The John Innes Centre Publications Repository contains details of all publications resulting from our researchers.

The repository also includes Open Access publications, which can be identified by the icons found on search results.

 Green open access publications are marked by the PDF icon. Click on the publication title, or the PDF icon, and read a pre-print PDF version of the publication.  Gold open access publications have the gold open padlock icon. You can read the full version of these papers on the publishing journal’s website without a subscription. 

The creation of this publications repository was funded by BBSRC.

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Galdon-Armero J., Fullana-Pericas M., Mulet P. A., Conesa M. A., Martin C., Galmes J. (2018)

The ratio of trichomes to stomata is associated with water use efficiency in tomato.

Plant Journal

Publisher's version: 10.1111/tpj.14055

ID: 59529

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Trichomes are specialised structures that originate from the aerial epidermis of plants, and play key roles in the interaction between the plant and the environment. In this study, we investigated differences in trichome phenotypes in four lines selected from the S. lycopersicum x S. pennellii introgression line (IL) population for their differences in trichome density, and their impact on plant performance under water deficit conditions. We performed comparative analyses at morphological and photosynthetic levels of plants grown under well-watered (WW) and also under water-deficit (WD) conditions in the field. Under WD conditions, we observed higher trichome density in ILs 11-3 and 4-1 and lower stomatal size in IL 4-1 compared to plants grown under WW conditions. Intrinsic water use efficiency (WUEi ) was higher under WD conditions in IL 11-3, and plant-level water use efficiency (WUEb ) was also higher in IL 11-3 and M82 in WD plants. The ratio of trichomes-to-stomata (T/S) was positively correlated with WUEi and WUEb , indicating an important role for both trichomes and stomata in drought tolerance in tomato and offering a promising way to select for improved water use efficiency of major crops. This article is protected by copyright. All rights reserved.

Dudnik A., Almeida A. F., Andrade R., Breitel D., Love N., Thole V., Trick M., Vain P., Martin C. R., Forster J. (2018)

BacHBerry: BACterial Hosts for production of Bioactive phenolics from bERRY fruits

Phytochemistry Reviews (17) 291-326

Publisher's version: 10.1007/s11101-017-9532-2

ID: 59154

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BACterial Hosts for production of Bioactive phenolics from bERRY fruits (BacHBerry) was a 3-year project funded by the Seventh Framework Programme (FP7) of the European Union that ran between November 2013 and October 2016. The overall aim of the project was to establish a sustainable and economically-feasible strategy for the production of novel high-value phenolic compounds isolated from berry fruits using bacterial platforms. The project aimed at covering all stages of the discovery and pre-commercialization process, including berry collection, screening and characterization of their bioactive components, identification and functional characterization of the corresponding biosynthetic pathways, and construction of Gram-positive bacterial cell factories producing phenolic compounds. Further activities included optimization of polyphenol extraction methods from bacterial cultures, scale-up of production by fermentation up to pilot scale, as well as societal and economic analyses of the processes. This review article summarizes some of the key findings obtained throughout the duration of the project.


Tomato has a relatively short growth cycle (fruit ready to pick within 65-85 days from planting) and a relatively high yield (the average for globe tomatoes is 3-9 kg fruit per plant rising to as much as 40 kg fruit per plant). Tomatoes also produce large amounts of important primary and secondary metabolites which can serve as intermediates or substrates for producing valuable new compounds. As a model crop, tomato already has a broad range of tools and resources available for biotechnological applications, either increased nutrients for health-promoting biofortified foods or as a production system for high-value compounds. These advantages make tomato an excellent chassis for the production of important metabolites. We summarize recent achievements in metabolic engineering of tomato and suggest new candidate metabolites which could be targets for metabolic engineering. We offer a scheme for how to establish tomato as a chassis for industrial-scale production of high-value metabolites.

Scarano A., Butelli E., De Santis S., Cavalcanti E., Hill L., De Angelis M., Giovinazzo G., Chieppa M., Martin C., Santino A. (2018)

Combined Dietary Anthocyanins, Flavonols, and Stilbenoids Alleviate Inflammatory Bowel Disease Symptoms in Mice.

Frontiers in nutrition (4) 75

Publisher's version: 10.3389/fnut.2017.00075

ID: 58217

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Dietary polyphenols are associated with a wide range of health benefits, protecting against chronic diseases and promoting healthy aging. Dietary polyphenols offer a complementary approach to the treatment of inflammatory bowel diseases (IBDs), a group of common chronic intestinal inflammation syndromes for which there is no cure. Tomato is widely consumed but its content of polyphenols is low. We developed a tomato variety, Bronze, enriched in three distinct classes of polyphenols: flavonols, anthocyanins, and stilbenoids. Using Bronze tomatoes as a dietary supplement as well as Indigo (high anthocyanins and flavonols), ResTom (high stilbenoids) and wild-type tomatoes, we examined the effects of the different polyphenols on the host gut microbiota, inflammatory responses, and the symptoms of chronic IBD, in a mouse model. Bronze tomatoes significantly impacted the symptoms of IBD. A similar result was observed using diets supplemented with red grape skin containing flavonols, anthocyanins, and stilbenoids, suggesting that effective protection is provided by different classes of polyphenols acting synergistically.


Specialized secondary metabolites serve not only to protect plants against abiotic and biotic challenges, but have also been used extensively by humans to combat diseases. Due to the great importance of medicinal plants for health, we need to find new and sustainable ways to improve the production of the specialized metabolites. In addition to direct extraction, recent progress in metabolic engineering of plants offers an alternative supply option. We argue that metabolic engineering for producing the secondary metabolites in plants may have distinct advantages over microbial production platforms, and thus propose new approaches of plant metabolic engineering, which are inspired by an ancient Chinese irrigation system. Metabolic engineering strategies work at three levels: introducing biosynthetic genes, using transcription factors, and improving metabolic flux including increasing the supply of precursors, energy, and reducing power. In addition, recent progress in biotechnology contributes markedly to better engineering, such as the use of specific promoters and the deletion of competing branch pathways. We propose that next-generation plant metabolic engineering will improve current engineering strategies, for the purpose of producing valuable metabolites in plants on industrial scales.

Tomlinson M. L., Butelli E., Martin C., Carding S. R. (2017)

Flavonoids from Engineered Tomatoes Inhibit Gut Barrier Pro-inflammatory Cytokines and Chemokines,viaSAPK/JNK and p38 MAPK Pathways.

Frontiers in nutrition (4) 61

Publisher's version: 10.3389/fnut.2017.00061

ID: 58241

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Flavonoids are a diverse group of plant secondary metabolites, known to reduce inflammatory bowel disease symptoms. How they achieve this is largely unknown. Our study focuses on the gut epithelium as it receives high topological doses of dietary constituents, maintains gut homeostasis, and orchestrates gut immunity. Dysregulation leads to chronic gut inflammation,viadendritic cell (DC)-driven immune responses. Tomatoes engineered for enriched sets of flavonoids (anthocyanins or flavonols) provided a unique and complex naturally consumed food matrix to study the effect of diet on chronic inflammation. Primary murine colonic epithelial cell-based inflammation assays consist of chemokine induction, apoptosis and proliferation, and effects on kinase pathways. Primary murine leukocytes and DCs were used to assay effects on transmigration. A murine intestinal cell line was used to assay wound healing. Engineered tomato extracts (enriched in anthocyanins or flavonols) showed strong and specific inhibitory effects on a set of key epithelial pro-inflammatory cytokines and chemokines. Chemotaxis assays showed a resulting reduction in the migration of primary leukocytes and DCs. Activation of epithelial cell SAPK/JNK and p38 MAPK signaling pathways were specifically inhibited. The epithelial wound healing-associated STAT3 pathway was unaffected. Cellular migration, proliferation, and apoptosis assays confirmed that wound healing processes were not affected by flavonoids. We show flavonoids target epithelial pro-inflammatory kinase pathways, inhibiting chemotactic signals resulting in reduced leukocyte and DC chemotaxis. Thus, both anthocyanins and flavonols modulate epithelial cells to become hyporesponsive to bacterial stimulation. Our results identify a viable mechanism to explain thein vivoanti-inflammatory effects of flavonoids.

Martin C., Li J. (2017)

Medicine is not health care, food is health care: plant metabolic engineering, diet and human health.

New Phytologist (Epub ahead of print) Epub ahead of print

Publisher's version: 10.1111/nph.14730

ID: 57059

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Plants make substantial contributions to our health through our diets, providing macronutrients for energy and growth as well as essential vitamins and phytonutrients that protect us from chronic diseases. Imbalances in our food can lead to deficiency diseases or obesity and associated metabolic disorders, increased risk of cardiovascular diseases and cancer. Nutritional security is now a global challenge which can be addressed, at least in part, through plant metabolic engineering for nutritional improvement of foods that are accessible to and eaten by many. We review the progress that has been made in nutritional enhancement of foods, both improvements through breeding and through biotechnology and the engineering principles on which increased phytonutrient levels are based. We also consider the evidence, where available, that such foods do enhance health and protect against chronic diseases.

Zhao Q., Cui M. Y., Levsh O., Yang D., Liu J., Li J., Hill L., Yang L., Hu Y., Weng J. K., Chen X. Y., Martin C. (2017)

Two CYP82D Enzymes Function as Flavone Hydroxylases in the Biosynthesis of Root-Specific 4'-Deoxyflavones in Scutellaria baicalensis.

Molecular Plant (In press corrected proof) In press corrected proof

Publisher's version: 10.1016/j.molp.2017.08.009

ID: 57548

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Baicalein, wogonin, and their glycosides are major bioactive compounds found in the medicinal plant Scutellaria baicalensis Georgi. These flavones can induce apoptosis in a variety of cancer cell lines but have no effect on normal cells. Furthermore, they have many additional benefits for human health, such as anti-oxidant, antiviral, and liver-protective properties. Here, we report the isolation and characterization of two CYP450 enzymes, SbCYP82D1.1 and SbCYP82D2, which function as the flavone 6-hydroxylase (F6H) and flavone 8-hydroxylase (F8H), respectively, in S. baicalensis. SbCYP82D1.1 has broad substrate specificity for flavones such as chrysin and apigenin and is responsible for biosynthesis of baicalein and scutellarein in roots and aerial parts of S. baicalensis, respectively. When the expression of SbCYP82D1.1 is knocked down, baicalin and baicalein levels are reduced significantly while chrysin glycosides accumulate in hairy roots. SbCYP82D2 is an F8H with high substrate specificity, accepting only chrysin as its substrate to produce norwogonin, although minor 6-hydroxylation activity can also be detected. Phylogenetic analysis suggested that SbCYP82D2 might have evolved from SbCYP82D1.1 via gene duplication followed by neofunctionalization, whereby the ancestral F6H activity is partially retained in the derived SbCYP82D2.

D'Amelia V., Aversano R., Ruggiero A., Batelli G., Appelhagen I., Dinacci C., Hill L., Martin C., Carputo D. (2017)

Subfunctionalization of duplicate MYB genes in Solanum commersonii generated the cold-induced ScAN2 and the anthocyanin regulator ScAN1.

Plant, Cell & Environment (XX) 111-123

Publisher's version: 10.1111/pce.12966

ID: 56627

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Wild potato species are useful sources of allelic diversity and loci lacking in the cultivated potato. In these species, the presence of anthocyanins in leaves has been associated with a greater tolerance to cold stress. However, the molecular mechanisms that allow potatoes to withstand cold exposure remain unclear. Here, we show that the expression of AN2, a MYB transcription factor, is induced by low temperatures in wild, cold-tolerant Solanum commersonii, and not in susceptible Solanum tuberosum varieties. We found that AN2 is a paralog of the potato anthocyanin regulator AN1, showing similar interaction ability with basic helix-loop-helix (bHLH) co-partners. Their sequence diversity resulted in a different capacity to promote accumulation of phenolics when tested in tobacco. Indeed, functional studies demonstrated that AN2 is less able to induce anthocyanins than AN1, but nevertheless it has a strong ability to induce accumulation of hydroxycinnamic acid derivatives. We propose that the duplication of R2R3 MYB genes resulted in subsequent subfunctionalization, where AN1 specialized in anthocyanin production and AN2 conserved the ability to respond to cold stress, inducing mainly the synthesis of hydroxycinnamic acid derivatives. These results contribute to understanding the evolutionary significance of gene duplication on phenolic compound regulation.

Kallam K., Appelhagen I., Luo J., Albert N., Zhang H., Deroles S., Hill L., Findlay K., Andersen Ø. M., Davies K., Martin C. (2017)

Aromatic Decoration Determines the Formation of Anthocyanic Vacuolar Inclusions.

Current Biology (Curr Biol. 2017 Mar 8. pii: S0960-9822(17)30164-1.) pii: S0960-9822(17)30164-1.

Publisher's version: 10.1016/j.cub.2017.02.027

ID: 55893

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Anthocyanins are some of the most widely occurring secondary metabolites in plants, responsible for the orange, red, purple, and blue colors of flowers and fruits and red colors of autumn leaves. These pigments accumulate in vacuoles, and their color is influenced by chemical decorations, vacuolar pH, the presence of copigments, and metal ions. Anthocyanins are usually soluble in the vacuole, but in some plants, they accumulate as discrete sub-vacuolar structures. Studies have distinguished intensely colored intra-vacuolar bodies observed in the cells of highly colored tissues, termed anthocyanic vacuolar inclusions (AVIs), from more globular, membrane-bound anthocyanoplasts. We describe a system in tobacco that adds additional decorations to the basic anthocyanin, cyanidin 3-O-rutinoside, normally formed by this species. Using this system, we have been able to establish which decorations underpin the formation of AVIs, the conditions promoting AVI formation, and, consequently, the mechanism by which they form.

Butelli E., Garcia-Lor A., Licciardello C., Las Casas G., Hill L., Recupero G. R., Keremane M. L., Ramadugu C., Krueger R., Xu Q., Deng X., Fanciullino A. L., Froelicher Y., Navarro L., Martin C. (2017)

Changes in Anthocyanin Production during Domestication of Citrus.

Plant Physiology (173) 2225-2242

Publisher's version: 10.1104/pp.16.01701

ID: 56012

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Mandarin (Citrus reticulata), citron (Citrus medica), and pummelo (Citrus maxima) are important species of the genus Citrus and parents of the interspecific hybrids that constitute the most familiar commercial varieties of Citrus: sweet orange, sour orange, clementine, lemon, lime, and grapefruit. Citron produces anthocyanins in its young leaves and flowers, as do species in genera closely related to Citrus, but mandarins do not, and pummelo varieties that produce anthocyanins have not been reported. We investigated the activity of the Ruby gene, which encodes a MYB transcription factor controlling anthocyanin biosynthesis, in different accessions of a range of Citrus species and in domesticated cultivars. A white mutant of lemon lacks functional alleles of Ruby, demonstrating that Ruby plays an essential role in anthocyanin production in Citrus Almost all the natural variation in pigmentation by anthocyanins in Citrus species can be explained by differences in activity of the Ruby gene, caused by point mutations and deletions and insertions of transposable elements. Comparison of the allelic constitution of Ruby in different species and cultivars also helps to clarify many of the taxonomic relationships in different species of Citrus, confirms the derivation of commercial varieties during domestication, elucidates the relationships within the subgenus Papeda, and allows a new genetic classification of mandarins.

Ewas M., Gao Y., Wang S., Liu X., Zhang H., Nishawy E. M. E., Ali F., Shahzad R., Ziaf K., Subthain H., Martin C., Luo J. (2016)

Manipulation of S1MX1 for enhanced carotenoids accumulation and drought resistance in tomato

Science Bulletin (61(18)) 1413-1418

Publisher's version: 10.1007/s11434-016-1108-9

ID: 56730

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Plants are the ultimate source of nutrients in the human diet. To ensure adequate availability of high quality food for an increasing world population, traits including improved tolerance of stresses and nutrient levels need to be selected in crops, both individually and in combination. Here we report the identification of SlMX1 encoding a MIXTA-like MYB transcription factor in tomato that simultaneously modulates drought resistance and metabolic processes through regulating key structural and regulatory genes of the corresponding pathways. Over-expression of SlMX1 results in substantially increased drought tolerance and improved fruit quality, while knocking down SlMX1 resulted in the opposite phenotypes. Our study indicates an effective way with multiple beneficial traits by genetic engineering of a single regulatory gene and can be a novel approach to breeding crops.

Zhao Q., Chen X. Y., Martin C. (2016)

Scutellaria baicalensis, the golden herb from the garden of Chinese medicinal plants.

Science bulletin (61) 1391-1398

Publisher's version: 10.1007/s11434-016-1136-5

ID: 56622

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Scutellaria baicalensis Georgi, or Chinese skullcap, has been widely used as a medicinal plant in China for thousands of years, where the preparation from its roots is called Huang-Qin. It has been applied in the treatment of diarrhea, dysentery, hypertension, hemorrhaging, insomnia, inflammation and respiratory infections. Flavones such as baicalin, wogonoside and their aglycones baicalein wogonin are the major bioactive compounds extracted from the root of S. baicalensis. These flavones have been reported to have various pharmacological functions, including anti-cancer, hepatoprotection, antibacterial and antiviral, antioxidant, anticonvulsant and neuroprotective effects. In this review, we focus on clinical applications and the pharmacological properties of the medicinal plant and the flavones extracted from it. We also describe biotechnological and metabolic methods that have been used to elucidate the biosynthetic pathways of the bioactive compounds in Scutellaria.

Matros A., Mock H. P., Oertel S., Wendell M., Hvoslef-Eide A. K., Pahlke G., Marko D., Appelhagen I., Martin C. (2016)

From specialized cell cultures to high quality fine chemicals: ANTHOcyanin production PLatform Using Suspension cultures (ANTHOPLUS)

Journal of International Society of Antioxidants in Nutrition & Health (9) 3(4)

Publisher's version: 10.18143/JISANH_v3i4_1306

ID: 56810

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Zhao Q., Zhang Y., Wang G., Hill L., Weng J. K., Chen X. Y., Xue H., Martin C. (2016)

A specialized flavone biosynthetic pathway has evolved in the medicinal plant Scutellaria baicalensis

Science Advances (2) 4

Publisher's version: 10.1126/sciadv.1501780

ID: 52919

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Wogonin and baicalein are bioactive flavones in the popular Chinese herbal remedy Huang-Qin (Scutellaria baicalensis Georgi). These specialized flavones lack a 4′-hydroxyl group on the B ring (4′-deoxyflavones) and induce apoptosis in a wide spectrum of human tumor cells in vitro and inhibit tumor growth in vivo in different mouse tumor models. Root-specific flavones (RSFs) from Scutellaria have a variety of reported additional beneficial effects including antioxidant and antiviral properties. We describe the characterization of a new pathway for the synthesis of these compounds, in which pinocembrin (a 4′-deoxyflavanone) serves as a key intermediate. Although two genes encoding flavone synthase II (FNSII) are expressed in the roots of S. baicalensis, FNSII-1 has broad specificity for flavanones as substrates, whereas FNSII-2 is specific for pinocembrin. FNSII-2 is responsible for the synthesis of 4′-deoxyRSFs, such as chrysin and wogonin, wogonoside, baicalein, and baicalin, which are synthesized from chrysin. A gene encoding a cinnamic acid–specific coenzyme A ligase (SbCLL-7), which is highly expressed in roots, is required for the synthesis of RSFs by FNSII-2, as demonstrated by gene silencing. A specific isoform of chalcone synthase (SbCHS-2) that is highly expressed in roots producing RSFs is also required for the synthesis of chrysin. Our studies reveal a recently evolved pathway for biosynthesis of specific, bioactive 4′-deoxyflavones in the roots of S. baicalensis.

Garcia-Seco D., Zhang Y., Gutierrez-Mañero F. J., Martin C., Ramos-Solano B. (2015)

Application of Pseudomonas fluorescens to Blackberry under Field Conditions Improves Fruit Quality by Modifying Flavonoid Metabolism.

PLoS One (10) e0142639

Publisher's version: 10.1371/journal.pone.0142639

ID: 52578

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Application of a plant growth promoting rhizobacterium (PGPR), Pseudomonas fluorescens N21.4, to roots of blackberries (Rubus sp.) is part of an optimised cultivation practice to improve yields and quality of fruit throughout the year in this important fruit crop. Blackberries are especially rich in flavonoids and therefore offer potential benefits for human health in prevention or amelioration of chronic diseases. However, the phenylpropanoid pathway and its regulation during ripening have not been studied in detail, in this species. PGPR may trigger flavonoid biosynthesis as part of an induced systemic response (ISR) given the important role of this pathway in plant defence, to cause increased levels of flavonoids in the fruit. We have identified structural genes encoding enzymes of the phenylpropanoid and flavonoid biosynthetic pathways catalysing the conversion of phenylalanine to the final products including flavonols, anthocyanins and catechins from blackberry, and regulatory genes likely involved in controlling the activity of pathway branches. We have also measured the major flavonols, anthocyanins and catechins at three stages during ripening. Our results demonstrate the coordinated expression of flavonoid biosynthetic genes with the accumulation of anthocyanins, catechins, and flavonols in developing fruits of blackberry. Elicitation of blackberry plants by treatment of roots with P.fluorescens N21.4, caused increased expression of some flavonoid biosynthetic genes and an accompanying increase in the concentration of selected flavonoids in fruits. Our data demonstrate the physiological mechanisms involved in the improvement of fruit quality by PGPR under field conditions, and highlight some of the genetic targets of elicitation by beneficial bacteria.

Zhang Y., Butelli E., Alseekh S., Tohge T., Rallapalli G., Luo J., Kawar P. G., Hill L., Santino A., Fernie A. R., Martin C. (2015)

Multi-level engineering facilitates the production of phenylpropanoid compounds in tomato.

Nature Communications (6) 8635

Publisher's version: 10.1038/ncomms9635

ID: 52035

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Phenylpropanoids comprise an important class of plant secondary metabolites. A number of transcription factors have been used to upregulate-specific branches of phenylpropanoid metabolism, but by far the most effective has been the fruit-specific expression of AtMYB12 in tomato, which resulted in as much as 10% of fruit dry weight accumulating as flavonols and hydroxycinnamates. We show that AtMYB12 not only increases the demand of flavonoid biosynthesis but also increases the supply of carbon from primary metabolism, energy and reducing power, which may fuel the shikimate and phenylalanine biosynthetic pathways to supply more aromatic amino acids for secondary metabolism. AtMYB12 directly binds promoters of genes encoding enzymes of primary metabolism. The enhanced supply of precursors, energy and reducing power achieved by AtMYB12 expression can be harnessed to engineer high levels of novel phenylpropanoids in tomato fruit, offering an effective production system for bioactives and other high value ingredients.

Patron N. J., Orzaez D., Marillonnet S., Warzecha H., Matthewman C., Youles M., Raitskin O., Leveau A., Farré G., Rogers C., Smith A., Hibberd J., Webb A. A., Locke J., Schornack S., Ajioka J., Baulcombe D. C., Zipfel C., Kamoun S., Jones J. D., Kuhn H., Robatzek S., Van Esse H. P., Sanders D., Oldroyd G., Martin C., Field R., O'Connor S., Fox S., Wulff B., Miller B., Breakspear A., Radhakrishnan G., Delaux P. M., Loqué D., Granell A., Tissier A., Shih P., Brutnell T. P., Quick W. P., Rischer H., Fraser P. D., Aharoni A., Raines C., South P. F., Ané J. M., Hamberger B. R., Langdale J., Stougaard J., Bouwmeester H., Udvardi M., Murray J. A., Ntoukakis V., Schäfer P., Denby K., Edwards K. J., Osbourn A., Haseloff J. (2015)

Standards for plant synthetic biology: a common syntax for exchange of DNA parts.

New Phytologist (208) 13-9

Publisher's version: 10.1111/nph.13532

ID: 55372

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Inventors in the field of mechanical and electronic engineering can access multitudes of components and, thanks to standardization, parts from different manufacturers can be used in combination with each other. The introduction of BioBrick standards for the assembly of characterized DNA sequences was a landmark in microbial engineering, shaping the field of synthetic biology. Here, we describe a standard for Type IIS restriction endonuclease-mediated assembly, defining a common syntax of 12 fusion sites to enable the facile assembly of eukaryotic transcriptional units. This standard has been developed and agreed by representatives and leaders of the international plant science and synthetic biology communities, including inventors, developers and adopters of Type IIS cloning methods. Our vision is of an extensive catalogue of standardized, characterized DNA parts that will accelerate plant bioengineering.

Tohge T., Zhang Y., Peterek S., Matros A., Rallapalli G., Tandrón Y. A., Butelli E., Kallam K., Hertkorn N., Mock H. P., Martin C., Fernie A. R. (2015)

Ectopic expression of snapdragon transcription factors facilitates the identification of genes encoding enzymes of anthocyanin decoration in tomato.

Plant Journal (83) 686-704

Publisher's version: 10.1111/tpj.12920

ID: 51898

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Given the potential health benefits of polyphenolic compounds in the diet, there is a growing interest in the generation of food crops enriched with health-protective flavonoids. We undertook a series of metabolite analyses of tomatoes ectopically expressing the Delila and Rosea1 transcription factor genes from snapdragon (Antirrhinum majus), paying particular attention to changes in phenylpropanoids compared to controls. These analyses revealed multiple changes, including depletion of rutin and naringenin chalcone, and enhanced levels of anthocyanins and phenylacylated flavonol derivatives. We isolated and characterized the chemical structures of the two most abundant anthocyanins, which were shown by NMR spectroscopy to be delphinidin-3-(4'''-O-trans-p-coumaroyl)-rutinoside-5-O-glucoside and petunidin-3-(4'''-O-trans-p-coumaroyl)-rutinoside-5-O-glucoside. By performing RNA sequencing on both purple fruit and wild-type fruit, we obtained important information concerning the relative expression of both structural and transcription factor genes. Integrative analysis of the transcript and metabolite datasets provided compelling evidence of the nature of all anthocyanin biosynthetic genes, including those encoding species-specific anthocyanin decoration enzymes. One gene, SlFdAT1 (Solyc12g088170), predicted to encode a flavonoid-3-O-rutinoside-4'''-phenylacyltransferase, was characterized by assays of recombinant protein and over-expression assays in tobacco. The combined data are discussed in the context of both our current understanding of phenylpropanoid metabolism in Solanaceous species, and evolution of flavonoid decorating enzymes and their transcriptional networks in various plant species.

Patron N. J., Orzaez D., Marillonnet S., Warzecha H., Matthewman C., Youles M., Raitskin O., Leveau A., Farré G., Rogers C., Smith A., Hibberd J., Webb A. A., Locke J., Schornack S., Ajioka J., Baulcombe D. C., Zipfel C., Kamoun S., Jones J. D., Kuhn H., Robatzek S., Van Esse H. P., Sanders D., Oldroyd G., Martin C., Field R., O'Connor S., Fox S., Wulff B., Miller B., Breakspear A., Radhakrishnan G., Delaux P. M., Loqué D., Granell A., Tissier A., Shih P., Brutnell T. P., Quick W. P., Rischer H., Fraser P. D., Aharoni A., Raines C., South P. F., Ané J. M., Hamberger B. R., Langdale J., Stougaard J., Bouwmeester H., Udvardi M., Murray J. A., Ntoukakis V., Schäfer P., Denby K., Edwards K. J., Osbourn A., Haseloff J. (2015)

Standards for plant synthetic biology: a common syntax for exchange of DNA parts.

New Phytologist (208) 1319

Publisher's version: 10.1111/nph.13532

ID: 51594

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Inventors in the field of mechanical and electronic engineering can access multitudes of components and, thanks to standardization, parts from different manufacturers can be used in combination with each other. The introduction of BioBrick standards for the assembly of characterized DNA sequences was a landmark in microbial engineering, shaping the field of synthetic biology. Here, we describe a standard for Type IIS restriction endonuclease-mediated assembly, defining a common syntax of 12 fusion sites to enable the facile assembly of eukaryotic transcriptional units. This standard has been developed and agreed by representatives and leaders of the international plant science and synthetic biology communities, including inventors, developers and adopters of Type IIS cloning methods. Our vision is of an extensive catalogue of standardized, characterized DNA parts that will accelerate plant bioengineering.

Zhang Y., de Stefano R., Robine M., Butelli E., Bulling K., Hill L., Rejzek M., Martin C., Schoonbeek H. J. (2015)

Different ROS-Scavenging Properties of Flavonoids Determine Their Abilities to Extend Shelf Life of Tomato.

Plant Physiology (169(3)) 1568-1583

Publisher's version: 10.1104/pp.15.00346

ID: 51528

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The shelf-life of tomato (Solanum lycopersicum) fruit is determined by the processes of over-ripening and susceptibility to pathogens. Post-harvest shelf life is one of the most important traits for commercially grown tomatoes. We compared the shelf life of tomato fruit that accumulate different flavonoids and found that delayed over-ripening is associated with increased total antioxidant capacity caused by the accumulation of flavonoids in the fruit. However, reduced susceptibility to Botrytis cinerea, a major post-harvest fungal pathogen of tomato, is conferred by specific flavonoids only. We demonstrate an association between flavonoid structure, selective scavenging ability for different free radicals and reduced susceptibility to B. cinerea. Our study provides mechanistic insight into how flavonoids influence shelf life of tomato, information which could be used to improve the shelf life of tomato, and potentially of other soft fruit.

Williams M., Lockhart P., Martin C. (2015)

Digital teaching tools and global learning communities

F1000 Research (4:59) 59

Publisher's version: 10.12688/f1000research.6150.1

ID: 49174

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In 2009, we started a project to support the learning of university-level sciences, called Teaching Tools in Plant Biology.  Articles in this series are published by the plant science journal The Plant Cell (published by the American Society of Plant Biologists).  Five years on, we investigated how the published materials are being used through an analysis of the Google Analytics page views distribution and through a user survey.  Our results suggest that this project has had a broad, global impact in supporting higher education, and also that the materials are used differently by individuals in terms of their role (infrastructure, independent learner, student) and geographical location.  We also report on our ongoing efforts to develop a global learning community that encourages discussion and resource sharing.

Garcia-Seco D., Zhang Y., Gutierrez-Mañero F. J., Martin C., Ramos-Solano B. (2015)

RNA-Seq analysis and transcriptome assembly for blackberry (Rubus sp. Var. Lochness) fruit.

BMC Genomics (16) 5

Publisher's version: 10.1186/s12864-014-1198-1

ID: 49187

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There is an increasing interest in berries, especially blackberries in the diet, because of recent reports of their health benefits due to their high content of flavonoids. A broad range of genomic tools are available for other Rosaceae species but these tools are still lacking in the Rubus genus, thus limiting gene discovery and the breeding of improved varieties.

Moglia A., Lanteri S., Comino C., Hill L., Knevitt D., Cagliero C., Rubiolo P., Bornemann S., Martin C. (2014)

Dual catalytic activity of hydroxycinnamoyl-coenzyme A quinate transferase from tomato allows it to moonlight in the synthesis of both mono- and dicaffeoylquinic acids.

Plant Physiology (166) 1777-87

Publisher's version: 10.1104/pp.114.251371

ID: 49024

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Tomato (Solanum lycopersicum), like other Solanaceous species, accumulates high levels of antioxidant caffeoylquinic acids, which are strong bioactive molecules and protect plants against biotic and abiotic stresses. Among these compounds, the monocaffeoylquinic acids (e.g. chlorogenic acid [CGA]) and the dicaffeoylquinic acids (diCQAs) have been found to possess marked antioxidative properties. Thus, they are of therapeutic interest both as phytonutrients in foods and as pharmaceuticals. Strategies to increase diCQA content in plants have been hampered by the modest understanding of their biosynthesis and whether the same pathway exists in different plant species. Incubation of CGA with crude extracts of tomato fruits led to the formation of two new products, which were identified by liquid chromatography-mass spectrometry as diCQAs. This chlorogenate:chlorogenate transferase activity was partially purified from ripe fruit. The final protein fraction resulted in 388-fold enrichment of activity and was subjected to trypsin digestion and mass spectrometric sequencing: a hydroxycinnamoyl-Coenzyme A:quinate hydroxycinnamoyl transferase (HQT) was selected as a candidate protein. Assay of recombinant HQT protein expressed in Escherichia coli confirmed its ability to synthesize diCQAs in vitro. This second activity (chlorogenate:chlorogenate transferase) of HQT had a low pH optimum and a high Km for its substrate, CGA. High concentrations of CGA and relatively low pH occur in the vacuoles of plant cells. Transient assays demonstrated that tomato HQT localizes to the vacuole as well as to the cytoplasm of plant cells, supporting the idea that in this species, the enzyme catalyzes different reactions in two subcellular compartments.

Schwinn K. E., Boase M. R., Bradley J. M., Lewis D. H., Deroles S. C., Martin C. R., Davies K. M. (2014)

MYB and bHLH transcription factor transgenes increase anthocyanin pigmentation in petunia and lisianthus plants, and the petunia phenotypes are strongly enhanced under field conditions.

Frontiers In Plant Science (5) 603

Publisher's version: 10.3389/fpls.2014.00603

ID: 49177

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Petunia line Mitchell [MP, Petunia axillaris × (P. axillaris × P. hybrida)] and Eustoma grandiflorum (lisianthus) plants were produced containing a transgene for over-expression of the R2R3-MYB transcription factor [TF; ROSEA1 (ROS1)] that up-regulates flavonoid biosynthesis in Antirrhinum majus. The petunia lines were also crossed with previously produced MP lines containing a Zea mays flavonoid-related basic helix-loop-helix TF transgene (LEAF COLOR, LC), which induces strong vegetative pigmentation when these 35S:LC plants are exposed to high-light levels. 35S:ROS1 lisianthus transgenics had limited changes in anthocyanin pigmentation, specifically, precocious pigmentation of flower petals and increased pigmentation of sepals. RNA transcript levels for two anthocyanin biosynthetic genes, chalcone synthase and anthocyanidin synthase, were increased in the 35S:ROS1 lisianthus petals compared to those of control lines. With MP, the 35S:ROS1 calli showed novel red pigmentation in culture, but this was generally not seen in tissue culture plantlets regenerated from the calli or young plants transferred to soil in the greenhouse. Anthocyanin pigmentation was enhanced in the stems of mature 35S:ROS1 MP plants, but the MP white-flower phenotype was not complemented. Progeny from a 35S:ROS1 × 35S:LC cross had novel pigmentation phenotypes that were not present in either parental line or MP. In particular, there was increased pigment in the petal throat region, and the anthers changed from yellow to purple pigmentation. An outdoor field trial was conducted with the 35S:ROS1, 35S:LC, 35S:ROS1 × 35S:LC and control MP lines. Field conditions rapidly induced intense foliage pigmentation in 35S:LC plants, a phenotype not observed in control MP or equivalent 35S:LC plants maintained in a greenhouse. No difference in plant stature, seed germination, or plant survival was observed between transgenic and control plants.

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