The pea gene NA encodes ent-kaurenoic acid oxidase

The mutation of ent-kaurenoic acid oxidase, a key enzyme involved in gibberellin biosynthesis, confers a dwarf phenotype to cucumber

KEY MESSAGE

A dwarf mutant with short branches (csdf) was identified from EMS-induced mutagenesis. Bulked segregant analysis sequencing and map-based cloning revealed CsKAO encoding ent-kaurenoic acid oxidase as the causal gene. Plant architecture is the primary target of artificial selection during domestication and improvement based on the determinate function for fruit yield. Plant architecture is regulated by complicated genetic networks, more underlying mechanism remains to be elucidated. Here, we identified a dwarf mutant (csdf) in an EMS-induced cucumber population, and genetic analysis revealed the mutated phenotype is controlled by a single recessive gene. Optical microanalysis showed the decrease in cell length is mainly contribute to the dwarf phenotype. By strategy of BSA-seq combined with map-based cloning, CsaV3_6G006520 (CsKAO) on chromosome 6 was identified as the candidate gene for csdf. Gene cloning and sequence alignment revealed a G to A mutation in the sixth exon, which causes the premature stop codon in CsKAO of csdf. Expression analysis revealed CsKAO was expressed in various tissues with abundant transcripts, and has significant differences between WT and csdf. Gene annotation indicated CsKAO encodes a cytochrome P450 family ent-kaurenoic acid oxidase which functioned in GA biosynthesis. GA-relevant analysis showed that endogenous GA contents were significantly decreased and the dwarfism phenotype could be restored by exogenous GA3 treatment; while, some of the representative enzyme genes involved in the GA pathway were up-regulated in csdf. Besides, IAA content is decreased in the terminal bud and increased in the lateral bud in csdf as well as several IAA-related genes are differentially expressed. Overall, those findings suggest that CsKAO regulated plant height via the influence on GAs pathways, and IAA might interact with GAs on plant architecture morphogenesis in cucumber.

Cell-layer specific roles for gibberellins in nodulation and root development

Gibberellins (GA) have a profound influence on the formation of lateral root organs. However, the precise role this hormone plays in the cell-specific events during lateral root formation, rhizobial infection and nodule organogenesis, including interactions with auxin and cytokinin (CK), is not clear. We performed epidermal- and endodermal-specific complementation of the severely GA-deficient na pea (Pisum sativum) mutant with Agrobacterium rhizogenes. Gibberellin mutants were used to examine the spatial expression pattern of CK (TCSn)- and auxin (DR5)-responsive promoters and hormone levels. We found that GA produced in the endodermis promote lateral root and nodule organogenesis and can induce a mobile signal(s) that suppresses rhizobial infection. By contrast, epidermal-derived GA suppress infection but have little influence on root or nodule development. GA suppress the CK-responsive TCSn promoter in the cortex and are required for normal auxin activation during nodule primordia formation. Our findings indicate that GA regulate the checkpoints between infection thread (IT) penetration of the cortex and invasion of nodule primordial cells and promote the subsequent progression of nodule development. It appears that GA limit the progression and branching of IT in the cortex by restricting CK response and activate auxin response to promote nodule primordia development.

Innovations in functional genomics and molecular breeding of pea: exploring advances and opportunities

The garden pea (Pisum sativum L.) is a significant cool-season legume, serving as crucial food sources, animal feed, and industrial raw materials. The advancement of functional genomics over the past two decades has provided substantial theoretical foundations and progress to pea breeding. Notably, the release of the pea reference genome has enhanced our understanding of plant architecture, symbiotic nitrogen fixation (SNF), flowering time, floral organ development, seed development, and stress resistance. However, a considerable gap remains between pea functional genomics and molecular breeding. This review summarizes the current advancements in pea functional genomics and breeding while highlighting the future challenges in pea molecular breeding.

The determination of peanut (Arachis hypogaea L.) pod-sizes during the rapid-growth stage by phytohormones

BACKGROUND

Pod size is an important yield target trait for peanut breeding. However, the molecular mechanism underlying the determination of peanut pod size still remains unclear.

RESULTS

In this study, two peanut varieties with contrasting pod sizes were used for comparison of differences on the transcriptomic and endogenous hormonal levels. Developing peanut pods were sampled at 10, 15, 20, 25 and 30 days after pegging (DAP). Our results showed that the process of peanut pod-expansion could be divided into three stages: the gradual-growth stage, the rapid-growth stage and the slow-growth stage. Cytological analysis confirmed that the faster increase of cell-number during the rapid-growth stage was the main reason for the formation of larger pod size in Lps. Transcriptomic analyses showed that the expression of key genes related to the auxin, the cytokinin (CK) and the gibberellin (GA) were mostly up-regulated during the rapid-growth stage. Meanwhile, the cell division-related differentially expressed genes (DEGs) were mostly up-regulated at 10DAP which was consistent with the cytological-observation. Additionally, the absolute quantification of phytohormones were carried out by liquid-chromatography coupled with the tandem-mass-spectrometry (LC-MS/MS), and results supported the findings from comparative transcriptomic studies.

CONCLUSIONS

It was speculated that the differential expression levels of TAA1 and ARF (auxin-related), IPT and B-ARR (CK-related), KAO, GA20ox and GA3ox (GA-related), and certain cell division-related genes (gene-LOC112747313 and gene-LOC112754661) were important participating factors of the determination-mechanism of peanut pod sizes. These results were informative for the elucidation of the underlying regulatory network in peanut pod-growth and would facilitate further identification of valuable target genes.

SlZF3 regulates tomato plant height by directly repressing SlGA20ox4 in the gibberellic acid biosynthesis pathway

Plant height is an important target trait for crop genetic improvement. Our previous work has identified a salt-tolerant C2H2 zinc finger, SlZF3, and its overexpression lines also showed a semi-dwarf phenotype, but the molecular mechanism remains to be elucidated. Here, we characterized the dwarf phenotype in detail. The dwarfism is caused by a decrease in stem internode cell elongation and deficiency of bioactive gibberellic acids (GAs), and can be rescued by exogenous GA3 treatment. Gene expression assays detected reduced expression of genes in the GA biosynthesis pathway of the overexpression lines, including SlGA20ox4. Several protein-DNA interaction methods confirmed that SlZF3 can directly bind to the SlGA20ox4 promoter and inhibit its expression, and the interaction can also occur for SlKS and SlKO. Overexpression of SlGA20ox4 in the SlZF3-overexpressing line can recover the dwarf phenotype. Therefore, SlZF3 regulates plant height by directly repressing genes in the tomato GA biosynthesis pathway.

Manipulating GA-Related Genes for Cereal Crop Improvement

The global population is projected to experience a rapid increase in the future, which poses a challenge to global food sustainability. The "Green Revolution" beginning in the 1960s allowed grain yield to reach two billion tons in 2000 due to the introduction of semi-dwarfing genes in cereal crops. Semi-dwarfing genes reduce the gibberellin (GA) signal, leading to short plant stature, which improves the lodging resistance and harvest index under modern fertilization practices. Here, we reviewed the literature on the function of GA in plant growth and development, and the role of GA-related genes in controlling key agronomic traits that contribute to grain yield in cereal crops. We showed that: (1) GA is a significant phytohormone in regulating plant development and reproduction; (2) GA metabolism and GA signalling pathways are two key components in GA-regulated plant growth; (3) GA interacts with other phytohormones manipulating plant development and reproduction; and (4) targeting GA signalling pathways is an effective genetic solution to improve agronomic traits in cereal crops. We suggest that the modification of GA-related genes and the identification of novel alleles without a negative impact on yield and adaptation are significant in cereal crop breeding for plant architecture improvement. We observed that an increasing number of GA-related genes and their mutants have been functionally validated, but only a limited number of GA-related genes have been genetically modified through conventional breeding tools and are widely used in crop breeding successfully. New genome editing technologies, such as the CRISPR/Cas9 system, hold the promise of validating the effectiveness of GA-related genes in crop development and opening a new venue for efficient and accelerated crop breeding.

Genome-wide association study for morphological traits and resistance to Peryonella pinodes in the USDA pea single plant plus collection

Peas (Pisum sativum) are the second most cultivated pulse crop in the world. They can serve as human food, fodder, and cover crop. The most serious foliar disease of pea cultivars worldwide is Ascochyta blight, which can be caused by several pathogens. Of these, Peyronella pinodes is the most aggressive and prevalent worldwide. Several traits, including resistance to Peyronella pinodes, stem diameter, internode length between nodes 2-3 and 5-6, and area of 7th leaf, were measured in 269 entries of the pea single plant plus collection. The heritability (H2) of the morphological traits was relatively high, while disease resistance had low heritability. Using 53,196 single-nucleotide polymorphism markers to perform a genome-wide association study to identify genomic loci associated with variation in all the traits measured, we identified 27 trait-locus associations, 5 of which were associated with more than 1 trait.

BrKAO2 mutations disrupt leafy head formation in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

The role of BrKAO2 in leafy head formation was confirmed by using two allelic Chinese cabbage mutants. Chinese cabbage yield and quality are determined by leafy head formation. Cloning and characterising the key genes regulating leafy head formation are essential for its varietal improvement. We used an EMS-mutagenised population of the heading type 'FT' Chinese cabbage line and identified two allelic non-heading mutants, i.e. nhm3-1 and nhm3-2. Genetic analysis showed that the mutant trait was controlled by a single recessive gene. MutMap and Kompetitive Allele Specific PCR genotyping revealed that BraA05g012440.3C was the candidate gene, which encodes ent-kaurenoic acid oxidase 2 in gibberellin (GA) biosynthetic pathway. It was named BrKAO2. Two non-synonymous mutations in the second BrKAO2 exon, respectively, accounted for the mutant phenotypes of nhm3-1 and nhm3-2. BrKAO2 was expressed during all leaf development stages, and there were no significant differences between the wild type and mutants in terms of BrKAO2 expression. The mutant phenotypes were restored to the wild type via exogenous GA3 application. RNA-Seq was performed on wild-type 'FT', nhm3-1, and nhm3-1 + GA3 rosette leaves, and several key genes involved in GA biosynthesis, signal transduction, and leafy head development were identified. These findings indicate that BrKAO2 is responsible for the leafy head formation in nhm3 mutants.

High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height

BACKGROUND

Coconut is an important tropical oil and fruit crop whose evolutionary position renders it a fantastic species for the investigation of the evolution of monocot chromosomes and the subsequent differentiation of ancient plants.

RESULTS

Here, we report the assembly and annotation of reference-grade genomes of Cn. tall and Cn. dwarf, whose genome sizes are 2.40 Gb and 2.39 Gb, respectively. The comparative analysis reveals that the two coconut subspecies diverge about 2-8 Mya while the conserved Arecaceae-specific whole-genome duplication (ω WGD) occurs approximately 47-53 Mya. It additionally allows us to reconstruct the ancestral karyotypes of the ten ancient monocot chromosomes and the evolutionary trajectories of the 16 modern coconut chromosomes. Fiber synthesis genes in Cn. tall, related to lignin and cellulose synthesis, are found at a higher copy number and expression level than dwarf coconuts. Integrated multi-omics analysis reveals that the difference in coconut plant height is the result of altered gibberellin metabolism, with both the GA20ox copy number and a single-nucleotide change in the promoter together leading to the difference in plant height between Cn. tall and Cn. dwarf.

CONCLUSION

We provide high-quality coconut genomes and reveal the genetic basis of trait differences between two coconuts through multi-omics analysis. We also reveal that the selection of plant height has been targeted for the same gene for millions of years, not only in natural selection of ancient plant as illustrated in coconut, but also for artificial selection in cultivated crops such as rice and maize.

Arabidopsis G-Protein β Subunit AGB1 Negatively Regulates DNA Binding of MYB62, a Suppressor in the Gibberellin Pathway

Plant G proteins are versatile components of transmembrane signaling transduction pathways. The deficient mutant of heterotrimeric G protein leads to defects in plant growth and development, suggesting that it regulates the GA pathway in Arabidopsis. However, the molecular mechanism of G protein regulation of the GA pathway is not understood in plants. In this study, two G protein β subunit (AGB1) mutants, agb1-2 and N692967, were dwarfed after exogenous application of GA₃. AGB1 interacts with the DNA-binding domain MYB62, a GA pathway suppressor. Transgenic plants were obtained through overexpression of MYB62 in two backgrounds including the wild-type (MYB62/WT Col-0) and agb1 mutants (MYB62/agb1) in Arabidopsis. Genetic analysis showed that under GA₃ treatment, the height of the transgenic plants MYB62/WT and MYB62/agb1 was lower than that of WT. The height of MYB62/agb1 plants was closer to MYB62/WT plants and higher than that of mutants agb1-2 and N692967, suggesting that MYB62 is downstream of AGB1 in the GA pathway. qRT-PCR and competitive DNA binding assays indicated that MYB62 can bind MYB elements in the promoter of GA2ox7, a GA degradation gene, to activate GA2ox7 transcription. AGB1 affected binding of MYB62 on the promoter of GA2ox7, thereby negatively regulating th eactivity of MYB62.

The influence of ethylene, gibberellins and brassinosteroids on energy and nitrogen-fixation metabolites in nodule tissue

Legume nodules are a unique plant organ that contain nitrogen-fixing rhizobial bacteria. For this interaction to be mutually beneficial, plant and bacterial metabolism must be precisely co-ordinated. Plant hormones are known to play essential roles during the establishment of legume-rhizobial symbioses but their role in subsequent nodule metabolism has not been explored in any depth. The plant hormones brassinosteroids, ethylene and gibberellins influence legume infection, nodule number and in some cases nodule function. In this paper, the influence of these hormones on nodule metabolism was examined in a series of well characterised pea mutants with altered hormone biosynthesis or response. A targeted set of metabolites involved in nutrient exchange and nitrogen fixation was examined in nodule tissue of mutant and wild type plants. Gibberellin-deficiency had a major negative impact on the level of several major dicarboxylates supplied to rhizobia by the plant and also led to a significant deficit in the amino acids involved in glutamine-aspartate transamination, consistent with the limited bacteroid development and low fixation rate of gibberellin-deficient na mutant nodules. In contrast, no major effects of brassinosteroid-deficiency or ethylene-insensitivity on the key metabolites in these pathways were found. Therefore, although all three hormones influence infection and nodule number, only gibberellin is important for the establishment of a functional nodule metabolome.

No Home without Hormones: How Plant Hormones Control Legume Nodule Organogenesis

The establishment of symbiotic nitrogen fixation requires the coordination of both nodule development and infection events. Despite the evolution of a variety of anatomical structures, nodule organs serve a common purpose in establishing a localized area that facilitates efficient nitrogen fixation. As in all plant developmental processes, the establishment of a new nodule organ is regulated by plant hormones. During nodule initiation, regulation of plant hormone signaling is one of the major targets of symbiotic signaling. We review the role of major developmental hormones in the initiation of the nodule organ and argue that the manipulation of plant hormones is a key requirement for engineering nitrogen fixation in non-legumes as the basis for improved food security and sustainability.

Cloning and Functional Analysis of Dwarf Gene Mini Plant 1 (MNP1) in Medicago truncatula

Plant height is a vital agronomic trait that greatly determines crop yields because of the close relationship between plant height and lodging resistance. Legumes play a unique role in the worldwide agriculture; however, little attention has been given to the molecular basis of their height. Here, we characterized the first dwarf mutant mini plant 1 (mnp1) of the model legume plant Medicago truncatula. Our study found that both cell length and the cell number of internodes were reduced in a mnp1 mutant. Using the forward genetic screening and subsequent whole-genome resequencing approach, we cloned the MNP1 gene and found that it encodes a putative copalyl diphosphate synthase (CPS) implicated in the first step of gibberellin (GA) biosynthesis. MNP1 was highly homologous to Pisum sativum LS. The subcellular localization showed that MNP1 was located in the chloroplast. Further analysis indicated that GA3 could significantly restore the plant height of mnp1-1, and expression of MNP1 in a cps1 mutant of Arabidopsis partially rescued its mini-plant phenotype, indicating the conservation function of MNP1 in GA biosynthesis. Our results provide valuable information for understanding the genetic regulation of plant height in M. truncatula.

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.

Hormonal and enzymatic responses of maize seedlings to chilling stress as affected by triazoles seed treatments

Triazole fungicides have been used for seed treatment to control soilborne diseases of maize, but seedlings coming from triazole-coated seed show serious phytotoxicity under chilling stress. To understand this phytotoxic impact, maize seed was treated with four triazoles fungicides and the corresponding seedlings were analysed on growth and gene expression. We found that maize seed coated with difenoconazole and tebuconazole exhibited either no or increased effects on germination and growth of maize at 25 °C, regardless of chemical concentrations. When maize seedlings were subjected to chilling treatment, however, their growth was significantly inhibited, and the inhibition was positively correlated with the rate of triazole application. Mesocotyl length decreased by 32.19-44.73% by difenoconazole, and 23.53-32.08% by tebuconazolet at rates of 1:50 and 1:25, respectively. However, myclobutanil did not have any effects at any temperatures. The contents of the gibberellin GA12 and abscisic acid in maize seedlings developed from difenoconazole- or tebuconazole-coated seed were significantly increased under chilling stress. The expression of two key catabolic enzyme genes, GA2ox3 and GA2ox4, was significantly up-regulated immediately following chilling stress and 2 days after recovery at 25 °C in the seedlings treated with difenoconazole or tebuconazole. This imbalance in phytohormones may explain why difenoconazole- or tebuconazole-coated seed more likely results in the phytotoxicity of maize seedlings under a low temperature condition during seed emergence and seedling growth. Since myclobutanil did not have this negative effect, it can be applied for seed coating in areas where temperatures are low during early seedling growth.

Morphological, transcriptomics and phytohormone analysis shed light on the development of a novel dwarf mutant of cabbage (Brassica oleracea)

Plant dwarf mutants generally exhibit delayed growth, delayed development, short internodes, and abnormal leaves and flowers and are ideal materials to explore the molecular mechanism of plant growth and development. In the current study, we first discovered a spontaneous cabbage (Brassica oleracea) dwarf mutant 99-198dw, which exhibits a dwarf stature, wrinkled leaves, non-heading, and substantially reduced self-fertility compared with the wild-type 99-198; however, the underlying molecular mechanism of its dwarfism is unknown. Here, we performed comparative phenotype, transcriptome and phytohormone analyses between 99-198 and 99-198dw. Cytological analysis showed that an increase in cell size, a reduction in cell layers, chloroplast degradation and a reduction in mitochondria were observed in 99-198dw. RNA-Seq showed that a total of 3801 differentially expressed genes (DEGs) were identified, including 2203 upregulated and 1598 downregulated genes in the dwarf mutant. Key genes in stress-resistant pathways were mostly upregulated, including salicylic acid (SA), jasmonic acid (JA), abscisic acid (ABA), ethylene (ET), etc., while the DEGs reported to be related to plant height, such as those involved in the gibberellin (GA), brassinolide (BR), indole-3-acetic acid (IAA), and strigolactone (SL) pathways were mostly downregulated. In addition, the DEGs in the cell division pathway were all downregulated, which is consistent with the cytokinesis defects detected by cytological analysis. The changes in the GA4, JA, ET, SA and ABA contents measured by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) absolute quantification were consistent with the transcriptome analysis. Further hormone treatment tests showed that the exogenous application of GA, BR, 6BA, paclobutrazol (PC), etc. did not rescue the phenotype, implying that the change in phytohormones is due to but not the cause of the dwarf trait. It was speculated that mutation of certain DEG related to cell division or participating in signalling pathway of phytohormones like GA, BR, IAA, and SL were the cause of dwarf. These results are informative for the elucidation of the underlying regulatory network in 99-198dw and enrich our understanding of plant dwarf traits at the molecular level.

Gibberellin Signaling Is Required for Far-Red Light-Induced Shoot Elongation in Pinus tabuliformis Seedlings

Gibberellin (GA) is known to play an important role in low red/far-red (R:FR) light ratio-mediated hypocotyl and petiole elongation in Arabidopsis (Arabidopsis thaliana). However, the regulatory relationship between low R:FR and GAs remains unclear, especially in gymnosperms. To increase our understanding of the molecular basis of low R:FR-mediated shoot elongation in pines and to determine whether there is an association between low R:FR and GAs action, we explored the morphological and transcriptomic changes triggered by low R:FR, GAs, and paclobutrazol (PAC), a GAs biosynthesis inhibitor, in Pinus tabuliformis seedlings. Transcriptome profiles revealed that low R:FR conditions and GAs have a common set of transcriptional targets in P. tabuliformis We provide evidence that the effect of low R:FR on shoot elongation in P. tabuliformis is at least partially modulated by GAs accumulation, which can be largely attenuated by PAC. GAs are also involved in the cross talk between different phytohormones in the low R:FR response. A GA biosynthesis gene, encoding ent-kaurenoic acid oxidase (KAO), was strongly stimulated by low R:FR without being affected by GAs feedback regulation or the photoperiod. We show that GA signaling is required for low R:FR-induced shoot elongation in P tabuliformis seedlings, and that there are different regulatory targets for low R:FR-mediated GA biosynthesis between conifers and angiosperms.

The Role of Gibberellins and Brassinosteroids in Nodulation and Arbuscular Mycorrhizal Associations

Plant hormones play key roles in nodulation and arbuscular mycorrhizal (AM) associations. These two agriculturally and ecologically important symbioses enable plants to gain access to nutrients, in particular, nitrogen in the case of nodulation and phosphorous in the case of AM. Work over the past few decades has revealed how symbioses with nitrogen-fixing rhizobia, restricted almost exclusively to legumes, evolved in part from ancient AM symbioses formed by more than 80% of land plants. Although overlapping, these symbiotic programs also have important differences, including the de novo development of a new organ found only in nodulation. One emerging area of research is the role of two plant hormone groups, the gibberellins (GAs) and brassinosteroids (BRs), in the development and maintenance of these symbioses. In this review, we compare and contrast the roles of these hormones in the two symbioses, including potential interactions with other hormones. This not only focuses on legumes, most of which can host both symbionts, but also examines the role of these in AM development in non-legumes. GA acts by suppressing DELLA, and this regulatory module acts to negatively influence both rhizobial and mycorrhizal infection but appears to promote nodule organogenesis. While an overall positive role for BRs in nodulation and AM has been suggested by studies using mutants disrupted in BR biosynthesis or response, application studies indicate that BR may play a more complex role in nodulation. Given the nature of these symbioses, with events regulated both spatially and temporally, future studies should examine in more detail how GAs and BRs may influence precise events during these symbioses, including interactions with other hormone groups.

Gibberellins promote nodule organogenesis but inhibit the infection stages of nodulation

Leguminous plant roots can form a symbiosis with soil-dwelling nitrogen-fixing rhizobia, leading to the formation of a new root organ, the nodule. Successful nodulation requires co-ordination of spatially separated events in the root, including infection in the root epidermis and nodule organogenesis deep in the root cortex. We show that the hormone gibberellin plays distinct roles in these epidermal and cortical programmes. We employed a unique set of genetic material in pea that includes severely gibberellin-deficient lines and della-deficient lines that enabled us to characterize all stages of infection and nodule development. We confirmed that gibberellin suppresses infection thread formation and show that it also promotes nodule organogenesis into nitrogen-fixing organs. In both cases, this is achieved through the action of DELLA proteins. This study therefore provides a mechanism to explain how both low and high gibberellin signalling can result in reduced nodule number and reveals a clear role for gibberellin in the maturation of nodules into nitrogen-fixing organs. We also demonstrate that gibberellin acts independently of ethylene in promoting nodule development.

Gibberellin biosynthesis and metabolism: A convergent route for plants, fungi and bacteria

Gibberellins (GAs) are natural complex biomolecules initially identified as secondary metabolites in the fungus Gibberella fujikuroi with strong implications in plant physiology. GAs have been identified in different fungal and bacterial species, in some cases related to virulence, but the full understanding of the role of these metabolites in the different organisms would need additional investigation. In this review, we summarize the current evidence regarding a common pathway for GA synthesis in fungi, bacteria and plant from the genes depicted as part of the GA production cluster to the enzymes responsible for the catalytic transformations and the biosynthetical routes involved. Moreover, we present the relationship between these observations and the biotechnological applications of GAs in plants, which has shown an enormous commercial impact.

Foliar Glyphosate Treatment Alters Transcript and Hormone Profiles in Crown Buds of Leafy Spurge and Induces Dwarfed and Bushy Phenotypes throughout its Perennial Lifecycle

Leafy spurge ( L.) is an invasive weed of North America and its perennial nature attributed to underground adventitious buds (UABs) that undergo seasonal cycles of para-, endo-, and ecodormancy. Recommended rates of glyphosate (∼1 kg ha) destroy aboveground shoots but plants still regenerate vegetatively; therefore, it is considered glyphosate-tolerant. However, foliar application of glyphosate at higher rates (2.2-6.7 kg ha) causes sublethal effects that induce UABs to produce stunted, bushy phenotypes. We investigated the effects of glyphosate treatment (±2.24 kg ha) on vegetative growth, phytohormone, and transcript profiles in UABs under controlled environments during one simulated seasonal cycle. Because shoots derived from UABs of foliar glyphosate-treated plants produced stunted, bushy phenotypes, we could not directly determine if these UABs transitioned through seasonally induced endo- and ecodormancy. However, transcript abundance for leafy spurge dormancy marker genes and principal component analyses suggested that UABs of foliar glyphosate-treated plants transitioned through endo- and ecodormancy. Glyphosate treatment increased shikimate abundance in UABs 7 d after treatment; however, the abundance of shikimate gradually decreased as UABs transitioned through endo- and ecodormancy. The dissipation of shikimate over time suggests that glyphosate's target site was no longer affected, but these changes did not reverse the altered phenotypes observed from UABs of foliar glyphosate-treated leafy spurge. Transcript profiles further indicated that foliar glyphosate treatment significantly affected phytohormone biosynthesis and signaling, particularly auxin transport; gibberellic acid, abscisic acid and jasmonic acid biosynthesis; ethylene responses; and detoxification and cell cycle processes in UABs. These results correlated well with the available phytohormone profiles and altered phenotypes.

Genetic Regulation of GA Metabolism during Vernalization, Floral Bud Initiation and Development in Pak Choi (Brassica rapa ssp. chinensis Makino)

Pak choi (Brassica rapa ssp. chinensis Makino) is a representative seed vernalization vegetable and premature bolting in spring can cause significant economic loss. Thus, it is critical to elucidate the mechanism of molecular regulation of vernalization and floral bud initiation to prevent premature bolting. Gibberellin (GA) is the key plant hormone involved in regulating plant development. To gain a better understanding of GA metabolism in pak choi, the content of GA in pak choi was measured at different stages of plant development using enzyme-linked immunosorbent assay. The results showed that the GA content increased significantly after low-temperature treatment (4°C) and then decreased rapidly with vegetative growth. During floral bud initiation, the GA content increased rapidly until it peaked upon floral bud differentiation. To elucidate these changes in GA content, the expression of homologous genes encoding enzymes directly involved in GA metabolism were analyzed. The results showed that the changes in the expression of four genes involved in GA synthesis (Bra035120 encoding ent-kaurene synthase, Bra009868 encoding ent-kaurene oxidase, Bra015394 encoding ent-kaurenoic acid oxidase, and Bra013890 encoding GA20-oxidase) were correlated with the changes in GA content. In addition, by comparing the expression of genes involved in GA metabolism at different growth stages, seven differentially expressed genes (Bra005596, Bra009285, Bra022565, Bra008362, Bra033324, Bra010802, and Bra030500) were identified. The differential expression of these genes were directly correlated with changes in GA content, suggesting that these genes were directly related to vernalization, floral bud initiation and development. These results contribute to the understanding of the molecular mechanism of changes in GA content during different developmental phases in pak choi.

Gene expression and metabolite profiling of gibberellin biosynthesis during induction of somatic embryogenesis in Medicago truncatula Gaertn

Gibberellins (GAs) are involved in the regulation of numerous developmental processes in plants including zygotic embryogenesis, but their biosynthesis and role during somatic embryogenesis (SE) is mostly unknown. In this study we show that during three week- long induction phase, when cells of leaf explants from non-embryogenic genotype (M9) and embryogenic variant (M9-10a) were forming the callus, all the bioactive gibberellins from non-13-hydroxylation (GA4, GA7) and 13-hydroxylation (GA1, GA5, GA3, GA6) pathways were present, but the contents of only a few of them differed between the tested lines. The GA53 and GA19 substrates synthesized by the 13-hydroxylation pathway accumulated specifically in the M9-10a line after the first week of induction; subsequently, among the bioactive gibberellins detected, only the content of GA3 increased and appeared to be connected with acquisition of embryogenic competence. We fully annotated 20 Medicago truncatula orthologous genes coding the enzymes which catalyze all the known reactions of gibberellin biosynthesis. Our results indicate that, within all the genes tested, expression of only three: MtCPS, MtGA3ox1 and MtGA3ox2, was specific to embryogenic explants and reflected the changes observed in GA53, GA19 and GA3 contents. Moreover, by analyzing expression of MtBBM, SE marker gene, we confirmed the inhibitory effect of manipulation in GAs metabolism, applying exogenous GA3, which not only impaired the production of somatic embryos, but also significantly decreased expression of this gene.

Gene expression and metabolite profiling of gibberellin biosynthesis during induction of somatic embryogenesis in Medicago truncatula Gaertn

Gibberellins (GAs) are involved in the regulation of numerous developmental processes in plants including zygotic embryogenesis, but their biosynthesis and role during somatic embryogenesis (SE) is mostly unknown. In this study we show that during three week- long induction phase, when cells of leaf explants from non-embryogenic genotype (M9) and embryogenic variant (M9-10a) were forming the callus, all the bioactive gibberellins from non-13-hydroxylation (GA4, GA7) and 13-hydroxylation (GA1, GA5, GA3, GA6) pathways were present, but the contents of only a few of them differed between the tested lines. The GA53 and GA19 substrates synthesized by the 13-hydroxylation pathway accumulated specifically in the M9-10a line after the first week of induction; subsequently, among the bioactive gibberellins detected, only the content of GA3 increased and appeared to be connected with acquisition of embryogenic competence. We fully annotated 20 Medicago truncatula orthologous genes coding the enzymes which catalyze all the known reactions of gibberellin biosynthesis. Our results indicate that, within all the genes tested, expression of only three: MtCPS, MtGA3ox1 and MtGA3ox2, was specific to embryogenic explants and reflected the changes observed in GA53, GA19 and GA3 contents. Moreover, by analyzing expression of MtBBM, SE marker gene, we confirmed the inhibitory effect of manipulation in GAs metabolism, applying exogenous GA3, which not only impaired the production of somatic embryos, but also significantly decreased expression of this gene.

Labeling Studies Clarify the Committed Step in Bacterial Gibberellin Biosynthesis

Bacteria have evolved gibberellin phytohormone biosynthesis independently of plants and fungi. Through 13C-labeling and NMR analysis, the mechanistically unusual "B" ring contraction catalyzed by a cytochrome P450 (CYP114), which is the committed step in gibberellin biosynthesis, was shown to occur via oxidative extrusion of carbon-7 from ent-kaurenoic acid in bacteria. This is identical to the convergently evolved chemical transformation in plants and fungi, suggesting a common semipinacol rearrangement mechanism potentially guided by carbon-4α carboxylate proximity.

Interactions between ethylene, gibberellins, and brassinosteroids in the development of rhizobial and mycorrhizal symbioses of pea

The regulation of arbuscular mycorrhizal development and nodulation involves complex interactions between the plant and its microbial symbionts. In this study, we use the recently identified ethylene-insensitive ein2 mutant in pea (Pisum sativum L.) to explore the role of ethylene in the development of these symbioses. We show that ethylene acts as a strong negative regulator of nodulation, confirming reports in other legumes. Minor changes in gibberellin1 and indole-3-acetic acid levels in ein2 roots appear insufficient to explain the differences in nodulation. Double mutants produced by crosses between ein2 and the severely gibberellin-deficient na and brassinosteroid-deficient lk mutants showed increased nodule numbers and reduced nodule spacing compared with the na and lk single mutants, but nodule numbers and spacing were typical of ein2 plants, suggesting that the reduced number of nodules innaandlkplants is largely due to the elevated ethylene levels previously reported in these mutants. We show that ethylene can also negatively regulate mycorrhizae development when ethylene levels are elevated above basal levels, consistent with a role for ethylene in reducing symbiotic development under stressful conditions. In contrast to the hormone interactions in nodulation, ein2 does not override the effect of lk or na on the development of arbuscular mycorrhizae, suggesting that brassinosteroids and gibberellins influence this process largely independently of ethylene.

The gibberellin biosynthetic genes AtKAO1 and AtKAO2 have overlapping roles throughout Arabidopsis development

Ent-kaurenoic acid oxidase (KAO), a class of cytochrome P450 monooxygenases of the subfamily CYP88A, catalyzes the conversion of ent-kaurenoic acid (KA) to gibberellin (GA) GA12 , the precursor of all GAs, thereby playing an important role in determining GA concentration in plants. Past work has demonstrated the importance of KAO activity for growth in various plant species. In Arabidopsis, this enzyme is encoded by two genes designated KAO1 and KAO2. In this study, we used various approaches to determine the physiological roles of KAO1 and KAO2 throughout plant development. Analysis of gene expression pattern reveals that both genes are mainly expressed in germinating seeds and young developing organs, thus suggesting functional redundancy. Consistent with this, kao1 and kao2 single mutants are indistinguishable from wild-type plants. By contrast, the kao1 kao2 double mutant exhibits typical non-germinating GA-dwarf phenotypes, similar to those observed in the severely GA-deficient ga1-3 mutant. Phenotypic characterization and quantitative analysis of endogenous GA contents of single and double kao mutants further confirm an overlapping role of KAO1 and KAO2 throughout Arabidopsis development.

Gibberellin deficiency pleiotropically induces culm bending in sorghum: an insight into sorghum semi-dwarf breeding

Regulation of symmetrical cell growth in the culm is important for proper culm development. So far, the involvement of gibberellin (GA) in this process has not yet been demonstrated in sorghum. Here, we show that GA deficiency resulting from any loss-of-function mutation in four genes (SbCPS1, SbKS1, SbKO1, SbKAO1) involved in the early steps of GA biosynthesis, not only results in severe dwarfism but also in abnormal culm bending. Histological analysis of the bent culm revealed that the intrinsic bending was due to an uneven cell proliferation between the lower and upper sides of culm internodes. GA treatment alleviated the bending and dwarfism in mutants, whereas the GA biosynthesis inhibitor, uniconazole, induced such phenotypes in wild-type plants--both in a concentration-dependent manner, indicating an important role of GA in controlling erectness of the sorghum culm. Finally, we propose that because of the tight relationship between GA deficiency-induced dwarfism and culm bending in sorghum, GA-related mutations have unlikely been selected in the history of sorghum breeding, as could be inferred from previous QTL and association studies on sorghum plant height that did not pinpoint GA-related genes.

Characterization of sck1, a novel Castanea mollissima mutant with the extreme short catkins and decreased gibberellin

A novel Chinese chestnut (Castanea mollissima Bl.) mutant with extreme short catkins, here was named sck1 and has been characterized in the present study. This sck1 caused 6-fold shorter than wild-type catkins. Endogenous gibberellic acids markedly decreased in the mutant, and application of exogenous GA(3) could partially restore the sck1 phenotype to the wild-type phenotype. Paclobutrazol (PP(333)), an antagonist of GAs biosynthesis, could significantly inhibit the wild-type catkins growth, and lead to a short catkins phenotype similar to the sck1. In addition, compared to the wild-type catkins, the mRNA expression level of ent-kaurenoic acid oxidase (KAO), a gibberellin biosynthesis key gene, was significantly down-regulated (P<0.01) in the sck1. Importantly, transient over-expression of a normal CmKAO gene in short catkins also could partially restore the wild-type phenotype. Real-time PCR and semi-quantitative analysis showed that the mRNA expression level of KAO was significantly up-regulated. In addition, transient RNA interference of CmKAO in wild-type catkins led the mRNA expression level of KAO decrease significantly and inhibited the wild-type catkins elongation strongly. Taken together, our results suggest that the lower gibberellic acids content that is due to decreased CmKAO expression level may contribute to the generation of the extreme short male catkins, sck1.

Gibberellin biosynthesis and its regulation

The GAs (gibberellins) comprise a large group of diterpenoid carboxylic acids that are ubiquitous in higher plants, in which certain members function as endogenous growth regulators, promoting organ expansion and developmental changes. These compounds are also produced by some species of lower plants, fungi and bacteria, although, in contrast to higher plants, the function of GAs in these organisms has only recently been investigated and is still unclear. In higher plants, GAs are synthesized by the action of terpene cyclases, cytochrome P450 mono-oxygenases and 2-oxoglutarate-dependent dioxygenases localized, respectively, in plastids, the endomembrane system and the cytosol. The concentration of biologically active GAs at their sites of action is tightly regulated and is moderated by numerous developmental and environmental cues. Recent research has focused on regulatory mechanisms, acting primarily on expression of the genes that encode the dioxygenases involved in biosynthesis and deactivation. The present review discusses the current state of knowledge on GA metabolism with particular emphasis on regulation, including the complex mechanisms for the maintenance of GA homoeostasis.

Expression dynamics of metabolic and regulatory components across stages of panicle and seed development in indica rice

Carefully analyzed expression profiles can serve as a valuable reference for deciphering gene functions. We exploited the potential of whole genome microarrays to measure the spatial and temporal expression profiles of rice genes in 19 stages of vegetative and reproductive development. We could verify expression of 22,980 genes in at least one of the tissues. Differential expression analysis with respect to five vegetative tissues and preceding stages of development revealed reproductive stage-preferential/-specific genes. By using subtractive logic, we identified 354 and 456 genes expressing specifically during panicle and seed development, respectively. The metabolic/hormonal pathways and transcription factor families playing key role in reproductive development were elucidated after overlaying the expression data on the public databases and manually curated list of transcription factors, respectively. During floral meristem differentiation (P1) and male meiosis (P3), the genes involved in jasmonic acid and phenylpropanoid biosynthesis were significantly upregulated. P6 stage of panicle, containing mature gametophytes, exhibited enrichment of transcripts involved in homogalacturonon degradation. Genes regulating auxin biosynthesis were induced during early seed development. We validated the stage-specificity of regulatory regions of three panicle-specific genes, OsAGO3, OsSub42, and RTS, and an early seed-specific gene, XYH, in transgenic rice. The data generated here provides a snapshot of the underlying complexity of the gene networks regulating rice reproductive development.

Expression dynamics of metabolic and regulatory components across stages of panicle and seed development in indica rice

Carefully analyzed expression profiles can serve as a valuable reference for deciphering gene functions. We exploited the potential of whole genome microarrays to measure the spatial and temporal expression profiles of rice genes in 19 stages of vegetative and reproductive development. We could verify expression of 22,980 genes in at least one of the tissues. Differential expression analysis with respect to five vegetative tissues and preceding stages of development revealed reproductive stage-preferential/-specific genes. By using subtractive logic, we identified 354 and 456 genes expressing specifically during panicle and seed development, respectively. The metabolic/hormonal pathways and transcription factor families playing key role in reproductive development were elucidated after overlaying the expression data on the public databases and manually curated list of transcription factors, respectively. During floral meristem differentiation (P1) and male meiosis (P3), the genes involved in jasmonic acid and phenylpropanoid biosynthesis were significantly upregulated. P6 stage of panicle, containing mature gametophytes, exhibited enrichment of transcripts involved in homogalacturonon degradation. Genes regulating auxin biosynthesis were induced during early seed development. We validated the stage-specificity of regulatory regions of three panicle-specific genes, OsAGO3, OsSub42, and RTS, and an early seed-specific gene, XYH, in transgenic rice. The data generated here provides a snapshot of the underlying complexity of the gene networks regulating rice reproductive development.

Mendel, 150 years on

Mendel's paper 'Versuche über Pflanzen-Hybriden' is the best known in a series of studies published in the late 18th and 19th centuries that built our understanding of the mechanism of inheritance. Mendel investigated the segregation of seven gene characters of pea (Pisum sativum), of which four have been identified. Here, we review what is known about the molecular nature of these genes, which encode enzymes (R and Le), a biochemical regulator (I) and a transcription factor (A). The mutations are: a transposon insertion (r), an amino acid insertion (i), a splice variant (a) and a missense mutation (le-1). The nature of the three remaining uncharacterized characters (green versus yellow pods, inflated versus constricted pods, and axial versus terminal flowers) is discussed.

The genes for gibberellin biosynthesis in wheat

The gibberellin biosynthesis pathway is well defined in Arabidopsis and features seven key enzymes including ent-copalyl diphosphate synthase (CPS), ent-kaurene synthase (KS), ent-kaurene oxidase (KO), ent-kaurenoic acid oxidase (KAO), GA 20-oxidase, GA 3-oxidase, and GA 2-oxidase. The Arabidopsis genes were used to identify their counterparts in wheat and the TaCPS, TaKS, TaKO, and TaKAO genes were cloned from Chinese Spring wheat. In order to determine their chromosome locations, expression patterns and feedback regulations, three TaCPS genes, three TaKS genes, three TaKO genes, and three TaKAO genes were cloned from Chinese Spring wheat. They are mainly located on chromosomes 7A, 7B, 7D and 2A, 2B and 2D. The expression patterns of TaCPS, TaKS, TaKO, and TaKAO genes in wheat leaves, young spikes, peduncles, the third and forth internodes were investigated using quantitative PCR. The results showed that all the genes were constitutively expressed in wheat, but their relative expression levels varied in different tissues. They were mainly transcribed in stems, secondly in leaves and spikes, and the least in peduncles. Feedback regulation of the TaCPS, TaKS, TaKO, and TaKAO genes was not evident. These results indicate that all the genes and their homologs may play important roles in the developmental processes of wheat, but each of the homologs may function differently in different tissues or during different developmental stages.

Interactions between GA, auxin, and UNI expression controlling shoot ontogeny, leaf morphogenesis, and auxin response in Pisum sativum (Fabaceae): or how the uni-tac mutant is rescued

PREMISE OF THE STUDY

Leaf morphogenesis, including that of compound leaves, provides the basis for the great diversity of leaf form among higher plants. Leaf form is an important character by which plants adapt to their environment. The common garden pea provides a developmental model system for understanding leaf development in the legumes and a contrasting one for other groups of plants.

METHODS

We used genetic, tissue culture, and physiological methods, as well as DR5::GUS expression and qRT-PCR, to explore the interactions between the hormones gibberellic acid (GA) and auxin and Unifoliata ( UNI ) gene expression that control leaf morphogenesis in pea.

KEY RESULTS

Rate of increase in leaf complexity during shoot ontogeny (i.e., heteroblasty) and adult leaf complexity are controlled by GA through UNI . Leaves on greenhouse-grown uni-tac mutants are rescued by weekly GA or auxin applications. Auxin responsiveness is reduced in uni-tac shoot and root tips and in wild-type shoot tips treated with auxin transport inhibitors. GA and auxin increase UNI mRNA levels in uni-tac as well as that of other transcription factors.

CONCLUSIONS

GA and auxin positively promote leaf dissection during leaf morphogenesis in pea by prolonging the time during which acropetally initiated pinna pairs are produced. GA-generated elaboration of leaf morphogenesis is in distinct contrast to that in other species, such as tomato and Cardamine . Instead, GA and auxin play common and supportive roles in pea leaf morphogenesis as they do in many other aspects of plant development

Molecular activities, biosynthesis and evolution of triterpenoid saponins

Saponins are bioactive compounds generally considered to be produced by plants to counteract pathogens and herbivores. Besides their role in plant defense, saponins are of growing interest for drug research as they are active constituents of several folk medicines and provide valuable pharmacological properties. Accordingly, much effort has been put into unraveling the modes of action of saponins, as well as in exploration of their potential for industrial processes and pharmacology. However, the exploitation of saponins for bioengineering crop plants with improved resistances against pests as well as circumvention of laborious and uneconomical extraction procedures for industrial production from plants is hampered by the lack of knowledge and availability of genes in saponin biosynthesis. Although the ability to produce saponins is rather widespread among plants, a complete synthetic pathway has not been elucidated in any single species. Current conceptions consider saponins to be derived from intermediates of the phytosterol pathway, and predominantly enzymes belonging to the multigene families of oxidosqualene cyclases (OSCs), cytochromes P450 (P450s) and family 1 UDP-glycosyltransferases (UGTs) are thought to be involved in their biosynthesis. Formation of unique structural features involves additional biosynthetical enzymes of diverse phylogenetic background. As an example of this, a serine carboxypeptidase-like acyltransferase (SCPL) was recently found to be involved in synthesis of triterpenoid saponins in oats. However, the total number of identified genes in saponin biosynthesis remains low as the complexity and diversity of these multigene families impede gene discovery based on sequence analysis and phylogeny. This review summarizes current knowledge of triterpenoid saponin biosynthesis in plants, molecular activities, evolutionary aspects and perspectives for further gene discovery.

The extreme dwarf phenotype of the GA-sensitive mutant of sunflower, dwarf2, is generated by a deletion in the ent-kaurenoic acid oxidase1 (HaKAO1) gene sequence

A dwarf mutant, dw arf 2 (dw2), was isolated from sunflower (Helianthus annuus). The most obvious alterations of dw2 plants were the lack of stem growth, reduced size of leaves, petioles and flower organs, retarded flower development. Pollen and ovules were produced but the filaments failed to extrude the anthers from the corolla. The dw2 phenotype was mainly because of reduced cell size. In dw2 leaves, the dark-green color was not so much due to higher pigment content, but was correlated with a changed leaf morphology. The mutant responded to the application of bioactive gibberellins (GAs). The levels of ent-7α-hydroxykaurenoic acid, GA(19), GA(20) and GA(1) in dw2 seedlings were severely decreased relative to those in its wild type (WT). ent-Kaurenoic acid was actively converted to ent-7α-hydroxykaurenoic acid in WT plants but quite poorly in dw2 plants. All together these data suggested that the dw2 mutation severely reduced the flux through the biosynthetic pathway leading to active GAs by hampering the conversion of ent-kaurenoic acid to GA(12). Two ent-kaurenoic acid oxidase (KAO) genes were identified. HaKAO1 was expressed everywhere in sunflower organs, while HaKAO2 was mainly expressed in roots. We demonstrated that a DNA deletion in HaKAO1 of dw2 generated aberrant mRNA-splicing, causing a premature stop codon in the amino acid sequence. In dw2 calli, Agrobacterium-mediated transfer of WT HaKAO1 cDNA restored the WT endogenous levels of GAs. In segregating BC(1) progeny, the deletion co-segregated with the dwarf phenotype. The deletion was generated near to a breakpoint of a more complex chromosome rearrangement.

Relationship between gibberellin, ethylene and nodulation in Pisum sativum

• Gibberellin (GA) deficiency resulting from the na mutation in pea (Pisum sativum) causes a reduction in nodulation. Nodules that do form are aberrant, having poorly developed meristems and a lack of enlarged cells. Studies using additional GA-biosynthesis double mutants indicate that this results from severe GA deficiency of the roots rather than simply dwarf shoot stature. • Double mutants isolated from crosses between na and three supernodulating pea mutants exhibit a supernodulation phenotype, but the nodule structures are aberrant. This suggests that severely reduced GA concentrations are not entirely inhibitory to nodule initiation, but that higher GA concentrations are required for proper nodule development. • na mutants evolve more than double the amount of ethylene produced by wild-type plants, indicating that low GA concentrations can promote ethylene production. The excess ethylene may contribute to the reduced nodulation of na plants, as application of an ethylene biosynthesis inhibitor increased na nodule numbers. However, these nodules were still aberrant in structure. • Constitutive GA signalling mutants also form significantly fewer nodules than wild-type plants. This suggests that there is an optimum degree of GA signalling required for nodule formation and that the GA signal, and not the concentration of bioactive GA per se, is important for nodulation.

EST analysis reveals putative genes involved in glycyrrhizin biosynthesis

Background

Glycyrrhiza uralensis is one of the most popular medicinal plants in the world and is also widely used in the flavoring of food and tobacco. Due to limited genomic and transcriptomic data, the biosynthetic pathway of glycyrrhizin, the major bioactive compound in G. uralensis, is currently unclear. Identification of candidate genes involved in the glycyrrhizin biosynthetic pathway will significantly contribute to the understanding of the biosynthetic and medicinal chemistry of this compound.

Results

We used the 454 GS FLX platform and Titanium regents to produce a substantial expressed sequence tag (EST) dataset from the vegetative organs of G. uralensis. A total of 59,219 ESTs with an average read length of 409 bp were generated. 454 ESTs were combined with the 50,666 G. uralensis ESTs in GenBank. The combined ESTs were assembled into 27,229 unique sequences (11,694 contigs and 15,535 singletons). A total of 20,437 unique gene elements representing approximately 10,000 independent transcripts were annotated using BLAST searches (e-value ≤ 1e-5) against the SwissProt, KEGG, TAIR, Nr and Nt databases. The assembled sequences were annotated with gene names and Gene Ontology (GO) terms. With respect to the genes related to glycyrrhizin metabolism, genes encoding 16 enzymes of the 18 total steps of the glycyrrhizin skeleton synthesis pathway were found. To identify novel genes that encode cytochrome P450 enzymes and glycosyltransferases, which are related to glycyrrhizin metabolism, a total of 125 and 172 unigenes were found to be homologous to cytochrome P450s and glycosyltransferases, respectively. The cytochrome P450 candidate genes were classified into 32 CYP families, while the glycosyltransferase candidate genes were classified into 45 categories by GO analysis. Finally, 3 cytochrome P450 enzymes and 6 glycosyltransferases were selected as the candidates most likely to be involved in glycyrrhizin biosynthesis through an organ-specific expression pattern analysis based on real-time PCR.

Conclusions

Using the 454 GS FLX platform and Titanium reagents, our study provides a high-quality EST database for G. uralensis. Based on the EST analysis, novel candidate genes related to the secondary metabolite pathway of glycyrrhizin, including novel genes encoding cytochrome P450s and glycosyltransferases, were found. With the assistance of organ-specific expression pattern analysis, 3 unigenes encoding cytochrome P450s and 6 unigenes encoding glycosyltransferases were selected as the candidates most likely to be involved in glycyrrhizin biosynthesis.

Licorice beta-amyrin 11-oxidase, a cytochrome P450 with a key role in the biosynthesis of the triterpene sweetener glycyrrhizin

Glycyrrhizin, a major bioactive compound derived from the underground parts of Glycyrrhiza (licorice) plants, is a triterpene saponin that possesses a wide range of pharmacological properties and is used worldwide as a natural sweetener. Because of its economic value, the biosynthesis of glycyrrhizin has received considerable attention. Glycyrrhizin is most likely derived from the triterpene beta-amyrin, an initial product of the cyclization of 2,3-oxidosqualene. The subsequent steps in glycyrrhizin biosynthesis are believed to involve a series of oxidative reactions at the C-11 and C-30 positions, followed by glycosyl transfers to the C-3 hydroxyl group; however, no genes encoding relevant oxidases or glycosyltransferases have been identified. Here we report the successful identification of CYP88D6, a cytochrome P450 monooxygenase (P450) gene, as a glycyrrhizin-biosynthetic gene, by transcript profiling-based selection from a collection of licorice expressed sequence tags (ESTs). CYP88D6 was characterized by in vitro enzymatic activity assays and shown to catalyze the sequential two-step oxidation of beta-amyrin at C-11 to produce 11-oxo-beta-amyrin, a possible biosynthetic intermediate between beta-amyrin and glycyrrhizin. CYP88D6 coexpressed with beta-amyrin synthase in yeast also catalyzed in vivo oxidation of beta-amyrin to 11-oxo-beta-amyrin. CYP88D6 expression was detected in the roots and stolons by RT-PCR; however, no amplification was observed in the leaves or stems, which is consistent with the accumulation pattern of glycyrrhizin in planta. These results suggest a role for CYP88D6 as a beta-amyrin 11-oxidase in the glycyrrhizin pathway.

Licorice beta-amyrin 11-oxidase, a cytochrome P450 with a key role in the biosynthesis of the triterpene sweetener glycyrrhizin

Glycyrrhizin, a major bioactive compound derived from the underground parts of Glycyrrhiza (licorice) plants, is a triterpene saponin that possesses a wide range of pharmacological properties and is used worldwide as a natural sweetener. Because of its economic value, the biosynthesis of glycyrrhizin has received considerable attention. Glycyrrhizin is most likely derived from the triterpene beta-amyrin, an initial product of the cyclization of 2,3-oxidosqualene. The subsequent steps in glycyrrhizin biosynthesis are believed to involve a series of oxidative reactions at the C-11 and C-30 positions, followed by glycosyl transfers to the C-3 hydroxyl group; however, no genes encoding relevant oxidases or glycosyltransferases have been identified. Here we report the successful identification of CYP88D6, a cytochrome P450 monooxygenase (P450) gene, as a glycyrrhizin-biosynthetic gene, by transcript profiling-based selection from a collection of licorice expressed sequence tags (ESTs). CYP88D6 was characterized by in vitro enzymatic activity assays and shown to catalyze the sequential two-step oxidation of beta-amyrin at C-11 to produce 11-oxo-beta-amyrin, a possible biosynthetic intermediate between beta-amyrin and glycyrrhizin. CYP88D6 coexpressed with beta-amyrin synthase in yeast also catalyzed in vivo oxidation of beta-amyrin to 11-oxo-beta-amyrin. CYP88D6 expression was detected in the roots and stolons by RT-PCR; however, no amplification was observed in the leaves or stems, which is consistent with the accumulation pattern of glycyrrhizin in planta. These results suggest a role for CYP88D6 as a beta-amyrin 11-oxidase in the glycyrrhizin pathway.

Dwarf plants of diploid Medicago sativa carry a mutation in the gibberellin 3-beta-hydroxylase gene

In this paper we describe the identification of a gene, MsDWF1 coding for a putative gibberellin 3-beta-hydroxylase (GA3ox), whose natural mutation is conditioning a dwarf growth phenotype in Medicago sativa. The dwarf phenotype could not be complemented with grafting, which indicates that the bioactive gibberellin compound necessary for shoot elongation is immobile. On the contrary, exogenously added gibberellic acid restored normal growth. The genetic position of the Msdwf1 gene was mapped to linkage group 2 (LG2) and the physical location was delimited by map-based cloning using Medicago truncatula genomic resources. Based on the similar appearance and behavior of the dwarf Medicago sativa plants to the pea stem length mutant (le) as well as the synthenic map position of the two genes it was postulated that MsDWF1 and pea Le are orthologs. The comparison of wild type and mutant allele sequences of MsGA3ox revealed an amino acid change in a conserved position in the mutant allele, which most probably impaired the function of the enzyme. Our results indicate that the dwarf phenotype was the consequence of this mutation.

Influence of electron transport proteins on the reactions catalyzed by Fusarium fujikuroi gibberellin monooxygenases

The multifunctional cytochrome P450 monooxygenases P450-1 and P450-2 from Fusarium fujikuroi catalyze the formation of GA14 and GA4, respectively, in the gibberellin (GA)-biosynthetic pathway. However, the activity of these enzymes is qualitatively and quantitatively different in mutants lacking the NADPH:cytochrome P450 oxidoreductase (CPR) compared to CPR-containing strains. 3beta-Hydroxylation, a major P450-1 activity in wild-type strains, was strongly decreased in the mutants relative to oxidation at C-6 and C-7, while synthesis of C19-GAs as a result of oxidative cleavage of C-20 by P450-2 was almost absent whereas the C-20 alcohol, aldehyde and carboxylic acid derivatives accumulated. Interaction of the monooxygenases with alternative electron transport proteins could account for these different product distributions. In the absence of CPR, P450-1 activities were NADH-dependent, and stimulated by cytochrome b5 or by added FAD. These properties as well as the decreased efficiency of P450-1 and P450-2 in the mutants are consistent with the participation of cytochrome b5:NADH cytochrome b5 reductase as redox partner of the gibberellin monooxygenases in the absence of CPR. We provide evidence, from either incubations of GA12 (C-20 methyl) with cultures of the mutant suspended in [18O]H2O or maintained under an atmosphere of [18O]O2:N2 (20:80), that GA15 (C-20 alcohol) and GA24 (C-20 aldehyde) are formed directly from dioxygen and not from hydrolysis of covalently enzyme-bound intermediates. Thus these partially oxidized GAs correspond to intermediates of the sequential oxidation of C-20 catalyzed by P450-2.

Developmental and embryo axis regulation of gibberellin biosynthesis during germination and young seedling growth of pea

The expression patterns of five genes (PsGA20ox1, PsGA20ox2, PsGA3ox1, PsGA2ox1, and PsGA2ox2) encoding five regulatory gibberellin (GA) biosynthesis enzymes (two GA 20-oxidases, a GA 3beta-hydroxylase, and two GA 2beta-hydroxylases) were examined to gain insight into how these genes coordinate GA biosynthesis during germination and early postgermination stages of the large-seeded dicotyledonous plant pea (Pisum sativum). At the time the developing embryo fills the seed coat, high mRNA levels of PsGA20ox2 (primarily responsible for conversion of C20-GAs to GA(20)), PsGA2ox1 (primarily responsible for conversion of GA(20) to GA(29)), and PsGA2ox2 (primarily responsible for conversion of GA(1) to GA(8)) were detected in the seeds, along with high GA(20) and GA(29) levels, the enzymatic products of these genes. Embryo maturation was accompanied by a large reduction in PsGA20ox2 and PsGA2ox1 mRNA and lower GA(20) and GA(29) levels. However, PsGA2ox2 transcripts remained high. Following seed imbibition, GA(20) levels in the cotyledons decreased, while PsGA3ox1 mRNA and GA(1) levels increased, implying that GA(20) was being used for de novo synthesis of GA(1). The presence of the embryo axis was required for stimulation of cotyledonary GA(1) synthesis at the mRNA and enzyme activity levels. As the embryo axis doubled in size, PsGA20ox1 and PsGA3ox1 transcripts increased, both GA(1) and GA(8) were detectable, PsGA2ox2 transcripts decreased, and PsGA2ox1 transcripts remained low. Cotyledonary-, root-, and shoot-specific expression of these GA biosynthesis genes and the resultant endogenous GA profiles support a key role for de novo GA biosynthesis in each organ during germination and early seedling growth of pea.

Cytochrome P450 mono-oxygenases in conifer genomes: discovery of members of the terpenoid oxygenase superfamily in spruce and pine

Diterpene resin acids, together with monoterpenes and sesquiterpenes, are the most prominent defence chemicals in conifers. These compounds belong to the large group of structurally diverse terpenoids formed by enzymes known as terpenoid synthases. CYPs (cytochrome P450-dependent mono-oxygenases) can further increase the structural diversity of these terpenoids. While most terpenoids are characterized as specialized or secondary metabolites, some terpenoids, such as the phytohormones GA (gibberellic acid), BRs (brassinosteroids) and ABA (abscisic acid), have essential functions in plant growth and development. To date, very few CYP genes involved in conifer terpenoid metabolism have been functionally characterized and were limited to two systems, yew (Taxus) and loblolly pine (Pinus taeda). The characterized yew CYP genes are involved in taxol diterpene biosynthesis, while the only characterized pine terpenoid CYP gene is part of DRA (diterpene resin acid) biosynthesis. These CYPs from yew and pine are members of two apparently conifer-specific CYP families within the larger CYP85 clan, one of four plant CYP multifamily clans. Other CYP families within the CYP85 clan were characterized from a variety of angiosperms with functions in terpenoid phytohormone metabolism of GA, BR, and ABA. The recent development of EST (expressed sequence tag) and FLcDNA (where FL is full-length) sequence databases and cDNA collections for species of two conifers, spruce (Picea) and pine, allows for the discovery of new terpenoid CYPs in gymnosperms by means of large-scale sequence mining, phylogenetic analysis and functional characterization. Here, we present a snapshot of conifer CYP data mining, discovery of new conifer CYPs in all but one family within the CYP85 clan, and suggestions for their functional characterization. This paper will focus on the discovery of conifer CYPs associated with diterpene metabolism and CYP with possible functions in the formation of GA, BR, and ABA in conifers.

Transcriptional analysis between two wheat near-isogenic lines contrasting in aluminum tolerance under aluminum stress

To understand the mechanisms of aluminum (Al) tolerance in wheat (Triticum aestivum L.), suppression subtractive hybridization (SSH) libraries were constructed from Al-stressed roots of two near-isogenic lines (NILs). A total of 1,065 putative genes from the SSH libraries was printed in a cDNA array. Relative expression levels of those genes were compared between two NILs at seven time points of Al stress from 15 min to 7 days. Fifty-seven genes were differentially expressed for at least one time point of Al treatment. Among them, 28 genes including genes for aluminum-activated malate transporter-1, ent-kaurenoic acid oxidase-1, beta-glucosidase, lectin, histidine kinase, and phospoenolpyruvate carboxylase showed more abundant transcripts in Chisholm-T and therefore may facilitate Al tolerance. In addition, a set of genes related to senescence and starvation of nitrogen, iron, and sulfur, such as copper chaperone homolog, nitrogen regulatory gene-2, yellow stripe-1, and methylthioribose kinase, was highly expressed in Chisholm-S under Al stress. The results suggest that Al tolerance may be co-regulated by multiple genes with diverse functions, and those genes abundantly expressed in Chisholm-T may play important roles in enhancing Al tolerance. The down-regulated genes in Chisholm-S may repress root growth and restrict uptake of essential nutrient elements, and lead to root senescence.

Ectopic expression of KNOTTED1-like homeobox protein induces expression of cytokinin biosynthesis genes in rice

Some phytohormones such as gibberellins (GAs) and cytokinins (CKs) are potential targets of the KNOTTED1-like homeobox (KNOX) protein. To enhance our understanding of KNOX protein function in plant development, we identified rice (Oryza sativa) genes for adenosine phosphate isopentenyltransferase (IPT), which catalyzes the rate-limiting step of CK biosynthesis. Molecular and biochemical studies revealed that there are eight IPT genes, OsIPT1 to OsIPT8, in the rice genome, including a pseudogene, OsIPT6. Overexpression of OsIPTs in transgenic rice inhibited root development and promoted axillary bud growth, indicating that OsIPTs are functional in vivo. Phenotypes of OsIPT overexpressers resembled those of KNOX-overproducing transgenic rice, although OsIPT overexpressers did not form roots or ectopic meristems, both of which are observed in KNOX overproducers. Expression of two OsIPT genes, OsIPT2 and OsIPT3, was up-regulated in response to the induction of KNOX protein function with similar kinetics to those of down-regulation of GA 20-oxidase genes, target genes of KNOX proteins in dicots. However, expression of these two OsIPT genes was not regulated in a feedback manner. These results suggest that OsIPT2 and OsIPT3 have unique roles in the developmental process, which is controlled by KNOX proteins, rather than in the maintenance of bioactive CK levels in rice. On the basis of these findings, we concluded that KNOX protein simultaneously decreases GA biosynthesis and increases de novo CK biosynthesis through the induction of OsIPT2 and OsIPT3 expression, and the resulting high-CK and low-GA condition is required for formation and maintenance of the meristem.

Hormone interactions and regulation of Unifoliata, PsPK2, PsPIN1 and LE gene expression in pea (Pisum sativum) shoot tips

The Unifoliata (Uni) gene plays a major role in development of the compound leaf in pea, but its regulation is unknown. In this study, we examined the effects of plant hormones on the expression of Uni, PsPK2 (the gene for a pea homolog of Arabidopsis PID, a regulator of PIN1 targeting), PsPIN1 (the major gene for a putative auxin efflux carrier) and LE (a gibberellin biosynthesis gene, GA3ox), and also examined mutual hormonal regulation of these genes, in pea shoot tips, including a number of mutants. The Uni promoter possessed putative auxin and gibberellin response elements. The PsPIN1 mRNA levels were increased in afila, which replaces leaflets with branched tendrils; and reduced in tendrilless, which replaces tendrils with leaflets, compared with the wild type (WT). In contrast, mRNA levels of LE were increased in uni and tendrilless and decreased in afila compared with the WT. Uni, PsPK2 and PsPIN1 are positively regulated by gibberellin and auxin, and were induced to higher levels by simultaneous application of auxin and gibberellin. Auxin induction of Uni, PsPK2 and PsPIN1 did not require de novo protein synthesis. LE was positively regulated by auxin and cytokinin. In conclusion, these results support the hypothesis that auxin and gibberellin positively regulate Uni, which controls pea compound leaf development. Also, Uni, PsPIN1, PsPK2 and LE are expressed differentially in the leaf mutants, suggesting that mutual regulation by auxin and gibberellin promotes compound leaf development.

The phytopathogen Rhodococcus fascians breaks apical dominance and activates axillary meristems by inducing plant genes involved in hormone metabolism

SUMMARY Rhodococcus fascians is a Gram-positive bacterium that interacts with many plant species and induces multiple shoots through a combination of activation of dormant axillary meristems and de novo meristem formation. Although phenotypic analysis of the symptoms of infected plants clearly demonstrates a disturbance of the phytohormonal balance and an activation of the cell cycle, the actual mechanism of symptom development and the targets of the bacterial signals are unknown. To elucidate the molecular pathways that are responsive to R. fascians infection, differential display was performed on Nicotiana tabacum as a host. Four differentially expressed genes could be identified that putatively encode a senescence-associated protein, a gibberellin 2-oxidase, a P450 monooxygenase and a proline dehydrogenase. The differential expression of the three latter genes was confirmed on infected Arabidopsis thaliana plants by quantitative reverse transcription polymerase chain reactions, supporting their general function in R. fascians-induced symptom development. The role of these genes in hormone metabolism, especially of gibberellin and abscisic acid, in breaking apical dominance and in activating axillary meristems, which are processes associated with symptom development, is discussed.