Publications by authors named "Saleh Alseekh"

99 Publications

The integration of MS-based metabolomics and multivariate data analysis allows for improved quality assessment of Zingiber officinale Roscoe.

Phytochemistry 2021 Jul 23;190:112843. Epub 2021 Jul 23.

Max Planck Institute for Biology of Ageing, Joseph Stelzmann Str. 9b, 50931, Cologne, Germany. Electronic address:

Ginger (Zingiber officinale Roscoe) is consumed for health-promoting effects and as a food condiment. Comprehensive phytochemical analysis, other than gingerols and shogaols, has not yet been deeply investigated. Hence, the current research aimed to establish a non-targeted metabolomics approach for the discrimination between fresh ginger rhizome samples collected from four different producing countries, i.e., China, India, Pakistan, and Peru. In addition, lab-dried samples were analyzed to trace drying-induced metabolites. A comprehensive extraction procedure was carried out resulting in production of polar and non-polar fractions. The polar fraction was analyzed by ultra-performance liquid chromatography coupled with Fourier transform tandem mass spectrometry (UPLC-C-FT-MS/MS) and gas chromatography coupled with time-of-flight mass spectrometry (GC-TOF-MS) post derivatization. UPLC-C-FT-MS/MS was used for analysis of non-polar fraction. Results revealed for identification of a total of 253 metabolites. In addition, multivariate data analysis (MVDA), including principal component analysis (PCA) demonstrated clustering of Asian specimens. Several metabolites with a characteristic pattern for the origin revealing the highest contents of bioactive metabolites in the Peruvian product. Moreover, chemical markers identified, including [6]-gingerol and [6]-shogaol discriminating between fresh and dried samples. Furthermore, abundances of some primary metabolites, including amino acids and cinnamic acid, have confirmed the biosynthetic pathway of gingerols and their transformation upon drying to shogaols. The proposed approach can be applied as a potential candidate for quality assessment of ginger and other medicinal plants.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.phytochem.2021.112843DOI Listing
July 2021

Towards Development, Maintenance, and Standardized Phenotypic Characterization of Single-Seed-Descent Genetic Resources for Lupins.

Curr Protoc 2021 Jul;1(7):e191

Legume Genomics Team, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland.

Well-characterized genetic resources are fundamental to maintain and provide the various genotypes for pre-breeding programs for the production of new cultivars (e.g., wild relatives, unimproved material, landraces). The aim of the current article is to provide protocols for the characterization of the genetic resources of two lupin crop species: the European Lupinus albus and the American Lupinus mutabilis. Intelligent nested collections of lupins derived from homozygous lines (single-seed descent) are being developed, established, and exploited using cutting-edge approaches for genotyping, phenotyping, data management, and data analysis within the INCREASE project (EU Horizon 2020). This will allow us to predict the phenotypic performance of genotyped lines, and will further boost research and development in lupins. Lupins stand out due to their high-quality seed protein (∼40% of seed dry weight) and other primary components in the seeds, which include fatty acids, dietary fiber, and minerals. The potential of lupins as a crop is highlighted by the multiple benefits of plant-based food in terms of food security, nutrition, human health, and sustainable production. The use of lupins in foods, along with other well-studied and widely used food legumes, will also provide a greatly diversified plant-based food palette to meet the Global Goals for Sustainable Development to improve people's lives by 2030. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Lupin seed phenotypic descriptors Basic Protocol 2: Lupin seed imaging Basic Protocol 3: Standardized phenotypic characterization of lupin genetic resources grown towards primary seed increase (development of single-seed descent genetic resources).
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/cpz1.191DOI Listing
July 2021

Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices.

Nat Methods 2021 Jul 8;18(7):747-756. Epub 2021 Jul 8.

CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.

Mass spectrometry-based metabolomics approaches can enable detection and quantification of many thousands of metabolite features simultaneously. However, compound identification and reliable quantification are greatly complicated owing to the chemical complexity and dynamic range of the metabolome. Simultaneous quantification of many metabolites within complex mixtures can additionally be complicated by ion suppression, fragmentation and the presence of isomers. Here we present guidelines covering sample preparation, replication and randomization, quantification, recovery and recombination, ion suppression and peak misidentification, as a means to enable high-quality reporting of liquid chromatography- and gas chromatography-mass spectrometry-based metabolomics-derived data.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41592-021-01197-1DOI Listing
July 2021

Plasticity of rosette size in response to nitrogen availability is controlled by an RCC1-family protein.

Plant Cell Environ 2021 Jul 6. Epub 2021 Jul 6.

Molecular Mechanisms of Plant Adaptation - group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.

Nitrogen (N) is fundamental to plant growth, development and yield. Genes underlying N utilization and assimilation are well-characterized, but mechanisms underpinning plasticity of different phenotypes in response to N remain elusive. Here, using Arabidopsis thaliana accessions, we dissected the genetic architecture of plasticity in early and late rosette diameter, flowering time and yield, in response to three levels of N in the soil. Furthermore, we found that the plasticity in levels of primary metabolites were related with the plasticities of the studied traits. Genome-wide association analysis identified three significant associations for phenotypic plasticity, one for early rosette diameter and two for flowering time. We confirmed that the gene At1g19880, hereafter named as PLASTICITY OF ROSETTE TO NITROGEN 1 (PROTON1), encoding for a regulator of chromatin condensation 1 (RCC1) family protein, conferred plasticity of rosette diameter in response to N. Treatment of PROTON1 T-DNA line with salt implied that the reduced plasticity of early rosette diameter was not a general growth response to stress. We further showed that plasticities of growth and flowering-related traits differed between environmental cues, indicating decoupled genetic programs regulating these traits. Our findings provide a prospective to identify genes that stabilize performance under fluctuating environments.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/pce.14146DOI Listing
July 2021

Genome-wide association studies: assessing trait characteristics in model and crop plants.

Cell Mol Life Sci 2021 Aug 1;78(15):5743-5754. Epub 2021 Jul 1.

Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.

GWAS involves testing genetic variants across the genomes of many individuals of a population to identify genotype-phenotype association. It was initially developed and has proven highly successful in human disease genetics. In plants genome-wide association studies (GWAS) initially focused on single feature polymorphism and recombination and linkage disequilibrium but has now been embraced by a plethora of different disciplines with several thousand studies being published in model and crop species within the last decade or so. Here we will provide a comprehensive review of these studies providing cases studies on biotic resistance, abiotic tolerance, yield associated traits, and metabolic composition. We also detail current strategies of candidate gene validation as well as the functional study of haplotypes. Furthermore, we provide a critical evaluation of the GWAS strategy and its alternatives as well as future perspectives that are emerging with the emergence of pan-genomic datasets.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00018-021-03868-wDOI Listing
August 2021

Tyr-Asp inhibition of glyceraldehyde 3-phosphate dehydrogenase affects plant redox metabolism.

EMBO J 2021 Aug 22;40(15):e106800. Epub 2021 Jun 22.

Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.

How organisms integrate metabolism with the external environment is a central question in biology. Here, we describe a novel regulatory small molecule, a proteogenic dipeptide Tyr-Asp, which improves plant tolerance to oxidative stress by directly interfering with glucose metabolism. Specifically, Tyr-Asp inhibits the activity of a key glycolytic enzyme, glyceraldehyde 3-phosphate dehydrogenase (GAPC), and redirects glucose toward pentose phosphate pathway (PPP) and NADPH production. In line with the metabolic data, Tyr-Asp supplementation improved the growth performance of both Arabidopsis and tobacco seedlings subjected to oxidative stress conditions. Moreover, inhibition of Arabidopsis phosphoenolpyruvate carboxykinase (PEPCK) activity by a group of branched-chain amino acid-containing dipeptides, but not by Tyr-Asp, points to a multisite regulation of glycolytic/gluconeogenic pathway by dipeptides. In summary, our results open the intriguing possibility that proteogenic dipeptides act as evolutionarily conserved small-molecule regulators at the nexus of stress, protein degradation, and metabolism.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.15252/embj.2020106800DOI Listing
August 2021

Multi-omics analyses reveal the roles of the ASR1 transcription factor in tomato fruits.

J Exp Bot 2021 Jun 8. Epub 2021 Jun 8.

Facultad de Agronomía. Cátedra de Genética. Universidad de Buenos Aires.

The transcription factor Asr1 (ABA, stress, ripening 1) plays multiple roles in the plant responses to abiotic stresses as well as being involved in the regulation of central metabolism in several plant species. However, despite the high expression levels of ASR1 in tomato fruits, large scale analyses to uncover its role in fruits are still lacking. In order to study its function in the context of fruit ripening, we performed a multi-omics analysis of Asr1-silenced transgenic tomato fruits at transcriptomics and metabolomics levels. Our results indicate that ASR1 is involved in several pathways implicated in the fruit ripening process, including cell wall, amino acid, and carotenoid metabolism as well as abiotic stress pathways. Moreover, we found that Asr1-silenced fruits are more susceptible to the infection by the necrotrophic fungus Botrytis cinerea. A literature search suggested that Asr1 could be regulated by the fruit ripening regulators NOR, CNR and FUL1/2, among others, which allowed us to situate it in the regulatory cascade of red ripe tomato fruits. These data thus extend the known range of functions of ASR1 underlying it to be an important auxiliary regulator of tomato ripening.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/jxb/erab269DOI Listing
June 2021

Towards the Development, Maintenance, and Standardized Phenotypic Characterization of Single-Seed-Descent Genetic Resources for Common Bean.

Curr Protoc 2021 May;1(5):e133

Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy.

The optimal use of legume genetic resources represents a key prerequisite for coping with current agriculture-related societal challenges, including conservation of agrobiodiversity, agricultural sustainability, food security, and human health. Among legumes, the common bean (Phaseolus vulgaris) is the most economically important for human consumption, and its evolutionary trajectories as a species have been crucial to determining the structure and level of its present and available genetic diversity. Genomic advances are considerably enhancing the characterization and assessment of important genetic variants. For this purpose, the development and availability of, and access to, well-described and efficiently managed genetic resource collections that comprise pure lines derived by single-seed-descent cycles will be paramount for the use of the reservoir of common bean variability and for the advanced breeding of legume crops. This is one of the main aims of the new and challenging European project INCREASE, which is the implementation of Intelligent Collections with appropriate standardized protocols that must be characterized, maintained, and made available, along with the related data, to users such as breeders and researchers. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Characterizing common bean seeds for seed trait descriptors Basic Protocol 2: Bean seed imaging Basic Protocol 3: Characterizing bean lines for plant trait descriptors specific for common bean Primary Seed Increase.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/cpz1.133DOI Listing
May 2021

Multi-omics analysis of early leaf development in .

Patterns (N Y) 2021 Apr 9;2(4):100235. Epub 2021 Apr 9.

Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.

The growth of plant organs is driven by cell division and subsequent cell expansion. The transition from proliferation to expansion is critical for the final organ size and plant yield. Exit from proliferation and onset of expansion is accompanied by major metabolic reprogramming, and in leaves with the establishment of photosynthesis. To learn more about the molecular mechanisms underlying the developmental and metabolic transitions important for plant growth, we used untargeted proteomics and metabolomics analyses to profile young leaves of a model plant representing proliferation, transition, and expansion stages. The dataset presented represents a unique resource comprising approximately 4,000 proteins and 300 annotated small-molecular compounds measured across 6 consecutive days of leaf growth. These can now be mined for novel developmental and metabolic regulators of plant growth and can act as a blueprint for studies aimed at better defining the interface of development and metabolism in other species.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.patter.2021.100235DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8085607PMC
April 2021

Ultra-high-performance liquid chromatography high-resolution mass spectrometry variants for metabolomics research.

Nat Methods 2021 Jul 10;18(7):733-746. Epub 2021 May 10.

Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.

Ultra-high-performance liquid chromatography high-resolution mass spectrometry (UHPLC-HRMS) variants currently represent the best tools to tackle the challenges of complexity and lack of comprehensive coverage of the metabolome. UHPLC offers flexible and efficient separation coupled with high-sensitivity detection via HRMS, allowing for the detection and identification of a broad range of metabolites. Here we discuss current common strategies for UHPLC-HRMS-based metabolomics, with a focus on expanding metabolome coverage.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41592-021-01116-4DOI Listing
July 2021

Using Precision Phenotyping to Inform de novo Domestication.

Plant Physiol 2021 Apr 12. Epub 2021 Apr 12.

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China.

An update on the use of precision phenotyping to assess the potential of lesser cultivated species as candidates for de novo domestication or similar development for future agriculture.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/plphys/kiab160DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8260140PMC
April 2021

Multi-omics approach reveals the contribution of KLU to leaf longevity and drought tolerance.

Plant Physiol 2021 03;185(2):352-368

Max-Planck-Institut für Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, Am Mühlenberg 1, 14476 Potsdam, Germany.

KLU, encoded by a cytochrome P450 CYP78A family gene, generates an important-albeit unknown-mobile signal that is distinct from the classical phytohormones. Multiple lines of evidence suggest that KLU/KLU-dependent signaling functions in several vital developmental programs, including leaf initiation, leaf/floral organ growth, and megasporocyte cell fate. However, the interactions between KLU/KLU-dependent signaling and the other classical phytohormones, as well as how KLU influences plant physiological responses, remain poorly understood. Here, we applied in-depth, multi-omics analysis to monitor transcriptome and metabolome dynamics in klu-mutant and KLU-overexpressing Arabidopsis plants. By integrating transcriptome sequencing data and primary metabolite profiling alongside phytohormone measurements, our results showed that cytokinin signaling, with its well-established function in delaying leaf senescence, was activated in KLU-overexpressing plants. Consistently, KLU-overexpressing plants exhibited significantly delayed leaf senescence and increased leaf longevity, whereas the klu-mutant plants showed early leaf senescence. In addition, proline biosynthesis and catabolism were enhanced following KLU overexpression owing to increased expression of genes associated with proline metabolism. Furthermore, KLU-overexpressing plants showed enhanced drought-stress tolerance and reduced water loss. Collectively, our work illustrates a role for KLU in positively regulating leaf longevity and drought tolerance by synergistically activating cytokinin signaling and promoting proline metabolism. These data promote KLU as a potential ideal genetic target to improve plant fitness.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/plphys/kiaa034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8133585PMC
March 2021

Domestication of Crop Metabolomes: Desired and Unintended Consequences.

Trends Plant Sci 2021 06 27;26(6):650-661. Epub 2021 Feb 27.

Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria. Electronic address:

The majority of the crops and vegetables of today were domesticated from their wild progenitors within the past 12 000 years. Considerable research effort has been expended on characterizing the genes undergoing positive and negative selection during the processes of crop domestication and improvement. Many studies have also documented how the contents of a handful of metabolites have been altered during human selection, but we are only beginning to unravel the true extent of the metabolic consequences of breeding. We highlight how crop metabolomes have been wittingly or unwittingly shaped by the processes of domestication, and highlight how we can identify new targets for metabolite engineering for the purpose of de novo domestication of crop wild relatives.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.tplants.2021.02.005DOI Listing
June 2021

Evolutionary gain of oligosaccharide hydrolysis and sugar transport enhanced carbohydrate partitioning in sweet watermelon fruits.

Plant Cell 2021 Jul;33(5):1554-1573

National Watermelon and Melon Improvement Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China.

How raffinose (Raf) family oligosaccharides, the major translocated sugars in the vascular bundle in cucurbits, are hydrolyzed and subsequently partitioned has not been fully elucidated. By performing reciprocal grafting of watermelon (Citrullus lanatus) fruits to branch stems, we observed that Raf was hydrolyzed in the fruit of cultivar watermelons but was backlogged in the fruit of wild ancestor species. Through a genome-wide association study, the alkaline alpha-galactosidase ClAGA2 was identified as the key factor controlling stachyose and Raf hydrolysis, and it was determined to be specifically expressed in the vascular bundle. Analysis of transgenic plants confirmed that ClAGA2 controls fruit Raf hydrolysis and reduces sugar content in fruits. Two single-nucleotide polymorphisms (SNPs) within the ClAGA2 promoter affect the recruitment of the transcription factor ClNF-YC2 (nuclear transcription factor Y subunit C) to regulate ClAGA2 expression. Moreover, this study demonstrates that C. lanatus Sugars Will Eventually Be Exported Transporter 3 (ClSWEET3) and Tonoplast Sugar Transporter (ClTST2) participate in plasma membrane sugar transport and sugar storage in fruit cell vacuoles, respectively. Knocking out ClAGA2, ClSWEET3, and ClTST2 affected fruit sugar accumulation. Genomic signatures indicate that the selection of ClAGA2, ClSWEET3, and ClTST2 for carbohydrate partitioning led to the derivation of modern sweet watermelon from non-sweet ancestors during domestication.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/plcell/koab055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8254481PMC
July 2021

Phytochromes control metabolic flux, and their action at the seedling stage determines adult plant biomass.

J Exp Bot 2021 04;72(8):3263-3278

Institute of Molecular Plant Sciences, School of Biological Sciences, Daniel Rutherford Building, Max Born Crescent, Kings Buildings, University of Edinburgh, Edinburgh, UK.

Phytochrome photoreceptors are known to regulate plastic growth responses to vegetation shade. However, recent reports also suggest an important role for phytochromes in carbon resource management, metabolism, and growth. Here, we use 13CO2 labelling patterns in multiallele phy mutants to investigate the role of phytochrome in the control of metabolic fluxes. We also combine quantitative data of 13C incorporation into protein and cell wall polymers, gas exchange measurements, and system modelling to investigate why biomass is decreased in adult multiallele phy mutants. Phytochrome influences the synthesis of stress metabolites such as raffinose and proline, and the accumulation of sugars, possibly through regulating vacuolar sugar transport. Remarkably, despite their modified metabolism and vastly altered architecture, growth rates in adult phy mutants resemble those of wild-type plants. Our results point to delayed seedling growth and smaller cotyledon size as the cause of the adult-stage phy mutant biomass defect. Our data signify a role for phytochrome in metabolic stress physiology and carbon partitioning, and illustrate that phytochrome action at the seedling stage sets the trajectory for adult biomass production.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/jxb/erab038DOI Listing
April 2021

The genetics underlying metabolic signatures in a brown rice diversity panel and their vital role in human nutrition.

Plant J 2021 Apr 10;106(2):507-525. Epub 2021 Mar 10.

International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.

Brown rice (Oryza sativa) possesses various nutritionally dense bioactive phytochemicals exhibiting a wide range of antioxidant, anti-cancer, and anti-diabetic properties known to promote various human health benefits. However, despite the wide claims made about the importance of brown rice for human nutrition the underlying metabolic diversity has not been systematically explored. Non-targeted metabolite profiling of developing and mature seeds of a diverse genetic panel of 320 rice cultivars allowed quantification of 117 metabolites. The metabolite genome-wide association study (mGWAS) detected genetic variants influencing diverse metabolic targets in developing and mature seeds. We further interlinked genetic variants on chromosome 7 (6.06-6.43 Mb region) with complex epistatic genetic interactions impacting multi-dimensional nutritional targets, including complex carbohydrate starch quality, the glycemic index, antioxidant catechin, and rice grain color. Through this nutrigenomics approach rare gene bank accessions possessing genetic variants in bHLH and IPT5 genes were identified through haplotype enrichment. These variants were associated with a low glycemic index, higher catechin levels, elevated total flavonoid contents, and heightened antioxidant activity in the whole grain with elevated anti-cancer properties being confirmed in cancer cell lines. This multi-disciplinary nutrigenomics approach thus allowed us to discover the genetic basis of human health-conferring diversity in the metabolome of brown rice.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/tpj.15182DOI Listing
April 2021

Diverting tyrosine: Data from untargeted metabolic analysis of tomato fruit accumulating L-DOPA.

Data Brief 2021 Feb 19;34:106678. Epub 2020 Dec 19.

Department of Metabolic Biology and Biological Chemistry, The John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.

L-DOPA, also known as Levodopa or L-3,4-dihydroxyphenylalanine, is synthesised in plants from the amino acid tyrosine, through oxidation. Conversion of tyrosine to L-DOPA constitues the first step of betalain biosynthesis in plants. Recently, the gene responsible for this step was identified in beetroot, , that is the source of yellow and purple betalain pigments. Overexpression of this gene, specifically in tomato fruit, led to accumulation of L-DOPA that otherwise is not detectable [1]. Co-expression of the Arabidopsis transcription factor, , in fruit, increased L-DOPA levels further. To study the metabolic changes in these fruit, we performed untargeted metabolite analysis of ripe fruit: GC-MS was performed to identify changes in primary metabolites, LC-MS analysis was used to identify alterations in specialised metabolites. These data can be used to study the impact of diversion of tyrosine in fruit, accompanied by the accumulation of L-DOPA and to identify new biological roles associated with the accumulation of these metabolites.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.dib.2020.106678DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7773851PMC
February 2021

An -Derived Biostimulant Protects Model and Crop Plants from Oxidative Stress.

Metabolites 2020 Dec 31;11(1). Epub 2020 Dec 31.

Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria.

Abiotic stresses, which at the molecular level leads to oxidative damage, are major determinants of crop yield loss worldwide. Therefore, considerable efforts are directed towards developing strategies for their limitation and mitigation. Here the superoxide-inducing agent paraquat (PQ) was used to induce oxidative stress in the model species and the crops tomato and pepper. Pre-treatment with the biostimulant SuperFifty (SF) effectively and universally suppressed PQ-induced leaf lesions, HO build up, cell destruction and photosynthesis inhibition. To further investigate the stress responses and SF-induced protection at the molecular level, we investigated the metabolites by GC-MS metabolomics. PQ induced specific metabolic changes such as accumulation of free amino acids (AA) and stress metabolites. These changes were fully prevented by the SF pre-treatment. Moreover, the metabolic changes of the specific groups were tightly correlating with their phenotypic characteristics. Overall, this study presents physiological and metabolomics data which shows that SF protects against oxidative stress in all three plant species.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/metabo11010024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7824492PMC
December 2020

Integrating multi-omics data for crop improvement.

J Plant Physiol 2021 Feb 17;257:153352. Epub 2020 Dec 17.

Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam, Golm, Germany; Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria. Electronic address:

Our agricultural systems are now in urgent need to secure food for a growing world population. To meet this challenge, we need a better characterization of plant genetic and phenotypic diversity. The combination of genomics, transcriptomics and metabolomics enables a deeper understanding of the mechanisms underlying the complex architecture of many phenotypic traits of agricultural relevance. We review the recent advances in plant genomics to see how these can be integrated with broad molecular profiling approaches to improve our understanding of plant phenotypic variation and inform crop breeding strategies.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jplph.2020.153352DOI Listing
February 2021

Long-Term Cd Exposure Alters the Metabolite Profile in Stem Tissue of .

Cells 2020 12 17;9(12). Epub 2020 Dec 17.

GreenTech Innovation Center, Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 5, Avenue des Hauts-Fourneaux, 4362 Esch-sur-Alzette, Luxembourg.

As a common pollutant, cadmium (Cd) is one of the most toxic heavy metals accumulating in agricultural soils through anthropogenic activities. The uptake of Cd by plants is the main entry route into the human food chain, whilst in plants it elicits oxidative stress by unbalancing the cellular redox status. was subjected to chronic Cd stress for five months. Targeted and untargeted metabolic analyses were performed. Long-term Cd exposure altered the amino acid composition with levels of asparagine, histidine and proline decreasing in stems but increasing in leaves. This suggests tissue-specific metabolic stress responses, which are often not considered in environmental studies focused on leaves. In stem tissue, profiles of secondary metabolites were clearly separated between control and Cd-exposed plants. Fifty-one secondary metabolites were identified that changed significantly upon Cd exposure, of which the majority are (iso)flavonoid conjugates. Cadmium exposure stimulated the phenylpropanoid pathway that led to the accumulation of secondary metabolites in stems rather than cell wall lignification. Those metabolites are antioxidants mitigating oxidative stress and preventing cellular damage. By an adequate adjustment of its metabolic composition, reaches a new steady state, which enables the plant to acclimate under chronic Cd stress.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/cells9122707DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7765984PMC
December 2020

Using Metabolomics to Assist Plant Breeding.

Methods Mol Biol 2021 ;2264:33-46

Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.

Recent methodological advances in both gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) have provided a deep understanding of metabolic regulation occurring in plant cells. The application of these techniques to agricultural systems is, however, subject to more complex interactions. Here we summarize a step-by-step modern metabolomics methodology that generates metabolome data toward the implementation of metabolomics in crop breeding. We describe a metabolic workflow, and provide guidelines for handling large sample numbers for the specific purpose of metabolic quantitative trait loci approaches.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-0716-1201-9_3DOI Listing
March 2021

Publisher Correction: Tomato multiomics at aPEELing resolution.

Nat Plants 2020 Dec;6(12):1506

Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41477-020-00825-6DOI Listing
December 2020

Pod indehiscence in common bean is associated with the fine regulation of PvMYB26.

J Exp Bot 2021 02;72(5):1617-1633

Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, via Brecce Bianche, Ancona, Italy.

In legumes, pod shattering occurs when mature pods dehisce along the sutures, and detachment of the valves promotes seed dispersal. In Phaseolus vulgaris (L)., the major locus qPD5.1-Pv for pod indehiscence was identified recently. We developed a BC4/F4 introgression line population and narrowed the major locus down to a 22.5 kb region. Here, gene expression and a parallel histological analysis of dehiscent and indehiscent pods identified an AtMYB26 orthologue as the best candidate for loss of pod shattering, on a genomic region ~11 kb downstream of the highest associated peak. Based on mapping and expression data, we propose early and fine up-regulation of PvMYB26 in dehiscent pods. Detailed histological analysis establishes that pod indehiscence is associated with the lack of a functional abscission layer in the ventral sheath, and that the key anatomical modifications associated with pod shattering in common bean occur early during pod development. We finally propose that loss of pod shattering in legumes resulted from histological convergent evolution and that it is the result of selection at orthologous loci.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/jxb/eraa553DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7921299PMC
February 2021

Metabolic engineering of tomato fruit enriched in L-DOPA.

Metab Eng 2021 05 23;65:185-196. Epub 2020 Nov 23.

Department of Metabolic Biology and Biological Chemistry, The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK. Electronic address:

L-DOPA, also known as Levodopa or L-3,4-dihydroxyphenylalanine, is a non-standard amino acid, and the gold standard drug for the treatment for Parkinson's Disease (PD). Recently, a gene encoding the enzyme that is responsible for its synthesis, as a precursor of the coloured pigment group betalains, was identified in beetroot, BvCYP76AD6. We have engineered tomato fruit enriched in L-DOPA through overexpression of BvCYP76AD6 in a fruit specific manner. Analysis of the transgenic fruit revealed the feasibility of accumulating L-DOPA in a non-naturally betalain-producing plant. Fruit accumulating L-DOPA also showed major effects on the fruit metabolome. Some of these changes included elevation of amino acids levels, changes in the levels of intermediates of the TCA and glycolysis pathways and reductions in the levels of phenolic compounds and nitrogen-containing specialised metabolites. Furthermore, we were able to increase the L-DOPA levels further by elevating the expression of the metabolic master regulator, MYB12, specifically in tomato fruit, together with BvCYP76AD6. Our study elucidated new roles for L-DOPA in plants, because it impacted fruit quality parameters including antioxidant capacity and firmness. The L-DOPA levels achieved in tomato fruit were comparable to the levels in other non-seed organs of L-DOPA - accumulating plants, offering an opportunity to develop new biological sources of L-DOPA by widening the repertoire of L-DOPA-accumulating plants. These tomato fruit could be used as an alternative source of this important pharmaceutical.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ymben.2020.11.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8054910PMC
May 2021

Metabolomic Analysis of Natural Variation in Arabidopsis.

Methods Mol Biol 2021 ;2200:393-411

Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.

Methodological advances in coupled-mass spectrometry (gas chromatography and liquid chromatography; GC-MS and LC-MS) have rendered the profiling of highly complex plant extracts relatively facile and allowed that their high-throughput use aids the investigation of a range of biological questions. Among these is the elucidation of the genetic factors underlying metabolite abundance. For this purpose genome-wide association studies (GWAS) are being widely adopted in Arabidopsis with the resultant quantitative trait loci being subjected to cross-validation by the use of recombinant inbred lines, introgression lines, and T-DNA insertional knockout lines.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-0716-0880-7_19DOI Listing
March 2021

Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data.

Nat Biotechnol 2021 02 9;39(2):169-173. Epub 2020 Nov 9.

Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.

We engineered a machine learning approach, MSHub, to enable auto-deconvolution of gas chromatography-mass spectrometry (GC-MS) data. We then designed workflows to enable the community to store, process, share, annotate, compare and perform molecular networking of GC-MS data within the Global Natural Product Social (GNPS) Molecular Networking analysis platform. MSHub/GNPS performs auto-deconvolution of compound fragmentation patterns via unsupervised non-negative matrix factorization and quantifies the reproducibility of fragmentation patterns across samples.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41587-020-0700-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7971188PMC
February 2021

Tomato multiomics at aPEELing resolution.

Nat Plants 2020 12;6(12):1394-1395

Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41477-020-00807-8DOI Listing
December 2020

Model-assisted identification of metabolic engineering strategies for Jatropha curcas lipid pathways.

Plant J 2020 09 23;104(1):76-95. Epub 2020 Jul 23.

Centre for Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria.

Efficient approaches to increase plant lipid production are necessary to meet current industrial demands for this important resource. While Jatropha curcas cell culture can be used for in vitro lipid production, scaling up the system for industrial applications requires an understanding of how growth conditions affect lipid metabolism and yield. Here we present a bottom-up metabolic reconstruction of J. curcas supported with labeling experiments and biomass characterization under three growth conditions. We show that the metabolic model can accurately predict growth and distribution of fluxes in cell cultures and use these findings to pinpoint energy expenditures that affect lipid biosynthesis and metabolism. In addition, by using constraint-based modeling approaches we identify network reactions whose joint manipulation optimizes lipid production. The proposed model and computational analyses provide a stepping stone for future rational optimization of other agronomically relevant traits in J. curcas.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/tpj.14906DOI Listing
September 2020

Mobile Transposable Elements Shape Plant Genome Diversity.

Trends Plant Sci 2020 11 28;25(11):1062-1064. Epub 2020 Aug 28.

Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Ruski Blvd. 139, Plovdiv, 4000, Bulgaria. Electronic address:

The presence of various types of structural variants, including transposons, make up the major part of the genomic differences among plant species. Two recent papers, Domínguez et al. and Alonge et al. explore specifically the impact that retrotransposons and other structural variants had on several tomato phenotypes of agricultural importance.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.tplants.2020.08.003DOI Listing
November 2020

Dissection of the domestication-shaped genetic architecture of lettuce primary metabolism.

Plant J 2020 11 14;104(3):613-630. Epub 2020 Sep 14.

Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.

Lettuce (Lactuca sativa L.) is an important vegetable crop species worldwide. The primary metabolism of this species is essential for its growth, development and reproduction as well as providing a considerable direct source of energy and nutrition for humans. Here, through investigating 77 primary metabolites in 189 accessions including all major horticultural types and wild lettuce L. serriola we showed that the metabolites in L. serriola were different from those in cultivated lettuce. The findings were consistent with the demographic model of lettuce and supported a single domestication event for this species. Selection signals among these metabolic traits were detected. Specifically, galactinol, malate, quinate and threonate were significantly affected by the domestication process and cultivar differentiation of lettuce. Galactinol and raffinose might have been selected during stem lettuce cultivation as an adaption to the local environments in China. Furthermore, we identified 154 loci significantly associated with the level of 51 primary metabolites. Three genes (LG8749721, LG8763094 and LG5482522) responsible for the levels of galactinol, raffinose, quinate and chlorogenic acid were further dissected, which may have been the target of domestication and/or affected by local adaptation. Additionally, our findings strongly suggest that human selection resulted in reduced quinate and chlorogenic acid levels in cultivated lettuce. Our study thus provides beneficial genetic resources for lettuce quality improvement and sheds light on the domestication and evolution of this important leafy green.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/tpj.14950DOI Listing
November 2020
-->