1 (CCA1)-binding site (CBS) on their promoters. Both the EE and CBS are known binding targets of the circadian regulatory protein CCA1. Here, we confirm that CCA1 binds the EE and CBS motifs on BAS1 and SOB7 promoters, respectively. Elevated accumulations of BAS1 and SOB7 transcripts in the CCA1 null mutant cca1-1 indicate that CCA1 is a repressor of their expression. When compared with either cca1-1 or the ATAF2 null mutant ataf2-2, the cca1-1 ataf2-2 double mutant shows higher SOB7 transcript accumulations and a stronger BR-insensitive phenotype of hypocotyl elongation in white light. CCA1 interacts with ATAF2 at both DNA-protein and protein-protein levels. ATAF2, BAS1, and SOB7 are all circadian regulated with distinct expression patterns. These results demonstrate that CCA1 and ATAF2 differentially suppress BAS1- and SOB7-mediated BR inactivation.

Regulation of Brassinosteroid Homeostasis in Higher Plants

Brassinosteroids (BRs) are known as one of the major classes of phytohormones essential for various processes during normal plant growth, development, and adaptations to biotic and abiotic stresses. Significant progress has been achieved on revealing mechanisms regulating BR biosynthesis, catabolism, and signaling in many crops and in model plant Arabidopsis. It is known that BRs control plant growth and development in a dosage-dependent manner. Maintenance of BR homeostasis is therefore critical for optimal functions of BRs. In this review, updated discoveries on mechanisms controlling BR homeostasis in higher plants in response to internal and external cues are discussed.

Inhibitors of Brassinosteroid Biosynthesis and Signal Transduction

Chemical inhibitors are invaluable tools for investigating protein function in reverse genetic approaches. Their application bears many advantages over mutant generation and characterization. Inhibitors can overcome functional redundancy, their application is not limited to species for which tools of molecular genetics are available and they can be applied to specific tissues or developmental stages, making them highly convenient for addressing biological questions. The use of inhibitors has helped to elucidate hormone biosynthesis and signaling pathways and here we review compounds that were developed for the plant hormones brassinosteroids (BRs). BRs are steroids that have strong growth-promoting capacities, are crucial for all stages of plant development and participate in adaptive growth processes and stress response reactions. In the last two decades, impressive progress has been made in BR inhibitor development and application, which has been instrumental for studying BR modes of activity and identifying and characterizing key players. Both, inhibitors that target biosynthesis, such as brassinazole, and inhibitors that target signaling, such as bikinin, exist and in a comprehensive overview we summarize knowledge and methodology that enabled their design and key findings of their use. In addition, the potential of BR inhibitors for commercial application in plant production is discussed.

CYP72A enzymes catalyse 13-hydrolyzation of gibberellins

Bioactive gibberellins (GAs or diterpenes) are essential hormones in land plants that control many aspects of plant growth and development. In flowering plants, 13-OH GAs (having low bioactivity-for example, GA₁) and 13-H GAs (having high bioactivity-for example, GA₄) frequently coexist in the same plant. However, the identity of the native Arabidopsis thaliana 13-hydroxylase GA and its physiological functions remain unknown. Here, we report that cytochrome P450 genes (CYP72A9 and its homologues) encode active GA 13-hydroxylases in Brassicaceae. Plants overexpressing CYP72A9 exhibited semi-dwarfism, which was caused by significant reduction in GA₄ levels. Biochemical assays revealed that recombinant CYP72A9 protein catalysed the conversion of 13-H GAs to the corresponding 13-OH GAs. CYP72A9 was expressed predominantly in developing seeds in Arabidopsis. Freshly harvested seeds of cyp72a9 mutants germinated more quickly than the wild type, whereas stratification-treated seeds and seeds from long-term storage did not. The evolutionary origin of GA 13-oxidases from the CYP72A subfamily was also investigated and discussed here.

Repeated evolution of cytochrome P450-mediated spiroketal steroid biosynthesis in plants

Diosgenin is a spiroketal steroidal natural product extracted from plants and used as the single most important precursor for the world steroid hormone industry. The sporadic occurrences of diosgenin in distantly related plants imply possible independent biosynthetic origins. The characteristic 5,6-spiroketal moiety in diosgenin is reminiscent of the spiroketal moiety present in anthelmintic avermectins isolated from actinomycete bacteria. How plants gained the ability to biosynthesize spiroketal natural products is unknown. Here, we report the diosgenin-biosynthetic pathways in himalayan paris (Paris polyphylla), a monocot medicinal plant with hemostatic and antibacterial properties, and fenugreek (Trigonella foenum-graecum), an eudicot culinary herb plant commonly used as a galactagogue. Both plants have independently recruited pairs of cytochromes P450 that catalyze oxidative 5,6-spiroketalization of cholesterol to produce diosgenin, with evolutionary progenitors traced to conserved phytohormone metabolism. This study paves the way for engineering the production of diosgenin and derived analogs in heterologous hosts.

BR deficiency causes increased sensitivity to drought and yield penalty in cotton

BACKGROUND

Brassinosteroids (BRs) play crucial roles in drought tolerance, but the underlying molecular mechanisms remain unclear in the important oilseed and fiber crop, cotton (Gossypium hirsutum L.).

RESULTS

To elucidate how BRs mediate drought tolerance in cotton, a cotton brassinosteroid (BR)-deficient mutant, pag1 (pagoda1), was employed for analysis. Importantly, the pag1 mutant showed increased sensitivity to drought stress, with shorter primary roots and fewer lateral roots. The number of stomata was significantly increased in the mutant, and the stomata aperture was much wider than that of the control plants. These mutant plants therefore showed an increased water loss rate. Furthermore, the abscisic acid (ABA) content, photosynthetic efficiency and starch content of the mutant were significantly lower than those of the wild type. The overall performance of the mutant plants was worse than that of the wild-type control under both normal and drought conditions. Moreover, Proteomic analysis revealed reduced levels of stress-related proteins in pag1 plants.

CONCLUSIONS

These results suggest that BRs may modulate the drought tolerance of cotton by regulating much genes that related to drought stress and multiple organ responses to drought, including root growth, stomata development, the stomata aperture and photosynthesis. This study provides an important basis for understanding drought resistance regulated by BRs and cultivating drought-resistant cotton lines.

Less Conserved LRRs Is Important for BRI1 Folding

Brassinosteroid insensitive 1 (BRI1) is a multidomain plant leucine-rich repeat receptor-like kinase (LRR-RLK), belongs to the LRR X subfamily. BRI1 perceives plant hormone brassinosteroids (BRs) through its extracellular domain that constitutes of LRRs interrupted by a 70 amino acid residue island domain (ID), which activates the kinase domain (KD) in its intracellular domain to trigger BR response. Thus, the KD and the ID of BRI1 are highly conserved and greatly contribute to BR functions. In fact, most bri1 mutants are clustered in or surrounded around the ID and the KD. However, the role of the less conserved LRR domains, particularly the first few LRRs after the signal peptide, is elusive. Here, we report the identification of a loss-of-function mutant bri1-235 that carries a mutation in the less conserved fourth LRR of BRI1 extracellular domain in Arabidopsis. This mutant had a base alteration from C to T, resulting in an amino acid substitution from serine to phenylalanine at the 156th position of BRI1. Compared with the wild-type plants, bri1-235 exhibited round leaves, prolonged life span, shorter stature, and approximately normal fertility under light conditions. The bri1-235 mutant was less sensitive to exogenous brassinolide under normal conditions. Importantly, both wild-type BRI1 expression and a sbi1 mutant that activates BRI1 rescued bri1-235 and resembled the wild type. Furthermore, bri1-235 protein was localized in endoplasmic reticulum rather than plasma membrane, suggestive of a cause for reducing BR sensitive in bri1-235. Taken together, our findings provide an insight into the role of the less conserved LRRs of BRI1, shedding light on the role of LRRs in a variety of LRR-RLKs that control numerous processes of plant growth, development, and stress response.

Transcriptome analyses of Paris polyphylla var. chinensis, Ypsilandra thibetica, and Polygonatum kingianum characterize their steroidal saponin biosynthesis pathway

Steroidal saponins, one of the most diverse groups of plant-derived natural products, elicit biological and pharmacological activities; however, the genes involved in their biosynthesis and the corresponding biosynthetic pathway in monocotyledon plants remain unclear. This study aimed to identify genes involved in the biosynthesis of steroidal saponins by performing a comparative analysis among transcriptomes of Paris polyphylla var. chinensis (PPC), Ypsilandra thibetica (YT), and Polygonatum kingianum (PK). De novo transcriptome assemblies generated 57,537, 140,420, and 151,773 unigenes from PPC, YT, and PK, respectively, of which 56.54, 47.81, and 44.30% were successfully annotated, respectively. Among the transcriptomes for PPC, YT, and PK, we identified 194, 169, and 131; 17, 14, and 26; and, 80, 122, and 113 unigenes corresponding to terpenoid backbone biosynthesis; sesquiterpenoid and triterpenoid biosynthesis; and, steroid biosynthesis pathways, respectively. These genes are putatively involved in the biosynthesis of cholesterol that is the primary precursor of steroidal saponins. Phylogenetic analyses indicated that lanosterol synthase may be exclusive to dicotyledon plant species, and the cytochrome P450 unigenes were closely related to clusters CYP90B1 and CYP734A1, which are UDP-glycosyltransferases unigenes homologous with the UGT73 family. Thus, unigenes of β-glucosidase may be candidate genes for catalysis of later period modifications of the steroidal saponin skeleton. Our data provide evidence to support the hypothesis that monocotyledons biosynthesize steroidal saponins from cholesterol via the cycloartenol pathway.

Genome-wide identification and expression analysis of brassinosteroid action-related genes during the shoot growth of moso bamboo

Brassinosteroids (BRs) are a group of plant steroid hormones that play crucial roles in a range of plant growth and development processes. BR action includes active BR formation by a complex biosynthesis process and driving BR biological function through signal transduction. Although the characterization of several BR action-related genes has been conducted in a few model plants, systematic information about these genes in bamboo is still lacking. We identified 64 genes related to BR action from the genome of moso bamboo (Phyllostachys edulis), including twenty that participated in BR biosynthesis and forty-four involved in BR signal transduction. The characteristics of all these candidate genes were identified by bioinformatics methods, including the gene structures, basic physical and chemical properties of proteins, conserved domains and evolutionary relationships. Based on the transcriptome data, the candidate genes demonstrated different expression patterns, which were further validated by qRT-PCR using templates from bamboo shoots with different heights. Thirty-four positive and three negative co-expression modules were identified by 44 candidate genes in the newly emerging bamboo shoot. The gene expression patterns and co-expression modules of BR action-related genes in bamboo shoots indicated that they might function to promote bamboo growth through BR biosynthesis and signal transduction processes. This study provides the first step towards the cloning and functional dissection of the role of BR action-related genes in moso bamboo, which also presents an excellent opportunity for genetic engineering using the candidate genes to improve bamboo quantity and quality.

Genome-wide identification and expression analysis of brassinosteroid biosynthesis and metabolism genes regulating apple tree shoot and lateral root growth

In plants, brassinosteroid biosynthesis and metabolism genes affect endogenous brassinosteroid metabolic processes as well as stem and root growth. However, there is little information available regarding these genes in apple. In this study, 22 brassinosteroid biosynthesis and metabolism genes were identified in apple (Malus domestica). These genes were named according to their chromosomal locations and the Arabidopsis thaliana homologs. Their conserved characteristic domains, evolutionary relationships, syntenic relationships, chemical characteristics, gene/protein structures, interactions among the encoded proteins, promoter sequences, and functions were investigated. These 22 genes were clustered with their A. thaliana homologs based on bioinformatics analyses, which suggested they are functionally similar in apple and A. thaliana. Tissue-specific expression levels revealed that most of these genes are important for stem growth and development, while several of these genes affect lateral root formation. The transcription patterns of these genes in shoot tips were investigated following diverse treatments [brassinosteroid (shoot tips and roots), brassinazole, auxin, and temperature]. Gene expression levels were also examined in different grafting combinations ('Nagafu No. 2'/Malling 9 and 'Nagafu No. 2'/'Nagafu No. 2') and shoot varieties ('Yanfu No. 6' and 'Nagafu No. 2'). The results indicated that these genes may be involved in apple stem and root growth. The comprehensive genome-wide analysis of brassinosteroid biosynthesis and metabolism genes presented herein may be useful for breeding new apple cultivars with increased vigor. The data also represent a rich genetic resource for future apple gene functional investigations that may have implications for the genetic improvement of apple tree species.

Changes in endogenous phytohormones regulated by microRNA-target mRNAs contribute to the development of Dwarf Autotetraploid Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

Polyploidization is considered as the major force that drives plant species evolution and biodiversity. The leaves of Chinese cabbage, an important vegetable crop valued for its nutritional quality, constitute the main edible organ. In this study, we found that autotetraploid Chinese cabbage (Brassica rapa ssp. pekinensis) generated from a doubled haploid (DH) line via isolated microspore culture exhibits a dwarf phenotype, along with thick leaves and delayed flowering. Abscisic acid (ABA) and brassinosteroid (BR) levels were significantly lower in autotetraploids compared to DHs. Comparative transcriptome analysis was performed to examine the gene regulatory network. A total of 13,225 differentially expressed genes (DEGs) were detected. Further microRNA (miRNA) analysis identified 102 DEGs that correspond to 35 differentially expressed miRNAs (DEMs). Subsequent screening of these 102 genes identified 13 key genes with 12 corresponding differentially expressed miRNAs that are related to leaf development and dwarfism. These 13 genes are involved in the regulation of various processes, including BR synthesis (dwarfing), plant growth, flowering time delay, ABA pathway-related growth and metabolism, leaf morphology and development, and cell extension. Two dwarfing-related genes (BraA01000252 and BraA05004386) regulated by two miRNAs (novel_15 and novel_54) were determined to be downregulated, indicating their possible role in leaf thickness and dwarfism in autotetraploid plants. We also propose two possible miRNA-dependent regulatory pathways that contribute to trait formation in autotetraploid Chinese cabbage. These results provide a theoretical basis for further work involving Chinese cabbage varieties by inducing polyploidy.

Arabidopsis BRASSINOSTEROID INACTIVATOR2 is a typical BAHD acyltransferase involved in brassinosteroid homeostasis

Brassinosteroids (BRs) are plant-specific steroidal hormones; BR homeostasis is crucial for various aspects of plant growth and development. However, to date, the BR inactivation process has not been thoroughly elucidated. In this study, we identified and characterized a novel BAHD family acyltransferase gene, BRASSINOSTEROID INACTIVATOR2 (BIA2), involved in BR inactivation. BIA2-overexpressing (OE-BIA2) plants displayed typical BR-deficient phenotypes, which were rescued by exogenous BR treatment. Real-time qRT-PCR and transcriptome analyses showed that expression levels of virtually all of the BR biosynthetic genes were increased, whereas the expression of many BR inactivation genes was reduced in OE-BIA2 plants. Root inhibition assays showed that the root growth of OE-BIA2 plants was inhibited. We obtained plants with an intermediate phenotype by crossing the OE-BIA2 plants with BRASSINOSTEROID-INSENSITIVE1 (BRI1)-overexpressing plants. The null BIA2 mutants had longer hypocotyls in the dark. BIA2 was predominantly expressed in roots, and its expression was induced by 24-epibrassinolide or dark treatment, but it exhibited a differential expression pattern compared with its homologue, BIA1. Furthermore, genetic transformation with point-mutant and deleted-BIA2 constructs confirmed that the HXXXD motif is essential for the function of BIA2. Taken together, these findings indicate that BIA2 is a typical BAHD acyltransferase that is involved in BR homeostasis and may inactivate bioactive BRs by esterification, particularly in roots and hypocotyls under dark conditions.

Changes in fenugreek transcriptome induced by methyl jasmonate and steroid precursors revealed by RNA-Seq

Changes in fenugreek transcriptome related to enhanced production of steroids were induced by methyl jasmonate, cholesterol and squalene, and recorded using RNA-seq. A total of 112,850 unigenes were obtained after de novo assembling of next generation sequencing data, and used for functional annotations. In steroidal saponins pathway, transcripts involved in mevalonate, terpenoid backbone and plant sterol synthesis were annotated. Overexpression of several transcripts from phytosterol biosynthesis pathway was confirmed by quantitative RT-PCR. In diosgenin biosynthesis pathway, fatty acid ω-hydroxylase (CYP86A2) and steroid 22-alpha-hydroxylase (CYP90B1) genes were annotated in all induced transcriptomes. Moreover, direct sequencing confirmed increased levels of CYP90B1, unspecific monooxygenase and 26-hydroxylase genes in plants with elevated level of diosgenin. New unigenes corresponding to enzymes involved in biosynthesis of diosgenin from cycloartenol via cholesterol were obtained and the role of CYP72A family in steroidal saponin biosynthesis was proposed. Additional support for biosynthetic pathway from cycloartenol to diosgenin was provided.

Next-generation sequencing of representational difference analysis products for identification of genes involved in diosgenin biosynthesis in fenugreek (Trigonella foenum-graecum)

Representational difference analysis of cDNA was performed and differential products were sequenced and annotated. Candidate genes involved in biosynthesis of diosgenin in fenugreek were identified. Detailed mechanism of diosgenin synthesis was proposed. Fenugreek (Trigonella foenum-graecum L.) is a valuable medicinal and crop plant. It belongs to Fabaceae family and has a unique potential to synthesize valuable steroidal saponins, e.g., diosgenin. Elicitation (methyl jasmonate) and precursor feeding (cholesterol and squalene) were used to enhance the content of sterols and steroidal sapogenins in in vitro grown plants for representational difference analysis of cDNA (cDNA-RDA). To identify candidate genes involved in diosgenin biosynthesis, differential, factor-specific libraries were subject to the next-generation sequencing. Approximately 9.9 million reads were obtained, trimmed, and assembled into 31,491 unigenes with an average length of 291 bp. Then, functional annotation and gene ontogeny enrichment analysis was performed by aligning all-unigenes with public databases. Within the transcripts related to sterol and steroidal saponin biosynthesis, we discovered novel candidate genes of diosgenin biosynthesis and validated their expression using quantitative RT-PCR analysis. Based on these findings, we supported the idea that diosgenin is biosynthesized from cycloartenol via cholesterol. This is the first report on the next-generation sequencing of cDNA-RDA products. Analysis of the transcriptomes enriched in low copy sequences contributed substantially to our understanding of the biochemical pathways of steroid synthesis in fenugreek.

Transcriptomic profiling of taproot growth and sucrose accumulation in sugar beet (Beta vulgaris L.) at different developmental stages

In sugar beet (Beta vulgaris L.), taproot weight and sucrose content are the important determinants of yield and quality. However, high yield and low sucrose content are two tightly bound agronomic traits. The advances in next-generation sequencing technology and the publication of sugar beet genome have provided a method for the study of molecular mechanism underlying the regulation of these two agronomic traits. In this work, we performed comparative transcriptomic analyses in the high taproot yield cultivar SD13829 and the high sucrose content cultivar BS02 at five developmental stages. More than 50,000,000 pair-end clean reads for each library were generated. When taproot turned into the rapid growth stage at the growth stage of 82 days after emergence (DAE), eighteen enriched gene ontology (GO) terms, including cell wall, cytoskeleton, and enzyme linked receptor protein signaling pathway, occurred in both cultivars. Differentially expressed genes (DEGs) of paired comparison in both cultivars were enriched in the cell wall GO term. For pathway enrichment analyses of DEGs that were respectively generated at 82 DAE compared to 59 DAE (the earlier developmental stage before taproot turning into the rapid growth stage), plant hormone signal transduction pathway was enriched. At 82 DAE, the rapid enlarging stage of taproot, several transcription factor family members were up-regulated in both cultivars. An antagonistic expression of brassinosteroid- and auxin-related genes was also detected. In SD13829, the growth strategy was relatively focused on cell enlargement promoted by brassinosteroid signaling, whereas in BS02, it was relatively focused on secondarily cambial cell division regulated by cytokinin, auxin and brassinosteroid signaling. Taken together, our data demonstrate that the weight and sucrose content of taproot rely on its growth strategy, which is controlled by brassinosteroid, auxin, cytokinin, and gibberellin.

Occurrence of brassinosteroids in non-flowering land plants, liverwort, moss, lycophyte and fern

Endogenous brassinosteroids (BRs) in non-flowering land plants were analyzed. BRs were found in a liverwort (Marchantia polymorpha), a moss (Physcomitrella patens), lycophytes (Selaginella moellendorffii and S. uncinata) and 13 fern species. A biologically active BR, castasterone (CS), was identified in most of these non-flowering plants but another biologically active BR, brassinolide, was not. It may be distinctive that levels of CS in non-flowering plants were orders of magnitude lower than those in flowering plants. 22-Hydroxycampesterol and its metabolites were identified in most of the non-flowering plants suggesting that the biosynthesis of BRs via 22-hydroxylation of campesterol occurs as in flowering plants. Phylogenetic analyses indicated that M. polymorpha, P. patens and S. moellendorffii have cytochrome P450s in the CYP85 clans which harbors BR biosynthesis enzymes, although the P450 profiles are simpler as compared with Arabidopsis and rice. Furthermore, these basal land plants were found to have multiple P450s in the CYP72 clan which harbors enzymes to catabolize BRs. These findings indicate that green plants were able to synthesize and inactivate BRs from the land-transition stage.

Effects of 24-epibrassinolide and green light on plastid gene transcription and cytokinin content of barley leaves

In order to evaluate whether brassinosteroids (BS) and green light regulate the transcription of plastid genes in a cross-talk with cytokinins (CKs), transcription rates of 12 plastid genes (ndhF, rrn23, rpoB, psaA, psaB, rrn16, psbA, psbD, psbK, rbcL, atpB, and trnE/trnY) as well as the accumulation of transcripts of some photoreceptors (PHYA, CRY2, CRY1A, and CRY1B) and signaling (SERK and CAS) genes were followed in detached etiolated barley leaves exposed to darkness, green or white light ±1μm 24-epibrassinolide (EBL). EBL in the dark was shown to up-regulate the transcription of 12 plastid genes, while green light activated 10 genes and the EBL combined with the green light affected the transcription of only two genes (psaB and rpoB). Green light inhibited the expression of photoreceptor genes, except for CRY1A. Under the green light, EBL practically did not affect the expression of CRY1A, CAS and SERK genes, but it reduced the influence of white light on the accumulation of CAS, CRY1A, CRY1B, and SERK gene transcripts. The total content of BS in the dark and under white light remained largely unchanged, while under green light the total content of BRs (brassinolide, castasterone, and 6-deoxocastasterone) and HBRs (28-homobrassinolide, 28-homocastasterone, and 6-deoxo-28-homocastasterone) increased. The EBL-dependent up-regulation of plastome transcription in the dark was accompanied by a significant decrease in CK deactivation by O-glucosylation. However, no significant effect on the content of active CKs was detected. EBL combined with green light moderately increased the contents of trans-zeatin and isopentenyladenine, but had a negative effect on cis-zeatin. The most significant promotive effect of EBL on active CK bases was observed in white light. The data obtained suggest the involvement of CKs in the BS- and light-dependent transcription regulation of plastid genes.

Identification and analysis of genes associated with the synthesis of bioactive constituents in Dendrobium officinale using RNA-Seq

Dendrobium officinale L. is an important traditional herb with high commercial value in China. Several bioactive constituents, including polysaccharides and alkaloids, reportedly make major contributions toward the excellent medicinal effect of D. officinale. In this study, the contents of polysaccharides and alkaloids in various organs of D. officinale were measured and compared. We took advantage of transcriptomes from four organs to explore biological mechanisms in the organ-specific distribution of active ingredients in D. officinale. Based on Kyoto Encyclopedia of Genes and Genomes pathways, unigenes related to the enzymes involved in fructose and mannose metabolism and unigenes associated with putative upstream elements of the alkaloid biosynthetic pathway were identified. A large number of candidates, including 35 full-length glycosyltransferase genes and 49 full-length P450 genes, were also identified based on the transcriptome data, and the organ-specific expression pattern of these genes was determined. Furthermore, differential expression of all candidate genes was analyzed in two Dendrobium species, D. nobile L. and D. officinale. The data will supply important clues to exploit useful genes involved in polysaccharide and alkaloid synthesis.

Functional analyses of Populus euphratica brassinosteroid biosynthesis enzyme genes DWF4 (PeDWF4) and CPD (PeCPD) in the regulation of growth and development of Arabidopsis thaliana

DWF4 and CPD are key brassinosteroids (BRs) biosynthesis enzyme genes. To explore the function of Populus euphratica DWF4 (PeDWF4) and CPD (PeCPD), Arabidopsis thaliana transgenic lines (TLs) expressing PeDWF4, PeCPD or PeDWF4 plus PeCPD, namely PeDWF4-TL, PeCPD-TL and PeCP/DW-TL, were characterized. Compared with wild type (WT), the changes of both PeDWF4-TL and PeCPD-TL in plant heights, silique and hypocotyls lengths and seed yields were similar, but in bolting time and stem diameters, they were opposite. PeCP/DW-TL was more in plant heights and the lengths of primary root, silique, and fruit stalk, but less in silique numbers and seed yields than either PeDWF4-TL or PeCPD-TL. PeDWF4 and PeCPD specially expressed in PeDWF4-TL or PeCPDTL, and the transcription level of PeDWF4 was higher than that of PeCPD. In PeCP/DW-TL, their expressions were all relatively reduced. Additionally, the expression of PeDWF4 and PeCPD differentially made the expression levels of AtDWF4, AtCPD, AtBR6OX2, AtFLC, AtTCP1 and AtGA5 change in the TLs. The total BRs contents were PeDWF4-TL greater than PeCP/DW-TL greater than WT greater than PeCPD-TL. These results imply that PeDWF4 is functionally not exactly the same as PeCPD and there may be a synergistic and antagonistic effects in physiology between both of them in the regulation of plant growth and development.

Identification and analysis of genes associated with the synthesis of bioactive constituents in Dendrobium officinale using RNA-Seq

Dendrobium officinale L. is an important traditional herb with high commercial value in China. Several bioactive constituents, including polysaccharides and alkaloids, reportedly make major contributions toward the excellent medicinal effect of D. officinale. In this study, the contents of polysaccharides and alkaloids in various organs of D. officinale were measured and compared. We took advantage of transcriptomes from four organs to explore biological mechanisms in the organ-specific distribution of active ingredients in D. officinale. Based on Kyoto Encyclopedia of Genes and Genomes pathways, unigenes related to the enzymes involved in fructose and mannose metabolism and unigenes associated with putative upstream elements of the alkaloid biosynthetic pathway were identified. A large number of candidates, including 35 full-length glycosyltransferase genes and 49 full-length P450 genes, were also identified based on the transcriptome data, and the organ-specific expression pattern of these genes was determined. Furthermore, differential expression of all candidate genes was analyzed in two Dendrobium species, D. nobile L. and D. officinale. The data will supply important clues to exploit useful genes involved in polysaccharide and alkaloid synthesis.

Brassinosteroid signaling converges with SUPPRESSOR OF PHYTOCHROME B4-#3 to influence the expression of SMALL AUXIN UP RNA genes and hypocotyl growth

Interactions between signaling pathways help guide plant development. In this study, we found that brassinosteroid (BR) signaling converges with SUPPRESSOR OF PHYTOCHROME B4-#3 (SOB3) to influence both the transcription of genes involved in cell elongation and hypocotyl growth. Specifically, SOB3 mutant hypocotyl phenotypes, which are readily apparent when the seedlings are grown in dim white light, were attenuated by treatment with either brassinolide (BL) or the BR biosynthesis inhibitor brassinazole (BRZ). Hypocotyls of SOB3 mutant seedlings grown in white light with a higher fluence rate also exhibited altered sensitivities to BL, further suggesting a connection to BR signaling. However, the impact of BL treatment on SOB3 mutants grown in moderate-intensity white light was reduced when polar auxin transport was inhibited. BL treatment enhanced transcript accumulation for all six members of the SMALL AUXIN UP RNA19 (SAUR19) subfamily, which promote cell expansion, are repressed by SOB3 and light, and are induced by auxin. Conversely, BRZ inhibited the expression of SAUR19 and its homologs. Expression of these SAURs was also enhanced in lines expressing a constitutively active form of the BR signaling component BZR1, further indicating that the transcription of SAUR19 subfamily members are influenced by this hormone signaling pathway. Taken together, these results indicate that SOB3 and BR signaling converge to influence the transcription of hypocotyl growth-promoting SAUR19 subfamily members.

Approaches to Study Light Effects on Brassinosteroid Sensitivity

Light perception and hormone signaling in plants are likely connected at multiple points. Light conditions, perceived by photoreceptors, control plant responses by altering hormone concentration, tissue sensitivity, or a combination of both. Whereas it is relatively straightforward to assess the light effects on hormone levels, hormone sensitivity is subjected to interpretation. In Arabidopsis thaliana seedlings, hypocotyl length is strongly affected by light conditions. As hypocotyl elongation also depends on brassinosteroids (BRs), assaying this response provides a valuable and easy way to measure the responsiveness of seedlings to BRs and the impact of light. We describe a simple protocol to evaluate the responsiveness of hypocotyls to commercial BRs and/or BR inhibitors under a range of light conditions. These assays can be used to establish whether light affects BR sensitivity or whether BRs affect light sensitivity. Overall, our protocol can be easily applied for deetiolation (under polychromatic or monochromatic light) and simulated shade treatments combined with BR treatments.

Triterpene Structural Diversification by Plant Cytochrome P450 Enzymes

Cytochrome P450 monooxygenases (P450s) represent the largest enzyme family of the plant metabolism. Plants typically devote about 1% of the protein-coding genes for the P450s to execute primary metabolism and also to perform species-specific specialized functions including metabolism of the triterpenes, isoprene-derived 30-carbon compounds. Triterpenes constitute a large and structurally diverse class of natural products with various industrial and pharmaceutical applications. P450-catalyzed structural modification is crucial for the diversification and functionalization of the triterpene scaffolds. In recent times, a remarkable progress has been made in understanding the function of the P450s in plant triterpene metabolism. So far, ∼80 P450s are assigned biochemical functions related to the plant triterpene metabolism. The members of the subfamilies CYP51G, CYP85A, CYP90B-D, CYP710A, CYP724B, and CYP734A are generally conserved across the plant kingdom to take part in plant primary metabolism related to the biosynthesis of essential sterols and steroid hormones. However, the members of the subfamilies CYP51H, CYP71A,D, CYP72A, CYP81Q, CYP87D, CYP88D,L, CYP93E, CYP705A, CYP708A, and CYP716A,C,E,S,U,Y are required for the metabolism of the specialized triterpenes that might perform species-specific functions including chemical defense toward specialized pathogens. Moreover, a recent advancement in high-throughput sequencing of the transcriptomes and genomes has resulted in identification of a large number of candidate P450s from diverse plant species. Assigning biochemical functions to these P450s will be of interest to extend our knowledge on triterpene metabolism in diverse plant species and also for the sustainable production of valuable phytochemicals.

Genetic architecture and evolution of the S locus supergene in Primula vulgaris

Darwin's studies on heterostyly in Primula described two floral morphs, pin and thrum, with reciprocal anther and stigma heights that promote insect-mediated cross-pollination. This key innovation evolved independently in several angiosperm families. Subsequent studies on heterostyly in Primula contributed to the foundation of modern genetic theory and the neo-Darwinian synthesis. The established genetic model for Primula heterostyly involves a diallelic S locus comprising several genes, with rare recombination events that result in self-fertile homostyle flowers with anthers and stigma at the same height. Here we reveal the S locus supergene as a tightly linked cluster of thrum-specific genes that are absent in pins. We show that thrums are hemizygous not heterozygous for the S locus, which suggests that homostyles do not arise by recombination between S locus haplotypes as previously proposed. Duplication of a floral homeotic gene 51.7 million years (Myr) ago, followed by its neofunctionalization, created the current S locus assemblage which led to floral heteromorphy in Primula. Our findings provide new insights into the structure, function and evolution of this archetypal supergene.

ARF7 increases the endogenous contents of castasterone through suppression of BAS1 expression in Arabidopsis thaliana

Homeostasis of brassinosteroids (BRs) maintained by the balance between their biosynthesis and inactivation is important to coordinate the diverse physiological and developmental responses of plants. Although BR signaling regulates the endogenous levels of BRs via negative feedback regulation, it remains largely unknown how the biosynthesis and inactivation of BR are triggered. BAS1 encodes CYP734A1, which inactivates the biologically active BRs via C-26 hydroxylation and is down-regulated by a BR-responsive transcription factor, BZR1. Here it is demonstrated that the expression of the BAS1 gene is regulated by auxin response factors (ARFs) in Arabidopsis thaliana. Two successive E-box motifs on the BAS1 promoter function as BZR1 binding sites and are essential for BR-regulated BAS1 expression. The expression of BAS1 is increased in the arf7 and arf7arf19 mutants. The endogenous level of bioactive BR, castasterone, is greatly decreased in those mutants. ARF7 can bind to the E-box motifs of the BAS1 promoter where BZR1 binds, suggesting that ARF7 and BZR1 mutually compete for the same cis-element of the BAS1 promoter. Additionally, ARF7 directly interacts with BZR1, which inhibits their DNA binding activities and regulation of BAS1 expression. In conclusion, auxin signaling via ARF7 directly modulates the expression of BAS1 by competition with BZR1, thereby increasing the level of castasterone and promoting growth and development in A. thaliana.

Identification and Characterization of Multiple Intermediate Alleles of the Key Genes Regulating Brassinosteroid Biosynthesis Pathways

Most of the early identified brassinosteroid signaling and biosynthetic mutants are null mutants, exhibiting extremely dwarfed phenotypes and male sterility. These null mutants are usually unable to be directly transformed via a routinely used Agrobacterium-mediated gene transformation system and therefore are less useful for genetic characterization of the brassinosteroid (BR)-related pathways. Identification of intermediate signaling mutants such as bri1-5 and bri1-9 has contributed drastically to the elucidation of BR signaling pathway using both genetic and biochemical approaches. However, intermediate mutants of key genes regulating BR biosynthesis have seldom been reported. Here we report identification of several intermediate BR biosynthesis mutants mainly resulted from leaky transcriptions due to the insertions of T-DNAs in the introns. These mutants are semi-dwarfed and fertile and capable to be transformed. These intermediate mutants could be useful tools for future discovery and analyses of novel components regulating BR biosynthesis and catabolism via genetic modifier screen.

A Conserved Cytochrome P450 Evolved in Seed Plants Regulates Flower Maturation

Global inspection of plant genomes identifies genes maintained in low copies across taxa and under strong purifying selection, which are likely to have essential functions. Based on this rationale, we investigated the function of the low-duplicated CYP715 cytochrome P450 gene family that appeared early in seed plants and evolved under strong negative selection. Arabidopsis CYP715A1 showed a restricted tissue-specific expression in the tapetum of flower buds and in the anther filaments upon anthesis. cyp715a1 insertion lines showed a strong defect in petal development, and transient alteration of pollen intine deposition. Comparative expression analysis revealed the downregulated expression of genes involved in pollen development, cell wall biogenesis, hormone homeostasis, and floral sesquiterpene biosynthesis, especially TPS21 and several key genes regulating floral development such as MYB21, MYB24, and MYC2. Accordingly, floral sesquiterpene emission was suppressed in the cyp715a1 mutants. Flower hormone profiling, in addition, indicated a modification of gibberellin homeostasis and a strong disturbance of the turnover of jasmonic acid derivatives. Petal growth was partially restored by the active gibberellin GA3 or the functional analog of jasmonoyl-isoleucine, coronatine. CYP715 appears to function as a key regulator of flower maturation, synchronizing petal expansion and volatile emission. It is thus expected to be an important determinant of flower-insect interaction.

Light and auxin responsive cytochrome P450s from Withania somnifera Dunal: cloning, expression and molecular modelling of two pairs of homologue genes with differential regulation

Cytochrome P450s (CYPs) catalyse a wide variety of oxygenation/hydroxylation reactions that facilitate diverse metabolic functions in plants. Specific CYP families are essential for the biosynthesis of species-specialized metabolites. Therefore, we investigated the role of different CYPs related to secondary metabolism in Withania somnifera, a medicinally important plant of the Indian subcontinent. In this study, complete complementary DNAs (cDNAs) of four different CYP genes were isolated and christened as WSCYP93Id, WSCYP93Sm, WSCYP734B and WSCYP734R. These cDNAs encoded polypeptides comprising of 498, 496, 522 and 550 amino acid residues with their deduced molecular mass of 56.7, 56.9, 59.4 and 62.2 kDa, respectively. Phylogenetic study and molecular modelling analysis of the four cloned WSCYPs revealed their categorization into two CYP families (CYP83B1 and CYP734A1) belonging to CYP71 and CYP72 clans, respectively. BLASTp searches showed similarity of 75 and 56 %, respectively, between the two CYP members of CYP83B1 and CYP734A1 with major variances exhibited in their N-terminal regions. The two pairs of homologues exhibited differential expression profiles in the leaf tissues of selected chemotypes of W. somnifera as well as in response to treatments such as methyl jasmonate, wounding, light and auxin. Light and auxin regulated two pairs of WSCYP homologues in a developing seedling in an interesting differential manner. Their lesser resemblance and homology with other CYP sequences suggested these genes to be more specialized and distinct ones. The results on chemotype-specific expression patterns of the four genes strongly suggested their key/specialized involvement of the CYPs in the biosynthesis of chemotype-specific metabolites, though their further biochemical characterization would reveal the specificity in more detail. It is revealed that WSCYP93Id and WSCYP93Sm may be broadly involved in the oxygenation reactions in the plant and, thereby, control various pathways involving such metabolic reactions in the plant. As a representative experimental validation of this notion, WSCYP93Id was heterologouly expressed in Escherichia coli and catalytic capabilities of the recombinant WSCYP93Id protein were evaluated using withanolides as substrates. Optimized assays with some major withanolides (withanone, withaferin A and withanolide A) involving spectrophotometric as well as high-pressure liquid chromatography (HPLC)-based evaluation (product detection) of the reactions showed conversion of withaferin A to a hydroxylated product. The genes belonging to other CYP group are possibly involved in some specialised synthesis such as that of brassinosteroids.

ATAF2 integrates Arabidopsis brassinosteroid inactivation and seedling photomorphogenesis

The Arabidopsis thaliana hypocotyl is a robust system for studying the interplay of light and plant hormones, such as brassinosteroids (BRs), in the regulation of plant growth and development. Since BRs cannot be transported between plant tissues, their cellular levels must be appropriate for given developmental fates. BR homeostasis is maintained in part by transcriptional feedback regulation loops that control the expression of key metabolic enzymes, including the BR-inactivating enzymes BAS1 (CYP734A1, formerly CYP72B1) and SOB7 (CYP72C1). Here, we find that the NAC transcription factor (TF) ATAF2 binds the promoters of BAS1 and SOB7 to suppress their expression. ATAF2 restricts the tissue-specific expression of BAS1 and SOB7 in planta. ATAF2 loss- and gain-of-function seedlings have opposite BR-response phenotypes for hypocotyl elongation. ATAF2 modulates hypocotyl growth in a light-dependent manner, with the photoreceptor phytochrome A playing a major role. The photomorphogenic phenotypes of ATAF2 loss- and gain-of-function seedlings are suppressed by treatment with the BR biosynthesis inhibitor brassinazole. Moreover, the disruption of BAS1 and SOB7 abolishes the short-hypocotyl phenotype of ATAF2 loss-of-function seedlings in low fluence rate white light, demonstrating an ATAF2-mediated connection between BR catabolism and photomorphogenesis. ATAF2 expression is suppressed by both BRs and light, which demonstrates the existence of an ATAF2-BAS1/SOB7-BR-ATAF2 feedback regulation loop, as well as a light-ATAF2-BAS1/SOB7-BR-photomorphogenesis pathway. ATAF2 also modulates root growth by regulating BR catabolism. As it is known to regulate plant defense and auxin biosynthesis, ATAF2 therefore acts as a central regulator of plant defense, hormone metabolism and light-mediated seedling development.

Global transcriptome analysis profiles metabolic pathways in traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao

BACKGROUND

Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao (A. mongolicus, family Leguminosae) is one of the most important traditional Chinese herbs. Among many secondary metabolites it produces, the effective bioactive constituents include isoflavonoids and triterpene saponins. The genomic resources regarding the biosynthesis of these metabolites in A. mongolicus are limited. Although roots are the primary material harvested for medical use, the biosynthesis of the bioactive compounds and its regulation in A. mongolicus are not well understood. Therefore, a global transcriptome analysis on A. mongolicus tissues was performed to identify the genes essential for the metabolism and to profile their expression patterns in greater details.

RESULTS

RNA-sequencing was performed for three different A. mongolicus tissues: leaf, stem, and root, using the Illumina Hiseq2000 platform. A total of 159.5 million raw sequence reads were generated, and assembled into 186,324 unigenes with an N50 of 1,524bp. Among them, 129,966 unigenes (~69.7%) were annotated using four public databases (Swiss-Prot, TrEMBL, CDD, Pfam), and 90,202, 63,946, and 78,326 unigenes were found to express in leaves, roots, and stems, respectively. A total of 8,025 transcription factors (TFs) were identified, in which the four largest families, bHLH, MYB, C3H, and WRKY, were implicated in regulation of tissue development, metabolisms, stress response, etc. Unigenes associated with secondary metabolism, especially those with isolavonoids and triterpene saponins biosynthesis were characterized and profiled. Most genes involved in the isoflavonoids biosynthesis had the lowest expression in the leaves, and the highest in the stems. For triterpene saponin biosynthesis, we found the genes in MVA and non-MVA pathways were differentially expressed among three examined tissues, indicating the parallel but compartmentally separated biosynthesis pathways of IPP and DMAPP in A. mongolicus. The first committed enzyme in triterpene saponin biosynthesis from A. mongolicus, cycloartenol synthase (AmCAS), which belongs to the oxidosqualene cyclase family, was cloned by us to study the astragalosides biosynthesis. Further co-expression analysis indicated the candidate CYP450s and glycosyltransferases (GTs) in the cascade of triterpene saponins biosynthesis. The presence of the large CYP450 families in A. mongolicus was further compared with those from Medicago truncatula and Arabidopsis thaliana, and the diversity and phylegenetic relationships of the CYP450 families were established.

CONCLUSION

A transcriptome study was performed for A. mongolicus tissues to construct and profile their metabolic pathways, especially for the important bioactive molecules. The results revealed a comprehensive profile for metabolic activities among tissues, pointing to the equal importance of leaf, stem, and root in A. mongolicus for the production of bioactive compounds. This work provides valuable resources for bioengineering and in vitro synthesis of the natural compounds for medical research and for potential drug development.