Identification of quantitative trait loci and candidate genes for primary metabolite content in strawberry fruit

Improvement of nutritional and organoleptic quality of fruits is a key goal in current strawberry breeding programs.The ratio of sugars to acids is a determinant factor contributing to fruit liking,although different sugars and acids contribute in varying degrees to this complex trait.A segregating F1 population of 95 individuals,previously characterized for several fruit quality characters,was used to map during 2 years quantitative trait loci(QTL)for 50 primary metabolites,L-ascorbic acid(L-AA)and other related traits such as soluble solid content(SSC),titratable acidity(TA),and pH.A total of 133 mQTL were detected above the established thresholds for 44 traits.Only 12.9%of QTL were detected in the 2 years,suggesting a large environmental influence on primary metabolite content.An objective of this study was the identification of key metabolites that were associated to the overall variation in SSC and acidity.As it was observed in previous studies,a number of QTL controlling several metabolites and traits were co-located in homoeology group V(HG V).mQTL controlling a large variance in raffinose,sucrose,succinic acid,and L-AA were detected in approximate the same chromosomal regions of different homoeologous linkage groups belonging to HG V.Candidate genes for selected mQTL are proposed based on their co-localization,on the predicted function,and their differential gene expression among contrasting F1 progeny lines.RNA-seq analysis from progeny lines contrasting in L-AA content detected 826 differentially expressed genes and identified Mannose-6-phosphate isomerase,FaM6PI1,as a candidate gene contributing to natural variation in ascorbic acid in strawberry fruit.

Genomic,transcriptomic,and metabolomic analysis of Oldenlandia corymbosa reveals the biosynthesis and mode of action of anti-cancer metabolites

Plants accumulate a vast array of secondary metabolites,which constitute a natural resource for pharmaceuticals.Oldenlandia corymbosa belongs to the Rubiaceae family,and has been used in traditional medicine to treat different diseases,including cancer.However,the active metabolites of the plant,their biosynthetic pathway and mode of action in cancer are unknown.To fill these gaps,we exposed this plant to eight different stress conditions and combined different omics data capturing gene expression,metabolic profiles,and anti-cancer activity.Our results show that O.corymbosa extracts are active against breast cancer cell lines and that ursolic acid is responsible for this activity.Moreover,we assembled a high-quality genome and uncovered two genes involved in the biosynthesis of ursolic acid.Finally,we also revealed that ursolic acid causes mitotic catastrophe in cancer cells and identified three high-confidence protein binding targets by Cellular Thermal Shift Assay(CETSA)and reverse docking.Altogether,these results constitute a valuable resource to further characterize the biosynthesis of active metabolites in the Oldenlandia group,while the mode of action of ursolic acid will allow us to further develop this valuable compound.

Plant cell cultures as heterologous bio-factories for secondary metabolite production

Synthetic biology has been developing rapidly in the last decade and is attracting increasing attention from many plant biologists.The production of high-value plant-specific secondary metabolites is,however,limited mostly to microbes.This is potentially problematic because of incorrect post-translational modification of proteins and differences in protein micro-compartmentalization,substrate availability,chaperone availability,product toxicity,and cytochrome p450 reductase enzymes.Unlike other heterologous systems,plant cells may be a promising alternative for the production of high-value metabolites.Several commercial plant suspension cell cultures from different plant species have been used successfully to produce valuable metabolites in a safe,low cost,and environmentally friendly manner.However,few metabolites are currently being biosynthesized using plant platforms,with the exception of the natural pigment anthocyanin.Both Arabidopsis thaliana and Nicotiana tabacum cell cultures can be developed by multiple gene transformations and CRISPR-Cas9 genome editing.Given that the introduction of heterologous biosynthetic pathways into Arabidopsis and N.tabacum is not widely used,the biosynthesis of foreign metabolites is currently limited;however,therein lies great potential.Here,we discuss the exemplary use of plant cell cultures and prospects for using A.thaliana and N.tabacum cell cultures to produce valuable plant-specific metabolites.

The metabolic changes that effect fruit quality during tomato fruit ripening

As the most valuable organ of tomato plants,fruit has attracted considerable attention which most focus on its quality formation during the ripening process.A considerable amount of research has reported that fruit quality is affected by metabolic shifts which are under the coordinated regulation of both structural genes and transcriptional regulators.In recent years,with the development of the next generation sequencing,molecular and genetic analysis methods,lots of genes which are involved in the chlorophyll,carotenoid,cell wall,central and secondary metabolism have been identified and confirmed to regulate pigment contents,fruit softening and other aspects of fruit flavor quality.Here,both research concerning the dissection of fruit quality related metabolic changes,the transcriptional and post-translational regulation of these metabolic pathways are reviewed.Furthermore,a weighted gene correlation network analysis of representative genes of fruit quality has been carried out and the potential of the combined application of the gene correlation network analysis,fine-mapping strategies and next generation sequencing to identify novel candidate genes determinants of fruit quality is discussed.

Metabolons,enzyme-enzyme assemblies that mediate substrate channeling,and their roles in plant metabolism

Metabolons are transientmulti-protein complexes of sequential enzymes that mediate substrate channeling.They differ from multi-enzyme complexes in that they are dynamic,rather than permanent,and as such have considerably lower dissociation constants.Despite the fact that a huge number of metabolons have been suggested to exist in plants,most of these claims are erroneous as only a handful of these have been proven to channelmetabolites.We believe that physical protein-protein interactions between consecutive enzymes of a pathway should rather be called enzyme-enzyme assemblies.In this review,we describe how metabolons are generally assembled by transient interactions and held together by both structural elements and non-covalent interactions.Experimental evidence for their existence comes fromprotein-protein interaction studies,which indicate that the enzymes physically interact,and direct substrate channelingmeasurements,which indicate that they functionally interact.Unfortunately,advances in cell biology and proteomics have far outstripped those in classical enzymology and flux measurements,rendering most reports reliant purely on interactome studies.Recent developments in co-fractionation mass spectrometry will likely further exacerbate this bias.Given this,only dynamic enzyme-enzyme assemblies in which both physical and functional interactions have been demonstrated should be termed metabolons.We discuss the level of evidence for the manifold plant pathways that have been postulated to contain metabolons and then list examples in both primary and secondary metabolism for which strong evidence has been provided to support these claims.In doing so,we pay particular attention to experimental and mathematical approaches to study metabolons as well as complexities that arise in attempting to follow them.Finally,we discuss perspectives for improving our understanding of these fascinating but enigmatic interactions.