Vliegensvlug door het DNA

Wageningse wetenschappers maken gebruik van twee nieuwe DNA-sequencers. Eén daarvan werkt 25 duizend keer sneller dan de apparatuur van vijftien jaar geleden

Metabolic engineering of flavonoids in tomato (Solanum lycopersicum): the potential for metabolomics

Flavonoids comprise a large and diverse group of polyphenolic plant secondary metabolites. In plants, flavonoids play important roles in many biological processes such as pigmentation of flowers, fruits and vegetables, plant-pathogen interactions, fertility and protection against UV light. Being natural plant compounds, flavonoids are an integral part of the human diet and there is increasing evidence that dietary polyphenols are likely candidates for the observed beneficial effects of a diet rich in fruits and vegetables on the prevention of several chronic diseases. Within the plant kingdom, and even within a single plant species, there is a large variation in the levels and composition of flavonoids. This variation is often due to specific mutations in flavonoid-related genes leading to quantitative and qualitative differences in metabolic profiles. The use of such specific flavonoid mutants with easily scorable, visible phenotypes has led to the isolation and characterisation of many structural and regulatory genes involved in the flavonoid biosynthetic pathway from different plant species. These genes have been used to engineer the flavonoid biosynthetic pathway in both model and crop plant species, not only from a fundamental perspective, but also in order to alter important agronomic traits, such as flower and fruit colour, resistance, nutritional value. This review describes the advances made in engineering the flavonoid pathway in tomato (Solanum lycopersicum). Three different approaches will be described; (I) Increasing endogenous tomato flavonoids using structural or regulatory genes; (II) Blocking specific steps in the flavonoid pathway by RNA interference strategies; and (III) Production of novel tomato flavonoids by introducing novel branches of the flavonoid pathway. Metabolite profiling is an essential tool to analyse the effects of pathway engineering approaches, not only to analyse the effect on the flavonoid composition itself, but also on other related or unrelated metabolic pathways. Metabolomics will therefore play an increasingly important role in revealing a more complete picture of metabolic perturbation and will provide additional novel insights into the effect of the introduced genes and the role of flavonoids in plant physiology and development

A comprehensive set of transcript sequences of the heavy metal hyperaccumulator Noccaea caerulescens

Noccaea caerulescens is an extremophile plant species belonging to the Brassicaceae family. It has adapted to grow on soils containing high, normally toxic, concentrations of metals such as nickel, zinc, and cadmium. Next to being extremely tolerant to these metals, it is one of the few species known to hyperaccumulate these metals to extremely high concentrations in their aboveground biomass. In order to provide additional molecular resources for this model metal hyperaccumulator species to study and understand the mechanism of adaptation to heavy metal exposure, we aimed to provide a comprehensive database of transcript sequences for N. caerulescens. In this study, 23,830 transcript sequences (isotigs) with an average length of 1025 bp were determined for roots, shoots and inflorescences of N. caerulescens accession “Ganges” by Roche GS-FLEX 454 pyrosequencing. These isotigs were grouped into 20,378 isogroups, representing potential genes. This is a large expansion of the existing N. caerulescens transcriptome set consisting of 3705 unigenes. When translated and compared to a Brassicaceae proteome set, 22,232 (93.2%) of the N. caerulescens isotigs (corresponding to 19,191 isogroups) had a significant match and could be annotated accordingly. Of the remaining sequences, 98 isotigs resembled non-plant sequences and 1386 had no significant similarity to any sequence in the GenBank database. Among the annotated set there were many isotigs with similarity to metal homeostasis genes or genes for glucosinolate biosynthesis. Only for transcripts similar to Metallothionein3 (MT3), clear evidence for an additional copy was found. This comprehensive set of transcripts is expected to further contribute to the discovery of mechanisms used by N. caerulescens to adapt to heavy metal exposur

The role of strigolactones in P deficiency induced transcriptional changes in tomato roots

BACKGROUND: Phosphorus (P) is an essential macronutrient for plant growth and development. Upon P shortage, plant responds with massive reprogramming of transcription, the Phosphate Starvation Response (PSR). In parallel, the production of strigolactones (SLs)—a class of plant hormones that regulates plant development and rhizosphere signaling molecules—increases. It is unclear, however, what the functional link is between these two processes. In this study, using tomato as a model, RNAseq was used to evaluate the time-resolved changes in gene expression in the roots upon P starvation and, using a tomato CAROTENOID CLEAVAGE DIOXYGENASES 8 (CCD8) RNAi line, what the role of SLs is in this. RESULTS: Gene ontology (GO)-term enrichment and KEGG analysis of the genes regulated by P starvation and P replenishment revealed that metabolism is an important component of the P starvation response that is aimed at P homeostasis, with large changes occurring in glyco-and galactolipid and carbohydrate metabolism, biosynthesis of secondary metabolites, including terpenoids and polyketides, glycan biosynthesis and metabolism, and amino acid metabolism. In the CCD8 RNAi line about 96% of the PSR genes was less affected than in wild-type (WT) tomato. For example, phospholipid biosynthesis was suppressed by P starvation, while the degradation of phospholipids and biosynthesis of substitute lipids such as sulfolipids and galactolipids were induced by P starvation. Around two thirds of the corresponding transcriptional changes depend on the presence of SLs. Other biosynthesis pathways are also reprogrammed under P starvation, such as phenylpropanoid and carotenoid biosynthesis, pantothenate and CoA, lysine and alkaloids, and this also partially depends on SLs. Additionally, some plant hormone biosynthetic pathways were affected by P starvation and also here, SLs are required for many of the changes (more than two thirds for Gibberellins and around one third for Abscisic acid) in the gene expression. CONCLUSIONS: Our analysis shows that SLs are not just the end product of the PSR in plants (the signals secreted by plants into the rhizosphere), but also play a major role in the regulation of the PSR (as plant hormone). SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-021-03124-0

Combining Genomics and Metabolomics for the Discovery of Regulatory Genes and Their Use in Metabolic Engineering to Produce ‘Healthy Foods’

Plants often accumulate their natural products to relatively low levels, so there is a lot of interest in breeding or engineering plants that produce higher levels. It has been shown that the most effective way to increase the accumulation of secondary metabolites is to increase the activity of genes that regulate the activity of the biosynthetic pathways that make different natural products. Regulatory genes of this type encode proteins called transcription factors. The biggest bottleneck in using this strategy to develop plants that accumulate significantly higher levels of important natural products is that not many transcription factors regulating secondary metabolism have yet been identified at the molecular level. Genes encoding transcription factors can be identified from model plants with sequenced genomes. The ability of such genes to regulate metabolism can be assayed by examination of mutants (reverse genetics) and by investigating the metabolic effects of high levels of expression of the genes. The combined techniques of metabolic fingerprinting and metabolite profiling of mutant and transgenic plants are allowing us to identify new genes encoding transcription factors controlling secondary metabolism, that can be used as tools for engineering natural product accumulatio

Dissecting disease-suppressive rhizosphere microbiomes by functional amplicon sequencing and 10× metagenomics

Microbial Biotechnolog

Genetic engineering of flavonoid biosynthesis in tomato

Planten beschikken over een enorme capaciteit om een breed scala aan secundaire metabolieten te produceren waarmee ze kunnen reageren op hun continu veranderende omgeving. Flavonoïden, een van de meest voorkomende soort secundaire metabolieten, zijn laagmoleculaire stoffen die van nature in vrijwel alle planten voorkomen. Ze zijn bij uiteenlopende natuurlijke processen betrokken. Zo ontstaat bijvoorbeeld de rode, blauwe en paarse kleur van veel bloemen door de aanwezigheid van anthocyanen, een specifieke klasse van flavonoïdpigmenten. Ook rijpe vruchten danken hun kleur vaak aan deze klasse van flavonoïden. Daarnaast spelen flavonoïden een rol bij processen zoals bescherming van planten tegen schadelijke UV-straling, afweer tegen infecties, pollenvorming en fertiliteit. Omdat flavonoïden wijdverspreid voorkomen in het plantenrijk, vormen deze stoffen een permanent onderdeel van ons plantaardig voedsel. Een deel van de gezondheidsbevorderende effecten van groenten en fruit wordt toegeschreven aan de aanwezigheid van bepaalde flavonoïden. Hoewel flavonoïden in vrijwel alle planten voorkomen, zijn sommige klassen specifiek voor een bepaalde plantensoort, terwijl deze ondervertegenwoordigd of geheel afwezig kunnen zijn in andere plantensoorten. Vanuit dit oogpunt kan het wenselijk zijn om te selecteren voor gewassen met bepaalde (hoeveelheden van) flavonoïden, dan wel de samenstelling daarvan aan te passen. Onderzoek naar de mogelijkheden om de productie van flavonoïden in planten te veranderen wordt veelal uitgevoerd om de aantrekkelijkheid van sierteeltgewassen óf de voedingswaarde van bepaalde gewassen te verhogen. Elio Schijlen onderzocht de genetische modificatie van de biosyntheseroute van flavonoïden in tomaat. Hiermee wil hij meer inzicht geven in de endogene flavonoïdbiosynthese én de mogelijkheden onderzoeken om nieuwe flavonoïden te produceren die van nature niet voorkomen in tomaten

A two-component system for seedless fruit development

The application relates to the field of plant biotechnology. A two component system for making hybrid plants capable of producing seedless fruits is provided. Using the two component system, for example seedless tomatoes, peppers, aubergines and melons can 5 be made. Also provided is a method for inducible seed set

Boosting beneficial phytochemicals in vegetable crop plants

Plants contain an astonishing diversity of biochemical pathways, which eventually result in the production and accumulation of innumerable phytochemical compounds. From an historical point of view, people have primarily selected plants on the basis of traits that are linked to the presence of beneficial phytochemicals. During the past decade, biotechnology has improved the possibilities of changing the biochemical composition of several crop plants and consequently has opened up new opportunities for targeted crop improvement or even for the development of new crops or converting existing crops for other uses. In this review, we will give an overview of strategies and progress made in modifications of some of the important compounds of importance to the food industry in particular. The focus is placed on the flavonoid, vitamin, essential amino acid and polyunsaturated fatty acid composition of vegetable crops and hence topics such as food quality improvement, food fortification, nutritional value and functional foods are broadly illustrate