Biochemical and Molecular Analyses of Gibberellin Biosynthesis in Fungi

Bioprocess of Gibberellic Acid by Fusarium fujikuroi: The Challenge of Regulation, Raw Materials, and Product Yields

Gibberellic acid (GA3) is a tetracyclic diterpenoid carboxylic acid synthesized by the secondary metabolism of Fusarium fujikuroi. This phytohormone is widely studied due to the advantages it offers as a plant growth regulator, such as growth stimulation, senescence delay, flowering induction, increased fruit size, and defense against abiotic or biotic stress, which improve the quality and yield of crops. Therefore, GA3 has been considered as an innovative strategy to improve agricultural production. However, the yields obtained at large scale are insufficient for the current market demand. This low productivity is attributed to the lack of adequate parameters to optimize the fermentation process, as well as the complexity of its regulation. Therefore, this article describes the latest advances for potentializing the GA3 production process, including an analysis of its origins from crops, the benefits of its application, the related biosynthetic metabolism, the maximum yields achieved from production processes, and their association with genetic engineering techniques for GA3 producers. This work provides a new perspective on the critical points of the production process, in order to overcome the limits surrounding this modern line of bioengineering.

The transcription factor STE12 influences growth on several carbon sources and production of dehydroacetic acid (DHAA) in Trichoderma reesei

The filamentous ascomycete Trichoderma reesei, known for its prolific cellulolytic enzyme production, recently also gained attention for its secondary metabolite synthesis. Both processes are intricately influenced by environmental factors like carbon source availability and light exposure. Here, we explore the role of the transcription factor STE12 in regulating metabolic pathways in T. reesei in terms of gene regulation, carbon source utilization and biosynthesis of secondary metabolites. We show that STE12 is involved in regulating cellulase gene expression and growth on carbon sources associated with iron homeostasis. STE12 impacts gene regulation in a light dependent manner on cellulose with modulation of several CAZyme encoding genes as well as genes involved in secondary metabolism. STE12 selectively influences the biosynthesis of the sorbicillinoid trichodimerol, while not affecting the biosynthesis of bisorbibutenolide, which was recently shown to be regulated by the MAPkinase pathway upstream of STE12 in the signaling cascade. We further report on the biosynthesis of dehydroacetic acid (DHAA) in T. reesei, a compound known for its antimicrobial properties, which is subject to regulation by STE12. We conclude, that STE12 exerts functions beyond development and hence contributes to balance the energy distribution between substrate consumption, reproduction and defense.

The soil-borne white root rot pathogen Rosellinia necatrix expresses antimicrobial proteins during host colonization

Rosellinia necatrix is a prevalent soil-borne plant-pathogenic fungus that is the causal agent of white root rot disease in a broad range of host plants. The limited availability of genomic resources for R. necatrix has complicated a thorough understanding of its infection biology. Here, we sequenced nine R. necatrix strains with Oxford Nanopore sequencing technology, and with DNA proximity ligation we generated a gapless assembly of one of the genomes into ten chromosomes. Whereas many filamentous pathogens display a so-called two-speed genome with more dynamic and more conserved compartments, the R. necatrix genome does not display such genome compartmentalization. It has recently been proposed that fungal plant pathogens may employ effectors with antimicrobial activity to manipulate the host microbiota to promote infection. In the predicted secretome of R. necatrix, 26 putative antimicrobial effector proteins were identified, nine of which are expressed during plant colonization. Two of the candidates were tested, both of which were found to possess selective antimicrobial activity. Intriguingly, some of the inhibited bacteria are antagonists of R. necatrix growth in vitro and can alleviate R. necatrix infection on cotton plants. Collectively, our data show that R. necatrix encodes antimicrobials that are expressed during host colonization and that may contribute to modulation of host-associated microbiota to stimulate disease development.

Understanding the Fermentation Potentiality For Gibberellic Acid (GA3) Production Using Fungi

Gibberellins represent an important group of potent phytohormones, growth-promoting, closely related diterpenoid acids biologically derived from tetracyclic diterpenoid hydrocarbon. Among these, gibberellic acid (GA3) has received the greatest attention. GA3 is a highly valued plant growth regulator which has various applications in agriculture. It is extensively used for beneficial effects including stem elongation, elimination of dormancy, sex expression, seed germination, flowering, and fruit senescence. Along with plants, many microbes are also producing GA3 as their secondary metabolite, and among these, fungi are reported to produce a higher amount of GA3. Fermentation technology based on submerged fermentation and solid-state fermentation for the production of GA3 has been used with its merits and demerits using Fusarium moniliforme fungus in the industry. Several mathematical models and optimization tools were also designed for enhancing the fermentative yield by researchers. The detailed analysis is essential to understand all the fermentation aspects, various unit parameters, process operation approaches, reduction in cost, and assessment of the possible uses of these models in the production of GA3 for higher yield. Recently, exclusive research is executed to lower down the production cost of GA3 approaching various strategies.

Targeted metabolome and transcriptome analyses reveal changes in gibberellin and related cell wall-acting enzyme-encoding genes during stipe elongation in Flammulina filiformis

Flammulina filiformis, a typical agaric fungus, is a widely cultivated and consumed edible mushroom. Elongation of its stipe (as the main edible part) is closely related to its yield and commercial traits; however, the endogenous hormones during stipe elongation and their regulatory mechanisms are not well understood. Gibberellin (GA) plays an important role in the regulation of plant growth, but little has been reported in macro fungi. In this study, we first treated F. filiformis stipes in the young stage with PBZ (an inhibitor of GA) and found that PBZ significantly inhibited elongation of the stipe. Then, we performed GA-targeted metabolome and transcriptome analyses of the stipe at both the young and elongation stages. A total of 13 types of GAs were detected in F. filiformis; the contents of ten of them, namely, GA3, GA4, GA8, GA14, GA19, GA20, GA24, GA34, GA44, and GA53, were significantly decreased, and the contents of three (GA5, GA9, and GA29) were significantly increased during stipe elongation. Transcriptome analysis showed that the genes in the terpenoid backbone biosynthesis pathway showed varying expression patterns: HMGS, HMGR, GPS, and FPPS were significantly upregulated, while CPS/KS had no significant difference in transcript level during stipe elongation. In total, 37 P450 genes were annotated to be involved in GA biosynthesis; eight of them were upregulated, twelve were downregulated, and the rest were not differentially expressed. In addition, four types of differentially expressed genes involved in stipe elongation were identified, including six signal transduction genes, five cell cycle-controlling genes, twelve cell wall-related enzymes and six transcription factors. The results identified the types and content of GAs and the expression patterns of their synthesis pathways during elongation in F. filiformis and revealed the molecular mechanisms by which GAs may affect the synthesis of cell wall components and the cell cycle of the stipe through the downstream action of cell wall-related enzymes, transcription factors, signal transduction and cell cycle control, thus regulating stipe elongation. This study is helpful for understanding the roles of GAs in stipe development in mushrooms and lays the foundation for the rational regulation of stipe length in agaric mushrooms during production.

Integration of Transcriptomic and Metabolomic Profiles Provides Insights into the Influence of Nitrogen on Secondary Metabolism in Fusarium sacchari

Nitrogen availability might play an essential role in plant diseases by enhancing fungal cell growth and influencing the expression of genes required for successful pathogenesis. Nitrogen availability could modulate secondary metabolic pathways as evidenced by the significant differential expression of several core genes involved in mycotoxin biosynthesis and genes encoding polyketide synthase/nonribosomal peptide synthetases, cytochrome P450 and carbohydrate-active enzymes in Fusarium sacchari, grown on different nitrogen sources. A combined analysis was carried out on the transcript and metabolite profiles of regulatory metabolic processes and the virulence of Fusarium sacchari grown on various nitrogen sources. The nitrogen regulation of the gibberellin gene cluster included the metabolic flux and multiple steps of gibberellin synthesis. UHPLC-MS/MS-based metabolome analysis revealed the coordination of these related transcripts and the accumulation of gibberellin metabolites. This integrated analysis allowed us to uncover additional information for a more comprehensive understanding of biological events relevant to fungal secondary metabolic regulation in response to nitrogen availability.

Comparative Analysis of Rhizosphere and Endophytic Microbial Communities Between Root Rot and Healthy Root of Psammosilene tunicoides

The wild resources of Psammosilene tunicoides have decreased sharply because of the long-term mining and excavation, which has led to the increased demand for its artificial cultivation. However, root rot represents a significant obstacle leading to a poor quality and product of P. tunicoides. Previous reports have not focused on root rot in P. tunicoides. Therefore, this study explores the rhizospheric and root endophytic microbial community structure and composition of healthy and root rot P. tunicoides to understand the mechanism underlying root rot. The properties of the rhizosphere soil were assessed using physiochemical methods, and the bacterial and fungal populations were studied through amplicon sequencing of the 16S rRNA genes and ITS regions in the root and soil. Compared to healthy samples, the pH, hydrolysis N, available P, and available K were significantly decreased in the diseased samples while the organic matter and total organic carbon were significantly increased in the diseased samples. Redundancy analysis (RDA) showed that soil environmental factors are related to changes in the root and rhizosphere soil microbial community of P. tunicoides indicating that the physiochemical properties of soil affect plant health. Alpha diversity analysis showed that the microbial communities of healthy and diseased samples were similar. Some bacterial and fungal genera were significantly increased or decreased (P < 0.05) in diseased P. tunicoides, and certain microbial factors that antagonized root rot were further explored. This study provides an abundant microbial resource for future studies and contributes to improving soil quality and P. tunicoides agricultural production.

Nuclear Genome Sequence and Gene Expression of an Intracellular Fungal Endophyte Stimulating the Growth of Cranberry Plants

Ericaceae thrive in poor soil, which we postulate is facilitated by microbes living inside those plants. Here, we investigate the growth stimulation of the American cranberry (Vaccinium macrocarpon) by one of its fungal endosymbionts, EC4. We show that the symbiont resides inside the epidermal root cells of the host but extends into the rhizosphere via its hyphae. Morphological classification of this fungus is ambiguous, but phylogenetic inference based on 28S rRNA identifies EC4 as a Codinaeella species (Chaetosphaeriaceae, Sordariomycetes, Ascomycetes). We sequenced the genome and transcriptome of EC4, providing the first 'Omics' information of a Chaetosphaeriaceae fungus. The 55.3-Mbp nuclear genome contains 17,582 potential protein-coding genes, of which nearly 500 have the capacity to promote plant growth. For comparing gene sets involved in biofertilization, we annotated the published genome assembly of the plant-growth-promoting Trichoderma hamatum. The number of proteins involved in phosphate transport and solubilization is similar in the two fungi. In contrast, EC4 has ~50% more genes associated with ammonium, nitrate/nitrite transport, and phytohormone synthesis. The expression of 36 presumed plant-growth-promoting EC4 genes is stimulated when the fungus is in contact with the plant. Thus, Omics and in-plantae tests make EC4 a promising candidate for cranberry biofertilization on nutrient-poor soils.

Effective biofertilizer Trichoderma spp. isolates with enzymatic activity and metabolites enhancing plant growth

Trichoderma species have been widely recognized as biofertilizer fungi for their ability to produce phytohormones and enhance plant growth. In our current study, fifteen strains of Trichoderma spp. (T1-T15) were screened for their capacity to produce phytohormones and metabolites eliciting plant growth. The stains were previously isolated from olive rhizosphere soil in northern Algeria. Plant growth promoting (PGP) potential of Trichoderma spp. was evaluated in vitro through the production of phosphatases, siderophores, hydrogen cyanide (HCN), and ammonia (NH3). Besides, plant growth phytohormones such as gibberellic acid and indole-3-acetic acid (IAA) were assessed quantitatively by a colorimetric assay. Results showed an effective potential of Trichoderma spp. in plant growth-promoting biomolecule production. Importantly, qualitative estimation of phosphate solubilization indicates that T10 gave the highest phosphate solubilization on medium Pikovskaya's with a solubilization index (SI) of 3, whereas, the high capacity nitrogen-fixing was related to T8. On the other hand, quantitative analysis of indole-3-acetic acid and gibberellic acid revealed a production varying between (1.30 μg mL^-1 to 21.15 μg mL^-1) and (0.53 μg mL^-1 to 7.87 μg mL^-1), respectively; the highest amount of both phytohormones was obtained by T11 isolate. Indeed, an analysis of ethyl acetate extracts of T11 isolate by high-performance liquid chromatography (HPLC) revealed a high amount (71.19 mg L^-1) of IAA. Overall, the results showed clearly that isolate T11 has promising plant growth-promoting properties. Hence, this native Trichoderma isolate (T11) identified as Trichoderma harzianum strain (OL587563) could be used later as biofertilizer for sustainable olive crop agriculture.

Genome-Wide Identification and Evolution Analysis of the Gibberellin Oxidase Gene Family in Six Gramineae Crops

The plant hormones gibberellins (GAs) regulate plant growth and development and are closely related to the yield of cash crops. The GA oxidases (GAoxs), including the GA2ox, GA3ox, and GA20ox subfamilies, play pivotal roles in GAs' biosynthesis and metabolism, but their classification and evolutionary pattern in Gramineae crops remain unclear. We thus conducted a comparative genomic study of GAox genes in six Gramineae representative crops, namely, Setaria italica (Si), Zea mays (Zm), Sorghum bicolor (Sb), Hordeum vulgare (Hv), Brachypodium distachyon (Bd), and Oryza sativa (Os). A total of 105 GAox genes were identified in these six crop genomes, belonging to the C19-GA2ox, C20-GA2ox, GA3ox, and GA20ox subfamilies. Based on orthogroup (OG) analysis, GAox genes were divided into nine OGs and the number of GAox genes in each of the OGs was similar among all tested crops, which indicated that GAox genes may have completed their family differentiations before the species differentiations of the tested species. The motif composition of GAox proteins showed that motifs 1, 2, 4, and 5, forming the 2OG-FeII_Oxy domain, were conserved in all identified GAox protein sequences, while motifs 11, 14, and 15 existed specifically in the GA20ox, C19-GA2ox, and C20-GA2ox protein sequences. Subsequently, the results of gene duplication events suggested that GAox genes mainly expanded in the form of WGD/SD and underwent purification selection and that maize had more GAox genes than other species due to its recent duplication events. The cis-acting elements analysis indicated that GAox genes may respond to growth and development, stress, hormones, and light signals. Moreover, the expression profiles of rice and maize showed that GAox genes were predominantly expressed in the panicles of the above two plants and the expression of several GAox genes was significantly induced by salt or cold stresses. In conclusion, our results provided further insight into GAox genes' evolutionary differences among six representative Gramineae and highlighted GAox genes that may play a role in abiotic stress.

Interactions of Gibberellins with Phytohormones and Their Role in Stress Responses

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

Biosynthesis and beneficial effects of microbial gibberellins on crops for sustainable agriculture

Soil microbes promote plant growth through several mechanisms such as secretion of chemical compounds including plant growth hormones. Among the phytohormones, auxins, ethylene, cytokinins, abscisic acid and gibberellins are the best understood compounds. Gibberellins were first isolated in 1935 from the fungus Gibberella fujikuroi and are synthesized by several soil microbes. The effect of gibberellins on plant growth and development has been studied, as has the biosynthesis pathways, enzymes, genes and their regulation. This review revisits the history of gibberellin research highlighting microbial gibberellins and their effects on plant health with an emphasis on the early discoveries and current advances that can find vital applications in agricultural practices.

The Current Status of Research on Gibberellin Biosynthesis

Gibberellins are produced by all vascular plants and several fungal and bacterial species that associate with plants as pathogens or symbionts. In the 60 years since the first experiments on the biosynthesis of gibberellic acid in the fungus Fusarium fujikuroi, research on gibberellin biosynthesis has advanced to provide detailed information on the pathways, biosynthetic enzymes and their genes in all three kingdoms, in which the production of the hormones evolved independently. Gibberellins function as hormones in plants, affecting growth and differentiation in organs in which their concentration is very tightly regulated. Current research in plants is focused particularly on the regulation of gibberellin biosynthesis and inactivation by developmental and environmental cues, and there is now considerable information on the molecular mechanisms involved in these processes. There have also been recent advances in understanding gibberellin transport and distribution and their relevance to plant development. This review describes our current understanding of gibberellin metabolism and its regulation, highlighting the more recent advances in this field.

Improvement of gibberellin production by a newly isolated Fusarium fujikuroi mutant

AIMS

To obtain and investigate the potential mechanism for GA₃ production in Fusarium fujikuroi GA-251, a high GA₃ producer.

METHODS AND RESULTS

Fusarium fujikuroi IMI 58289 was bred with Cobalt-60 (⁶⁰ Co) radiation and lithium chloride treatment. The best mutant strain GA-251 was obtained for the subsequent optimization of fermentation conditions. The yield of GA₃ by GA-251 was 2100 mg l^-1 , while the wild-type strain was 100 mg l^-1 , which is a 21-fold increase in the yield. To elucidate the mechanism of high GA₃ yield of GA-251, the genome was sequenced and compared with wild-type strain IMI 58289. The results showed 2295 single nucleotide polymorphisms, 1242 small indels and 30 structural variants. These mutations were analysed and enriched in the MAPK signalling pathway, the mRNA surveillance pathway and endocytosis. The potential reasons for the improved GA₃ biosynthesis were investigated.

CONCLUSIONS

The potential mechanism of high GA₃ yield was attributed to endocytosis pathway and histone modification proteins family.

SIGNIFICANCE AND IMPACT OF THE STUDY

A mutant strain GA-251 in this work that could potentially be utilized in the industrial yield of GA₃ . The comparative genome analysis would shed light onto the mechanism of yield improvement and be a theoretical guide for further metabolic engineering.

Microbial community overlap between the phyllosphere and rhizosphere of three plants from Yongxing Island, South China Sea

Phyllosphere and rhizosphere are unique and wide‐ranging habitats that harbor various microbial communities, which influence plant growth and health, and the productivity of the ecosystems. In this study, we characterized the shared microbiome of the phyllosphere and rhizosphere among three plants (Ipomoea pes‐caprae, Wedelia chinensis, and Cocos nucifera), to obtain an insight into the relationships between bacteria (including diazotrophic bacteria) and fungi, present on these host plants. Quantitative PCR showed that the abundances of the microbiome in the soil samples were significantly higher than those in the phyllosphere samples, though there was an extremely low abundance of fungi in bulk soil. High‐throughput sequencing showed that the alpha‐diversity of bacteria and fungi was higher in the rhizosphere than the phyllosphere samples associated with the same plant, while there was no obvious shift in the alpha‐diversity of diazotrophic communities between all the tested phyllosphere and soil samples. Results of the microbial composition showed that sample‐specific bacteria and fungi were found among the phyllosphere and rhizosphere of the different host plants. About 10%–27% of bacteria, including diazotrophs, and fungi overlapped between the phyllosphere and the rhizosphere of these host plants. No significant difference in microbial community structure was found among the tested rhizosphere samples, and soil properties had a higher influence on the soil microbial community structures than the host plant species.

Current advances in gibberellic acid (GA3) production, patented technologies and potential applications

Gibberellic acid is a plant growth hormone that promotes cell expansion and division. Studies have aimed at optimizing and reducing production costs, which could make its application economically viable for different cultivars. Gibberellins consist of a large family of plant growth hormones discovered in the 1930s, which are synthesized via the terpenes route from the geranylgeranyl diphosphate and feature a basic structure formed by an ent-gibberellane tetracyclic skeleton. Among them, only four have biological activity, including gibberellic acid (GA₃), which acts as a natural plant growth regulator, especially for stem elongation, seed germination, and increased fruit size. It can be obtained from plants, fungi, and bacteria. There are also some reports about microalgae GA₃ producers. Fungi, especially Gibberella fujikuroi, are preferred for GA₃ production via submerged fermentation or solid-state fermentation. Many factors may affect its production, some of which are related to the control and scale-up of fermentation parameters. Different GA₃ products are available on the market. They can be found in liquid or solid formulations containing only GA₃ or a mixture of other biological active gibberellins, which can be applied on a wide variety of cultivars, including crops and fruits. However, the product's cost still limits its large and continuous application. New low-cost and efficient GA₃ production alternatives are surely welcome. This review deals with the latest scientific and technological advances on production, recovery, formulation, and applications of this important plant growth hormone.

Inclusion complexes of GA3 and the plant growth regulation activities

Gibberellic acid (GA₃) is an important phytohormone that is applied in agriculture, nurseries, tissue culture, tea gardens, etc. However, it has some drawbacks such as potential hazardous effects on mammals and labile in the condition of a weak base or acid. In this study, the enhanced stability and bioavailability of GA₃ were achieved by forming the inclusion complexes of GA₃ with cyclodextrins (β- or γ-CD) and its derivative (HP-β-CD). In the preliminary plant growth regulation assay, GA₃/CDs displays superior bioactivity compared to pure GA₃ to help with the early seedling growth of cucumber and mung bean and the root growth of cucumber and mung bean, respectively. The results showed that there was a certain relationship between the inclusion ability, stability and bioactivity. The inclusion stability constants of gibberellin clathrate are consistent with the order of stabilities of the inclusion complex. Among these complexes, GA₃/HP-β-CD possess highest inclusion constant, and the binding ability of the HP-β-CD not only enhances the stability of gibberellic acid in the stability test but also plays a slow release role in the bioactivity assay. Therefore, the complex of GA₃ may be used as a promising plant growth regulator.

Fungal Diversity and Community Composition of Culturable Fungi in Stanhopea trigrina Cast Gibberellin Producers

Stanhopea tigrina is a Mexican endemic orchid reported as a threatened species. The naturally occurring microorganisms present in S. tigrina are unknown. In this work, we analyzed the diversity of endophytic and epiphytic culturable fungi in S. tigrina according to morphological and molecular identification. Using this combined approach, in this study we retrieved a total of 634 fungal isolates that presented filamentous growth, which were grouped in 134 morphotypes that were associated to 63 genera, showing that S. tigrina harbors a rich diversity of both endophytic and epiphytic fungi. Among these, the majority of the isolates corresponded to Ascomycetes, with Trichoderma and Penicillium as the most frequent genera followed by Fusarium and Aspergillus. Non-ascomycetes isolated were associated only to the genus Mucor (Mucoromycota) and Schizophyllum (Basidiomycota). Identified genera showed a differential distribution considering their epiphytic or endophytic origin, the tissue from which they were isolated, and the ability of the orchid to grow on different substrates. To our knowledge, this work constitutes the first study of the mycobiome of S. tigrina. Interestingly, 21 fungal isolates showed the ability to produce gibberellins. Almost half of the isolates were related to the gibberellin-producer genus Penicillium based on morphological and molecular identification. However, the rest of the isolates were related to the following genera, which have not been reported as gibberellin producers so far: Bionectria, Macrophoma, Nectria, Neopestalotiopsis, Talaromyces, Trichoderma, and Diplodia. Taken together, we found that S. tigrina possess a significant fungal diversity that could be a rich source of fungal metabolites with the potential to develop biotechnological approaches oriented to revert the threatened state of this orchid in the near future.

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.

The genome of the generalist plant pathogen Fusarium avenaceum is enriched with genes involved in redox, signaling and secondary metabolism

Fusarium avenaceum is a fungus commonly isolated from soil and associated with a wide range of host plants. We present here three genome sequences of F. avenaceum, one isolated from barley in Finland and two from spring and winter wheat in Canada. The sizes of the three genomes range from 41.6–43.1 MB, with 13217–13445 predicted protein-coding genes. Whole-genome analysis showed that the three genomes are highly syntenic, and share>95% gene orthologs. Comparative analysis to other sequenced Fusaria shows that F. avenaceum has a very large potential for producing secondary metabolites, with between 75 and 80 key enzymes belonging to the polyketide, non-ribosomal peptide, terpene, alkaloid and indole-diterpene synthase classes. In addition to known metabolites from F. avenaceum, fuscofusarin and JM-47 were detected for the first time in this species. Many protein families are expanded in F. avenaceum, such as transcription factors, and proteins involved in redox reactions and signal transduction, suggesting evolutionary adaptation to a diverse and cosmopolitan ecology. We found that 20% of all predicted proteins were considered to be secreted, supporting a life in the extracellular space during interaction with plant hosts.

Traversing the fungal terpenome

Fungi (Ascomycota and Basidiomycota) are prolific producers of structurally diverse terpenoid compounds. Classes of terpenoids identified in fungi include the sesqui-, di- and triterpenoids. Biosynthetic pathways and enzymes to terpenoids from each of these classes have been described. These typically involve the scaffold generating terpene synthases and cyclases, and scaffold tailoring enzymes such as e.g. cytochrome P450 monoxygenases, NAD(P)+ and flavin dependent oxidoreductases, and various group transferases that generate the final bioactive structures. The biosynthesis of several sesquiterpenoid mycotoxins and bioactive diterpenoids has been well-studied in Ascomycota (e.g. filamentous fungi). Little is known about the terpenoid biosynthetic pathways in Basidiomycota (e.g. mushroom forming fungi), although they produce a huge diversity of terpenoid natural products. Specifically, many trans-humulyl cation derived sesquiterpenoid natural products with potent bioactivities have been isolated. Biosynthetic gene clusters responsible for the production of trans-humulyl cation derived protoilludanes, and other sesquiterpenoids, can be rapidly identified by genome sequencing and bioinformatic methods. Genome mining combined with heterologous biosynthetic pathway refactoring has the potential to facilitate discovery and production of pharmaceutically relevant fungal terpenoids.

Connecting growth and defense: the emerging roles of brassinosteroids and gibberellins in plant innate immunity

Brassinosteroids (BRs) and gibberellins (GAs) are two groups of phytohormones that regulate many common developmental processes throughout the plant life cycle. Fueled by large-scale 'omics' technologies and the burgeoning field of plant computational biology, the past few years have witnessed paradigm-shifting advances in our understanding of how BRs and GA are perceived and their signals transduced. Accumulating evidence also implicates BR and GA in the coordination and integration of plant immune responses. Similarly to other growth regulators, BR and GA play ambiguous roles in molding pathological outcomes, the effects of which may depend not only on the pathogen's lifestyle and infection strategy, but also on specialized features of each interaction. Analysis of the underpinning molecular mechanisms points to a crucial role of GA-inhibiting DELLA proteins and the BR-regulated transcription factor BZR1. Acting at the interface of developmental and defense signaling, these proteins likely serve as central hubs for pathway crosstalk and signal integration, allowing appropriate modulation of plant growth and defense in response to various stimuli. In this review, we outline the latest discoveries dealing with BR and GA modulation of plant innate immunity and highlight interactions between BR and GA signaling, plant defense, and microbial virulence.

Biosynthesis of terpenoid natural products in fungi

Tens of thousands of terpenoid natural products have been isolated from plants and microbial sources. Higher fungi (Ascomycota and Basidiomycota) are known to produce an array of well-known terpenoid natural products, including mycotoxins, antibiotics, antitumor compounds, and phytohormones. Except for a few well-studied fungal biosynthetic pathways, the majority of genes and biosynthetic pathways responsible for the biosynthesis of a small number of these secondary metabolites have only been discovered and characterized in the past 5-10 years. This chapter provides a comprehensive overview of the current knowledge on fungal terpenoid biosynthesis from biochemical, genetic, and genomic viewpoints. Enzymes involved in synthesizing, transferring, and cyclizing the prenyl chains that form the hydrocarbon scaffolds of fungal terpenoid natural products are systematically discussed. Genomic information and functional evidence suggest differences between the terpenome of the two major fungal phyla--the Ascomycota and Basidiomycota--which will be illustrated for each group of terpenoid natural products.

Deciphering the cryptic genome: genome-wide analyses of the rice pathogen Fusarium fujikuroi reveal complex regulation of secondary metabolism and novel metabolites

The fungus Fusarium fujikuroi causes "bakanae" disease of rice due to its ability to produce gibberellins (GAs), but it is also known for producing harmful mycotoxins. However, the genetic capacity for the whole arsenal of natural compounds and their role in the fungus' interaction with rice remained unknown. Here, we present a high-quality genome sequence of F. fujikuroi that was assembled into 12 scaffolds corresponding to the 12 chromosomes described for the fungus. We used the genome sequence along with ChIP-seq, transcriptome, proteome, and HPLC-FTMS-based metabolome analyses to identify the potential secondary metabolite biosynthetic gene clusters and to examine their regulation in response to nitrogen availability and plant signals. The results indicate that expression of most but not all gene clusters correlate with proteome and ChIP-seq data. Comparison of the F. fujikuroi genome to those of six other fusaria revealed that only a small number of gene clusters are conserved among these species, thus providing new insights into the divergence of secondary metabolism in the genus Fusarium. Noteworthy, GA biosynthetic genes are present in some related species, but GA biosynthesis is limited to F. fujikuroi, suggesting that this provides a selective advantage during infection of the preferred host plant rice. Among the genome sequences analyzed, one cluster that includes a polyketide synthase gene (PKS19) and another that includes a non-ribosomal peptide synthetase gene (NRPS31) are unique to F. fujikuroi. The metabolites derived from these clusters were identified by HPLC-FTMS-based analyses of engineered F. fujikuroi strains overexpressing cluster genes. In planta expression studies suggest a specific role for the PKS19-derived product during rice infection. Thus, our results indicate that combined comparative genomics and genome-wide experimental analyses identified novel genes and secondary metabolites that contribute to the evolutionary success of F. fujikuroi as a rice pathogen.

Co-synergism of endophyte Penicillium resedanum LK6 with salicylic acid helped Capsicum annuum in biomass recovery and osmotic stress mitigation

BACKGROUND

Water-deficiency adversely affects crop growth by generating reactive oxygen species (ROS) at cellular level. To mitigate such stressful events, it was aimed to investigate the co-synergism of exogenous salicylic acid (SA) and symbiosis of endophytic fungus with Capsicum annuum L. (pepper).

RESULTS

The findings of the study showed that exogenous SA (10⁻⁶ M) application to endophyte (Penicillium resedanum LK6) infected plants not only increased the shoot length and chlorophyll content but also improved the biomass recovery of pepper plants under polyethylene glycol (15%) induced osmotic stress (2, 4 and 8 days). Endophyte-infected plants had low cellular injury and high photosynthesis rate. SA also enhanced the colonization rate of endophyte in the host-plant roots. Endophyte and SA, in combination, reduced the production of ROS by increasing the total polyphenol, reduce glutathione, catalase, peroxidase and polyphenol oxidase as compared to control plants. Osmotic stress pronounced the lipid peroxidation and superoxide anions formation in control plants as compared to endophyte and SA-treated plants. The endogenous SA contents were significantly higher in pepper plants treated with endophyte and SA under osmotic stress as compared to control.

CONCLUSION

Endophytic fungal symbiosis and exogenous SA application can help the plants to relieve the adverse effects of osmotic stress by decreasing losses in biomass as compared to non-inoculated plants. These findings suggest that SA application positively impact microbial colonization while in combination, it reprograms the plant growth under various intervals of drought stress. Such symbiotic strategy can be useful for expanding agriculture production in drought prone lands.

Characterization of the fungal gibberellin desaturase as a 2-oxoglutarate-dependent dioxygenase and its utilization for enhancing plant growth

The biosynthesis of gibberellic acid (GA(3)) by the fungus Fusarium fujikuroi is catalyzed by seven enzymes encoded in a gene cluster. While four of these enzymes are characterized as cytochrome P450 monooxygenases, the nature of a fifth oxidase, GA(4) desaturase (DES), is unknown. DES converts GA(4) to GA(7) by the formation of a carbon-1,2 double bond in the penultimate step of the pathway. Here, we show by expression of the des complementary DNA in Escherichia coli that DES has the characteristics of a 2-oxoglutarate-dependent dioxygenase. Although it has low amino acid sequence homology with known 2-oxoglutarate-dependent dioxygenases, putative iron- and 2-oxoglutarate-binding residues, typical of such enzymes, are apparent in its primary sequence. A survey of sequence databases revealed that homologs of DES are widespread in the ascomycetes, although in most cases the homologs must participate in non-gibberellin (GA) pathways. Expression of des from the cauliflower mosaic virus 35S promoter in the plant species Solanum nigrum, Solanum dulcamara, and Nicotiana sylvestris resulted in substantial growth stimulation, with a 3-fold increase in height in S. dulcamara compared with controls. In S. nigrum, the height increase was accompanied by a 20-fold higher concentration of GA(3) in the growing shoots than in controls, although GA(1) content was reduced. Expression of des was also shown to partially restore growth in plants dwarfed by ectopic expression of a GA 2-oxidase (GA-deactivating) gene, consistent with GA(3) being protected from 2-oxidation. Thus, des has the potential to enable substantial growth increases, with practical implications, for example, in biomass production.

Endophytic fungi produce gibberellins and indoleacetic acid and promotes host-plant growth during stress

We isolated and examined two endophytic fungi for their potential to secrete phytohormones viz. gibberellins (GAs) and indoleacetic acid (IAA) and mitigate abiotic stresses like salinity and drought. The endophytic fungi Phoma glomerata LWL2 and Penicillium sp. LWL3 significantly promoted the shoot and allied growth attributes of GAs-deficient dwarf mutant Waito-C and Dongjin-beyo rice. Analysis of the pure cultures of these endophytic fungi showed biologically active GAs (GA1, GA3, GA4 and GA7) in various quantities. The cultures of P. glomerata and Penicillium sp. also contained IAA. The culture application and endophytic-association with host-cucumber plants significantly increased the plant biomass and related growth parameters under sodium chloride and polyethylene glycol induced salinity and drought stress as compared to control plants. The endophytic symbiosis resulted in significantly higher assimilation of essential nutrients like potassium, calcium and magnesium as compared to control plants during salinity stress. Endophytic-association reduced the sodium toxicity and promoted the host-benefit ratio in cucumber plants as compared to non-inoculated control plants. The symbiotic-association mitigated stress by compromising the activities of reduced glutathione, catalase, peroxidase and polyphenol oxidase. Under stress conditions, the endophyte-infection significantly modulated stress through down-regulated abscisic acid, altered jasmonic acid, and elevated salicylic acid contents as compared to control. In conclusion, the two endophytes significantly reprogrammed the growth of host plants during stress conditions.

Geopyxins A-E, ent-kaurane diterpenoids from endolichenic fungal strains Geopyxis aff. majalis and Geopyxis sp. AZ0066: structure-activity relationships of geopyxins and their analogues

Four new ent-kaurane diterpenoids, geopyxins A-D (1-4), were isolated from Geopyxis aff. majalis, a fungus occurring in the lichen Pseudevernia intensa, whereas Geopyxis sp. AZ0066 inhabiting the same host afforded two new ent-kaurane diterpenoids, geopyxins E and F (5 and 6), together with 1 and 3. The structures of 1-6 were established on the basis of their spectroscopic data, while the absolute configurations were assigned using modified Mosher's ester method. Methylation of 1-3, 5, and 6 gave their corresponding methyl esters 7-11. On acetylation, 1 and 7 yielded their corresponding monoacetates 12 and 14 and diacetates 13 and 15. All compounds were evaluated for their cytotoxic and heat-shock induction activities. Compounds 2, 7-10, 12, 14, and 15 showed cytotoxic activity in the low micromolar range against all five cancer cell lines tested, but only compounds 7-9, 14, and 15 were found to activate the heat-shock response at similar concentrations. From a preliminary structure-activity perspective, the electrophilic α,β-unsaturated ketone carbonyl motif present in all compounds except 6 and 11 was found to be necessary but not sufficient for both cytotoxicity and heat-shock activation.

Endophytic fungal association via gibberellins and indole acetic acid can improve plant growth under abiotic stress: an example of Paecilomyces formosus LHL10

BACKGROUND

Endophytic fungi are little known for exogenous secretion of phytohormones and mitigation of salinity stress, which is a major limiting factor for agriculture production worldwide. Current study was designed to isolate phytohormone producing endophytic fungus from the roots of cucumber plant and identify its role in plant growth and stress tolerance under saline conditions.

RESULTS

We isolated nine endophytic fungi from the roots of cucumber plant and screened their culture filtrates (CF) on gibberellins (GAs) deficient mutant rice cultivar Waito-C and normal GAs biosynthesis rice cultivar Dongjin-byeo. The CF of a fungal isolate CSH-6H significantly increased the growth of Waito-C and Dongjin-byeo seedlings as compared to control. Analysis of the CF showed presence of GAs (GA1, GA3, GA4, GA8, GA9, GA12, GA20 and GA24) and indole acetic acid. The endophyte CSH-6H was identified as a strain of Paecilomyces formosus LHL10 on the basis of phylogenetic analysis of ITS sequence similarity. Under salinity stress, P. formosus inoculation significantly enhanced cucumber shoot length and allied growth characteristics as compared to non-inoculated control plants. The hypha of P. formosus was also observed in the cortical and pericycle regions of the host-plant roots and was successfully re-isolated using PCR techniques. P. formosus association counteracted the adverse effects of salinity by accumulating proline and antioxidants and maintaining plant water potential. Thus the electrolytic leakage and membrane damage to the cucumber plants was reduced in the association of endophyte. Reduced content of stress responsive abscisic acid suggest lesser stress convened to endophyte-associated plants. On contrary, elevated endogenous GAs (GA3, GA4, GA12 and GA20) contents in endophyte-associated cucumber plants evidenced salinity stress modulation.

CONCLUSION

The results reveal that mutualistic interactions of phytohormones secreting endophytic fungi can ameliorate host plant growth and alleviate adverse effects of salt stress. Such fungal strain could be used for further field trials to improve agricultural productivity under saline conditions.

Gibberellins – terpenoid plant hormones: Biological importance and chemical analysis

Gibberellins (GAs) are a large group of diterpenoid carboxylic acids, some members of which function as plant hormones controlling diverse aspects of growth and development. Biochemical, genetic, and genomic approaches have led to the identification of the majority of the genes that encode GA biosynthesis and deactivation enzymes. Recent studies have shown that both GA biosynthesis and deactivation pathways are tightly regulated by developmental, hormonal, and environmental signals, consistent with the role of GAs as key growth regulators. In this review, we summarize our current understanding of the GA biosynthesis and deactivation pathways in plants and fungi, and discuss methods for their qualitative and quantitative analysis. The challenges for their extraction and purification from plant tissues, which form complex matrices containing thousands of interfering substances, are discussed.

Exophiala sp. LHL08 reprograms Cucumis sativus to higher growth under abiotic stresses

Endophytic fungi are potential sources of secondary metabolites; however, they are little known for phytohormones secretion and amelioration of plant growth under abiotic stresses. We isolated a novel endophyte from the roots of Cucumis sativus and identified it as a strain of Exophiala sp. by sequencing internal transcribed spacer/large subunit rDNA and phylogenetic analysis. Prior to identification, culture filtrate (CF) of Exophiala sp. has shown significant growth promotion of Waito-C [a gibberellins (GAs)-deficient mutant cultivar] and Dongjin-byeo (normal GAs biosynthesis cultivar) rice seedlings. CF analysis of Exophiala sp. showed the presence of physiologically active GAs (GA₁, GA₃, GA₄ and GA₇) and inactive GAs (GA₅, GA₈, GA₉, GA₁₂ and GA₂₀). Exophiala sp. had higher GAs in its CF than wild-type strain of Gibberella fujikuroi except GA₃. Influence of Exophiala sp. was assessed on cucumber plant's growth and endogenous abscisic acid (ABA), salicylic acid (SA) and bioactive GAs under salinity and drought stresses. Exophiala sp.-treated plants have shown significantly higher growth and rescued the host plants from stress promulgated water deficit, osmotic and cellular damage. The altered levels of stress-responsive ABA showed low level of stress confined to endophyte-applied plants than control. Elevated levels of SA and bioactive GAs (GA₃ and GA₄) in endophyte-associated plants suggest stress-modulating response toward salinity and drought. In conclusion, symbiotic relations between Exophiala and cucumber have reprogrammed the host plant growth under abiotic stresses, thus indicating a possible threshold role of endophytic fungi in stress alleviation. This study could be extended for improving agricultural productivity under extreme environmental conditions.

Enzymatic (13)C labeling and multidimensional NMR analysis of miltiradiene synthesized by bifunctional diterpene cyclase in Selaginella moellendorffii

Diterpenes show diverse chemical structures and various physiological roles. The diversity of diterpene is primarily established by diterpene cyclases that catalyze a cyclization reaction to form the carbon skeleton of cyclic diterpene. Diterpene cyclases are divided into two types, monofunctional and bifunctional cyclases. Bifunctional diterpene cyclases (BDTCs) are involved in hormone and defense compound biosyntheses in bryophytes and gymnosperms, respectively. The BDTCs catalyze the successive two-step type-B (protonation-initiated cyclization) and type-A (ionization-initiated cyclization) reactions of geranylgeranyl diphosphate (GGDP). We found that the genome of a lycophyte, Selaginella moellendorffii, contains six BDTC genes with the majority being uncharacterized. The cDNA from S. moellendorffii encoding a BDTC-like enzyme, miltiradiene synthase (SmMDS), was cloned. The recombinant SmMDS converted GGDP to a diterpene hydrocarbon product with a molecular mass of 272 Da. Mutation in the type-B active motif of SmMDS abolished the cyclase activity, whereas (+)-copalyl diphosphate, the reaction intermediate from the conversion of GGDP to the hydrocarbon product, rescued the cyclase activity of the mutant to form a diterpene hydrocarbon. Another mutant lacking type-A activity accumulated copalyl diphosphate as the reaction intermediate. When the diterpene hydrocarbon was enzymatically synthesized from [U-(13)C(6)]mevalonate, all carbons were labeled with (13)C stable isotope (>99%). The fully (13)C-labeled product was subjected to (13)C-(13)C COSY NMR spectroscopic analyses. The direct carbon-carbon connectivities observed in the multidimensional NMR spectra demonstrated that the hydrocarbon product by SmMDS is miltiradiene, a putative biosynthetic precursor of tanshinone identified from the Chinese medicinal herb Salvia miltiorrhiza. Hence, SmMDS functions as a bifunctional miltiradiene synthase in S. moellendorffii. In this study, we demonstrate that one-dimensional and multidimensional (13)C NMR analyses of completely (13)C-labeled compound are powerful methods for biosynthetic studies.

Enzymatic total synthesis of gibberellin A₄ from acetate

Natural terpenoids have elaborate structures and various bioactivities, making difficult their synthesis and labeling with isotopes. We report here the enzymatic total synthesis of plant hormone gibberellins (GAs) with recombinant biosynthetic enzymes from stable isotope-labeled acetate. Mevalonate (MVA) is a key intermediate for the terpenoid biosynthetic pathway. ¹³C-MVA was synthesized from ¹³C-acetate via acetyl-CoA, using four enzymes or fermentation with a MVA-secreted yeast. The diterpene hydrocarbon, ent-kaurene, was synthesized from ¹³C-acetate and ¹³C-MVA with ten and six recombinant enzymes in one test tube, respectively. Four recombinant enzymes, P450 monooxygenases and soluble dioxygenases involved in the GA₄ biosynthesis from ent-kaurene via GA₁₂ were prepared in yeast and Escherichia coli. All intermediates and the final product GA₄ were uniformly labeled with ¹³C without dilution by natural abundance when [U-¹³C₂] acetate was used. The ¹³C-NMR and MS data for [U-¹³C₂₀] ent-kaurene confirmed ¹³C-¹³C coupling, and no dilution with the ¹²C atom was observed.