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Mellway RD, Lund ST. Interaction analysis of grapevine MIKC(c)-type MADS transcription factors and heterologous expression of putative véraison regulators in tomato. JOURNAL OF PLANT PHYSIOLOGY 2013; 170:1424-33. [PMID: 23787144 DOI: 10.1016/j.jplph.2013.05.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/15/2013] [Accepted: 05/16/2013] [Indexed: 05/06/2023]
Abstract
MIKC(c)-type MADS-domain transcription factors include important regulators of floral development that interact in protein complexes to control the development of floral organs, as described by the ABC model. Members of the SEPALLATA (SEP) and AGAMOUS (AG) MADS clades include proteins involved in stamen and carpel specification and certain members of these families, such as tomato (Solanum lycopersicon) SlRIN and SlTAGL1, have been shown to regulate fruit development and ripening initiation. A number of expression studies have shown that several floral homeotic MADS genes are expressed during grapevine (Vitis vinifera) berry development, including potential homologues of these characterized ripening regulators. To gain insight into the regulation of berry development and ripening in grapevine, we studied the interactions and functions of grapevine floral homeotic MADS genes. Using the yeast 2- and 3-hybrid systems, we determined that the complexes formed during fruit development and ripening may involve several classes of floral homeotic MADS proteins. We found that a heterologously expressed grapevine SEP gene, VviSEP4, is capable of partially complementing the non-ripening phenotype of the tomato rin mutant, indicating that a role for this gene in ripening regulation may be conserved in fleshy fruit ripening. We also found that ectopic expression of a grapevine AG clade gene, VviAG1, in tomato results in the development of fleshy sepals with the chemical characteristics of tomato fruit pericarp. Additionally, we performed 2-hybrid screens on a library prepared from Pinot noir véraison-stage berry and identified proteins that may interact with the MADS factors that are expressed during berry development and that may represent regulatory functions in grape berry development.
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Affiliation(s)
- Robin D Mellway
- Wine Research Centre, Faculty of Land and Food Systems, 230-2205 East Mall, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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52
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Toydemir G, Capanoglu E, Kamiloglu S, Boyacioglu D, de Vos RC, Hall RD, Beekwilder J. Changes in sour cherry (Prunus cerasus L.) antioxidants during nectar processing and in vitro gastrointestinal digestion. J Funct Foods 2013. [DOI: 10.1016/j.jff.2013.05.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Du X, Zeisel SH. Spectral deconvolution for gas chromatography mass spectrometry-based metabolomics: current status and future perspectives. Comput Struct Biotechnol J 2013; 4:e201301013. [PMID: 24688694 PMCID: PMC3962095 DOI: 10.5936/csbj.201301013] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 06/20/2013] [Accepted: 06/23/2013] [Indexed: 12/28/2022] Open
Abstract
Mass spectrometry coupled to gas chromatography (GC-MS) has been widely applied in the field of metabolomics. Success of this application has benefited greatly from computational workflows that process the complex raw mass spectrometry data and extract the qualitative and quantitative information of metabolites. Among the computational algorithms within a workflow, deconvolution is critical since it reconstructs a pure mass spectrum for each component that the mass spectrometer observes. Based on the pure spectrum, the corresponding component can be eventually identified and quantified. Deconvolution is challenging due to the existence of co-elution. In this review, we focus on progress that has been made in the development of deconvolution algorithms and provide thoughts on future developments that will expand the application of GC-MS in metabolomics.
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Affiliation(s)
- Xiuxia Du
- Department of Bioinformatics, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Steven H Zeisel
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, United States
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Gijsbers L, van Eekelen HDLM, de Haan LHJ, Swier JM, Heijink NL, Kloet SK, Man HY, Bovy AG, Keijer J, Aarts JMMJG, van der Burg B, Rietjens IMCM. Induction of peroxisome proliferator-activated receptor γ (PPARγ)-mediated gene expression by tomato (Solanum lycopersicum L.) extracts. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:3419-3427. [PMID: 23418723 DOI: 10.1021/jf304790a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Since beneficial effects related to tomato consumption partially overlap with those related to peroxisome proliferator-activated receptor γ (PPARγ) activation, our aim was to test extracts of tomato fruits and tomato components, including polyphenols and isoprenoids, for their capacity to activate PPARγ using the PPARγ2 CALUX reporter cell line. Thirty tomato compounds were tested; seven carotenoids and three polyphenols induced PPARγ2-mediated luciferase expression. Two extracts of tomato, one containing deglycosylated phenolic compounds and one containing isoprenoids, also induced PPARγ2-mediated expression at physiologically relevant concentrations. Furthermore, enzymatically hydrolyzed extracts of seven tomato varieties all induced PPARγ-mediated expression, with a 1.6-fold difference between the least potent and the most potent variety. The two most potent varieties had high flavonoid content, while the two least potent varieties had low flavonoid content. These data indicate that extracts of tomato are able to induce PPARγ-mediated gene expression in vitro and that some tomato varieties are more potent than others.
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Affiliation(s)
- Linda Gijsbers
- Division of Toxicology, Wageningen University, Wageningen, The Netherlands.
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55
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Wahyuni Y, Ballester AR, Tikunov Y, de Vos RCH, Pelgrom KTB, Maharijaya A, Sudarmonowati E, Bino RJ, Bovy AG. Metabolomics and molecular marker analysis to explore pepper (Capsicum sp.) biodiversity. Metabolomics 2013; 9:130-144. [PMID: 23335867 PMCID: PMC3548101 DOI: 10.1007/s11306-012-0432-6] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 05/09/2012] [Indexed: 11/25/2022]
Abstract
An overview of the metabolic diversity in ripe fruits of a collection of 32 diverse pepper (Capsicum sp.) accessions was obtained by measuring the composition of both semi-polar and volatile metabolites in fruit pericarp, using untargeted LC-MS and headspace GC-MS platforms, respectively. Accessions represented C. annuum, C. chinense, C. frutescens and C. baccatum species, which were selected based on variation in morphological characters, pungency and geographic origin. Genotypic analysis using AFLP markers confirmed the phylogenetic clustering of accessions according to Capsicum species and separated C. baccatum from the C. annuum-C. chinense-C. frutescens complex. Species-specific clustering was also observed when accessions were grouped based on their semi-polar metabolite profiles. In total 88 semi-polar metabolites could be putatively identified. A large proportion of these metabolites represented conjugates of the main pepper flavonoids (quercetin, apigenin and luteolin) decorated with different sugar groups at different positions along the aglycone. In addition, a large group of acyclic diterpenoid glycosides, called capsianosides, was found to be highly abundant in all C. annuum genotypes. In contrast to the variation in semi-polar metabolites, the variation in volatiles corresponded well to the differences in pungency between the accessions. This was particularly true for branched fatty acid esters present in pungent accessions, which may reflect the activity through the acyl branch of the metabolic pathway leading to capsaicinoids. In addition, large genetic variation was observed for many well-established pepper aroma compounds. These profiling data can be used in breeding programs aimed at improving metabolite-based quality traits such as flavour and health-related metabolites in pepper fruits. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11306-012-0432-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuni Wahyuni
- Wageningen UR Plant Breeding, 6708 PB Wageningen, The Netherlands
- Research Centre for Biotechnology, Indonesian Institute of Sciences, Jl. Raya Bogor KM. 46, Cibinong, Bogor, 16910 Indonesia
| | - Ana-Rosa Ballester
- Centre for Biosystems Genomics, 6700 PB Wageningen, The Netherlands
- Plant Research International, 6700 AA Wageningen, The Netherlands
- Present Address: Instituto de Agroquímica y Tecnología de Alimentos. Consejo Superior de Investigaciones Científicas (IATA-CSIC), Avenida Agustín Escardino 7, 46980 Paterna, Valencia Spain
| | - Yury Tikunov
- Wageningen UR Plant Breeding, 6708 PB Wageningen, The Netherlands
- Centre for Biosystems Genomics, 6700 PB Wageningen, The Netherlands
| | - Ric C. H. de Vos
- Centre for Biosystems Genomics, 6700 PB Wageningen, The Netherlands
- Plant Research International, 6700 AA Wageningen, The Netherlands
- Netherlands Metabolomics Centre, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | | | - Awang Maharijaya
- Wageningen UR Plant Breeding, 6708 PB Wageningen, The Netherlands
- Bogor Agricultural University, Jl. Raya Darmaga, 16680 Bogor, Indonesia
| | - Enny Sudarmonowati
- Research Centre for Biotechnology, Indonesian Institute of Sciences, Jl. Raya Bogor KM. 46, Cibinong, Bogor, 16910 Indonesia
| | - Raoul J. Bino
- Laboratory of Plant Physiology, Wageningen University, 6700 AR Wageningen, The Netherlands
| | - Arnaud G. Bovy
- Wageningen UR Plant Breeding, 6708 PB Wageningen, The Netherlands
- Centre for Biosystems Genomics, 6700 PB Wageningen, The Netherlands
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56
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Wehrens R, Carvalho E, Masuero D, de Juan A, Martens S. High-throughput carotenoid profiling using multivariate curve resolution. Anal Bioanal Chem 2012; 405:5075-86. [DOI: 10.1007/s00216-012-6555-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 10/29/2012] [Accepted: 11/06/2012] [Indexed: 12/20/2022]
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Rohrmann J, McQuinn R, Giovannoni JJ, Fernie AR, Tohge T. Tissue specificity and differential expression of transcription factors in tomato provide hints of unique regulatory networks during fruit ripening. PLANT SIGNALING & BEHAVIOR 2012; 7:1639-47. [PMID: 23073014 PMCID: PMC3578905 DOI: 10.4161/psb.22264] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Tissue specificity or dramatically different expression levels of transcription factors in different tissue types allows differential regulation of tissue development as well as alternate modes of metabolic regulation. Recently we reported (Rohrmann et al., 2011) the development of a quantitative real-time PCR platform (qRT-PCR) that allows accurate quantification of the expression level of approximately 1000 tomato transcription factors. Application of this platform to samples collected during a ripening time course of wild type tomato and the high pigment mutant hp1 allowed us to identify transcription factors of importance both to ripening per se and to the metabolic shifts that occur during this critical biological process. Here we extend the quantitative real-time PCR analyses to include samples from flower, leaf, stem and root of wild type tomato. Co-expression network analysis to identify both conserved and unique regulatory networks both between individual tissues of tomato and also in cross-species comparisons of specific tissues, suggested some key TF genes which are involved in photosynthesis and fruit development.
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Affiliation(s)
- Johannes Rohrmann
- Max-Planck Institute of Molecular Plant Physiology; Potsdam, Germany
| | - Ryan McQuinn
- Boyce Thompson Institute for Plant Research and USDA-ARS Robert W. Holley Center; Cornell University Campus; Ithaca, NY USA
| | - James J. Giovannoni
- Boyce Thompson Institute for Plant Research and USDA-ARS Robert W. Holley Center; Cornell University Campus; Ithaca, NY USA
| | | | - Takayuki Tohge
- Max-Planck Institute of Molecular Plant Physiology; Potsdam, Germany
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58
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Gijsbers L, van Eekelen HD, Nguyen TH, de Haan LH, van der Burg B, Aarts JM, Rietjens IM, Bovy AG. Induction of electrophile-responsive element (EpRE)-mediated gene expression by tomato extracts in vitro. Food Chem 2012; 135:1166-72. [DOI: 10.1016/j.foodchem.2012.05.073] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 05/16/2012] [Accepted: 05/17/2012] [Indexed: 12/31/2022]
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59
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Groot SPC, Surki AA, de Vos RCH, Kodde J. Seed storage at elevated partial pressure of oxygen, a fast method for analysing seed ageing under dry conditions. ANNALS OF BOTANY 2012; 110:1149-59. [PMID: 22967856 PMCID: PMC3478056 DOI: 10.1093/aob/mcs198] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 07/18/2012] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Despite differences in physiology between dry and relative moist seeds, seed ageing tests most often use a temperature and seed moisture level that are higher than during dry storage used in commercial practice and gene banks. This study aimed to test whether seed ageing under dry conditions can be accelerated by storing under high-pressure oxygen. methods: Dry barley (Hordeum vulgare), cabbage (Brassica oleracea), lettuce (Lactuca sativa) and soybean (Glycine max) seeds were stored between 2 and 7 weeks in steel tanks under 18 MPa partial pressure of oxygen. Storage under high-pressure nitrogen gas or under ambient air pressure served as controls. The method was compared with storage at 45 °C after equilibration at 85 % relative humidity and long-term storage at the laboratory bench. Germination behaviour, seedling morphology and tocopherol levels were assessed. KEY RESULTS The ageing of the dry seeds was indeed accelerated by storing under high-pressure oxygen. The morphological ageing symptoms of the stored seeds resembled those observed after ageing under long-term dry storage conditions. Barley appeared more tolerant of this storage treatment compared with lettuce and soybean. Less-mature harvested cabbage seeds were more sensitive, as was the case for primed compared with non-primed lettuce seeds. Under high-pressure oxygen storage the tocopherol levels of dry seeds decreased, in a linear way with the decline in seed germination, but remained unchanged in seeds deteriorated during storage at 45 °C after equilibration at 85 % RH. CONCLUSIONS Seed storage under high-pressure oxygen offers a novel and relatively fast method to study the physiology and biochemistry of seed ageing at different seed moisture levels and temperatures, including those that are representative of the dry storage conditions as used in gene banks and commercial practice.
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Affiliation(s)
- S P C Groot
- Plant Research International, Wageningen University and Research centre, PO Box 619, 6700 AP Wageningen, The Netherlands.
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60
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Fu W, Magnúsdóttir M, Brynjólfson S, Palsson BØ, Paglia G. UPLC-UV-MS(E) analysis for quantification and identification of major carotenoid and chlorophyll species in algae. Anal Bioanal Chem 2012; 404:3145-54. [PMID: 23052878 DOI: 10.1007/s00216-012-6434-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2012] [Revised: 09/14/2012] [Accepted: 09/18/2012] [Indexed: 12/23/2022]
Abstract
A fast method for quantification and identification of carotenoid and chlorophyll species utilizing liquid chromatography coupled with UV detection and mass spectrometry has been demonstrated and validated for the analysis of algae samples. This method allows quantification of targeted pigments and identification of unexpected compounds, providing isomers separation, UV detection, accurate mass measurements, and study of fragment ions for structural elucidation in a single run. This is possible using parallel alternating low- and high-energy collision spectral acquisition modes, which provide accurate mass full scan chromatograms and accurate mass high-energy chromatograms. Here, it is shown how this approach can be used to confirm carotenoid and chlorophyll species by identification of key diagnostic fragmentations during high-energy mode. The developed method was successfully applied for the analysis of Dunaliella salina samples during defined red LED lighting growth conditions, identifying 37 pigments including 19 carotenoid species and 18 chlorophyll species, and providing quantification of 7 targeted compounds. Limit of detections for targeted pigments ranged from 0.01 ng/mL for lutein to 0.24 ng/mL for chlorophyll a. Inter-run precision ranged for of 3 to 24 (RSD%) while inter-run inaccuracy ranged from -17 to 11.
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Affiliation(s)
- Weiqi Fu
- Center for Systems Biology, University of Iceland, Sturlugata 8, IS 101 Reykjavik, Iceland
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61
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Liu J, Tang X, Gao L, Gao Y, Li Y, Huang S, Sun X, Miao M, Zeng H, Tian X, Niu X, Zheng L, Giovannoni J, Xiao F, Liu Y. A role of tomato UV-damaged DNA binding protein 1 (DDB1) in organ size control via an epigenetic manner. PLoS One 2012; 7:e42621. [PMID: 22927934 PMCID: PMC3424292 DOI: 10.1371/journal.pone.0042621] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 07/10/2012] [Indexed: 11/24/2022] Open
Abstract
Epigenetic modification generally refers to phenotypic changes by a mechanism other than changes in DNA sequence and plays a significant role in developmental processes. In this study, we found that overexpression of one alternatively spliced tomato DDB1 transcript, DDB1(F) that is prevalently present in all tested tissues, resulted in reduction of organ size. Transgenic plants constitutively expressing the DDB1(F) from a strong cauliflower mosaic virus (CaMV) 35S promoter displayed moderately reduced size in vegetative organs (leaves and stems) and radically decreased size in reproductive organs (flowers, seeds and fruits), in which several genes encoding negative regulators for cell division were upregulated. Significantly, reduction of organ size conferred by overexpression of DDB1(F) transgene appears not to segregate in the subsequent generations, suggesting the phenotypic alternations are manipulated in an epigenetic manner and can be transmitted over generations. This notion was further substantiated by analysis of DNA methylation level at the SlWEE1 gene (encoding a negative regulator of cell division), revealing a correlation between less methylation in the promoter region and elevated expression level of this gene. Thus, our results suggest DDB1 plays an important role in regulation of the epigenetic state of genes involved in organogenesis, despite the underlying mechanism remains to be elucidated.
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Affiliation(s)
- Jikai Liu
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, China
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, China
| | - Xiaofeng Tang
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, China
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, China
| | - Lanyang Gao
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, China
| | - Yongfeng Gao
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, China
| | - Yuxiang Li
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, China
| | - Shengxiong Huang
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, China
| | - Xiaochun Sun
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, China
| | - Min Miao
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, China
- Department of Plant, Soil and Entomological Sciences, University of Idaho, Moscow, Idaho, United State of America
| | - Hui Zeng
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, China
| | - Xuefen Tian
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, China
| | - Xiangli Niu
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, China
| | - Lei Zheng
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, China
| | - Jim Giovannoni
- United States Department of Agriculture-Agricultural Research Service, Robert Holly Center and Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, United State of America
| | - Fangming Xiao
- Department of Plant, Soil and Entomological Sciences, University of Idaho, Moscow, Idaho, United State of America
| | - Yongsheng Liu
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, China
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, China
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Barry CS, Aldridge GM, Herzog G, Ma Q, McQuinn RP, Hirschberg J, Giovannoni JJ. Altered chloroplast development and delayed fruit ripening caused by mutations in a zinc metalloprotease at the lutescent2 locus of tomato. PLANT PHYSIOLOGY 2012; 159:1086-98. [PMID: 22623517 PMCID: PMC3387696 DOI: 10.1104/pp.112.197483] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 05/21/2012] [Indexed: 05/20/2023]
Abstract
The chloroplast is the site of photosynthesis in higher plants but also functions as the center of synthesis for primary and specialized metabolites including amino acids, fatty acids, starch, and diverse isoprenoids. Mutants that disrupt aspects of chloroplast function represent valuable tools for defining structural and biochemical regulation of the chloroplast and its interplay with whole-plant structure and function. The lutescent1 (l1) and l2 mutants of tomato (Solanum lycopersicum) possess a range of chlorophyll-deficient phenotypes including reduced rates of chlorophyll synthesis during deetiolation and enhanced rates of chlorophyll loss in leaves and fruits as they age, particularly in response to high-light stress and darkness. In addition, the onset of fruit ripening is delayed in lutescent mutants by approximately 1 week although once ripening is initiated they ripen at a normal rate and accumulation of carotenoids is not impaired. The l2 locus was mapped to the long arm of chromosome 10 and positional cloning revealed the existence of a premature stop codon in a chloroplast-targeted zinc metalloprotease of the M50 family that is homologous to the Arabidopsis (Arabidopsis thaliana) gene ETHYLENE-DEPENDENT GRAVITROPISM DEFICIENT AND YELLOW-GREEN1. Screening of tomato germplasm identified two additional l2 mutant alleles. This study suggests a role for the chloroplast in mediating the onset of fruit ripening in tomato and indicates that chromoplast development in fruit does not depend on functional chloroplasts.
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Affiliation(s)
- Cornelius S Barry
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA.
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63
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Monteiro CC, Rolão MB, Franco MR, Peters LP, Cia MC, Capaldi FR, Carvalho RF, Gratão PL, Rossi ML, Martinelli AP, Peres LE, Azevedo RA. Biochemical and histological characterization of tomato mutants. ACTA ACUST UNITED AC 2012; 84:573-85. [DOI: 10.1590/s0001-37652012005000022] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 03/09/2012] [Indexed: 12/22/2022]
Abstract
Biochemical responses inherent to antioxidant systems as well morphological and anatomical properties of photomorphogenic, hormonal and developmental tomato mutants were investigated. Compared to the non-mutant Micro-Tom (MT), we observed that the malondialdehyde (MDA) content was enhanced in the diageotropica (dgt) and lutescent (l) mutants, whilst the highest levels of hydrogen peroxide (H2O2) were observed in high pigment 1 (hp1) and aurea (au) mutants. The analyses of antioxidant enzymes revealed that all mutants exhibited reduced catalase (CAT) activity when compared to MT. Guaiacol peroxidase (GPOX) was enhanced in both sitiens (sit) and notabilis (not) mutants, whereas in not mutant there was an increase in ascorbate peroxidase (APX). Based on PAGE analysis, the activities of glutathione reductase (GR) isoforms III, IV, V and VI were increased in l leaves, while the activity of superoxide dismutase (SOD) isoform III was reduced in leaves of sit, epi, Never ripe (Nr) and green flesh (gf) mutants. Microscopic analyses revealed that hp1 and au showed an increase in leaf intercellular spaces, whereas sit exhibited a decrease. The au and hp1 mutants also exhibited a decreased in the number of leaf trichomes. The characterization of these mutants is essential for their future use in plant development and ecophysiology studies, such as abiotic and biotic stresses on the oxidative metabolism.
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64
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Gady ALF, Vriezen WH, Van de Wal MHBJ, Huang P, Bovy AG, Visser RGF, Bachem CWB. Induced point mutations in the phytoene synthase 1 gene cause differences in carotenoid content during tomato fruit ripening. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2012; 29:801-812. [PMID: 22408384 PMCID: PMC3285762 DOI: 10.1007/s11032-011-9591-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Accepted: 05/24/2011] [Indexed: 05/20/2023]
Abstract
In tomato, carotenoids are important with regard to major breeding traits such as fruit colour and human health. The enzyme phytoene synthase (PSY1) directs metabolic flux towards carotenoid synthesis. Through TILLING (Targeting Induced Local Lesions IN Genomes), we have identified two point mutations in the Psy1 gene. The first mutation is a knockout allele (W180*) and the second mutation leads to an amino acid substitution (P192L). Plants carrying the Psy1 knockout allele show fruit with a yellow flesh colour similar to the r, r mutant, with no further change in colour during ripening. In the line with P192L substitution, fruit remain yellow until 3 days post-breaker and eventually turn red. Metabolite profiling verified the absence of carotenoids in the W180* line and thereby confirms that PSY1 is the only enzyme introducing substrate into the carotenoid pathway in ripening fruit. More subtle effects on carotenoid accumulation were observed in the P192L line with a delay in lycopene and β-carotene accumulation clearly linked to a very slow synthesis of phytoene. The observation of lutein degradation with ripening in both lines showed that lutein and its precursors are still synthesised in ripening fruit. Gene expression analysis of key genes involved in carotenoid biosynthesis revealed that expression levels of genes in the pathway are not feedback-regulated by low levels or absence of carotenoid compounds. Furthermore, protein secondary structure modelling indicated that the P192L mutation affects PSY1 activity through misfolding, leading to the low phytoene accumulation.
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Affiliation(s)
- Antoine L. F. Gady
- Laboratory of Plant Breeding, Department of Plant Sciences, Wageningen-UR, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Graduate School Experimental Plant Sciences, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Wim H. Vriezen
- Nunhems Netherlands BV, P.O. Box 4005, 6080 AA Haelen, The Netherlands
| | | | - Pingping Huang
- Laboratory of Plant Breeding, Department of Plant Sciences, Wageningen-UR, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Graduate School Experimental Plant Sciences, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Present Address: Laboratory of Genetics, Department of Plant Sciences, Wageningen-UR, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Arnaud G. Bovy
- Laboratory of Plant Breeding, Department of Plant Sciences, Wageningen-UR, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Richard G. F. Visser
- Laboratory of Plant Breeding, Department of Plant Sciences, Wageningen-UR, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Christian W. B. Bachem
- Laboratory of Plant Breeding, Department of Plant Sciences, Wageningen-UR, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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65
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Brand A, Borovsky Y, Meir S, Rogachev I, Aharoni A, Paran I. pc8.1, a major QTL for pigment content in pepper fruit, is associated with variation in plastid compartment size. PLANTA 2012; 235:579-88. [PMID: 21987007 DOI: 10.1007/s00425-011-1530-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 09/25/2011] [Indexed: 05/03/2023]
Abstract
Studies on the genetic control of pigment content in pepper fruit have focused mainly on monogenic mutations leading to changes in fruit color. In addition to the qualitative variation in fruit color, quantitative variation in pigment content and color intensity exists in pepper giving rise to a range of color intensities. However, the genetic basis for this variation is poorly understood, hindering the development of peppers that are rich in these beneficial compounds. In this paper, quantitative variation in pigment content was studied in a cross between a dark-green Capsicum annuum pepper and a light-green C. chinense pepper. Two major pigment content QTLs that control chlorophyll content were identified, pc8.1 and pc10.1. The major QTL pc8.1, also affected carotenoid content in the ripe fruit. However, additional analyses in subsequent generations did not reveal a consistent effect of this QTL on carotenoid content in ripe fruit. Confocal microscopy analyses of green immature fruits of the parents and of near-isogenic lines for pc8.1 indicated that the QTL exerts its effect via increasing chloroplast compartment size in the dark-green genotypes, predominantly in a fruit-specific manner. Metabolic analyses indicated that in addition to chlorophyll, chloroplast-associated tocopherols and carotenoids are also elevated. Future identification of the genes controlling pigment content QTLs in pepper will provide a better understanding of this important trait and new opportunities for breeding peppers and other Solanaceae species with enhanced nutritional value.
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Affiliation(s)
- Arnon Brand
- Institute of Plant Sciences, The Volcani Center, Bet Dagan, Israel
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66
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Lenucci MS, Serrone L, De Caroli M, Fraser PD, Bramley PM, Piro G, Dalessandro G. Isoprenoid, lipid, and protein contents in intact plastids isolated from mesocarp cells of traditional and high-pigment tomato cultivars at different ripening stages. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:1764-75. [PMID: 22264157 DOI: 10.1021/jf204189z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
This study reports quali-quantitative analyses on isoprenoids, phospholipids, neutral lipids, phytosterols, and proteins in purified plastids isolated from fresh fruits of traditional (Donald and Incas) and high-pigment (Kalvert and HLY-18) tomato cultivars at four ripening stages. In all of the investigated cultivars, lycopene, β-catotene, lutein, and total carotenoids varied significantly during ripening. Chromoplasts of red-ripe tomato fruits of high-pigment cultivars accumulated twice as much as lycopene (307.6 and 319.2 μg/mg of plastid proteins in Kalvert and HLY-18, respectively) than ordinary cultivars (178.6 and 151.7 μg/mg of plastid proteins in Donald and Incas, respectively); differences in chlorophyll and α-tocopherol contents were also evidenced. Phospholipids and phytosterols increased during ripening, whereas triglycerides showed a general decrease. Regardless of the stage of ripening, palmitic acid was the major fatty acid in all cultivars (ranging from 35 to 52% of the total fatty acids), followed by stearic, oleic, linoleic, linolenic, and myristic acids, but their relative percentage was affected by ripening. Most of the bands detected on the SDS-PAGEs of plastid proteins were constantly present during chloroplast-to-chromoplast conversion, some others disappeared, and only one, with a molecular weight of ~41.6 kDa, was found to increase in intensity.
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Affiliation(s)
- Marcello S Lenucci
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA), Università del Salento, Lecce, Italy
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67
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Rohrmann J, Tohge T, Alba R, Osorio S, Caldana C, McQuinn R, Arvidsson S, van der Merwe MJ, Riaño-Pachón DM, Mueller-Roeber B, Fei Z, Nesi AN, Giovannoni JJ, Fernie AR. Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 68:999-1013. [PMID: 21851430 DOI: 10.1111/j.1365-313x.2011.04750.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Maturation of fleshy fruits such as tomato (Solanum lycopersicum) is subject to tight genetic control. Here we describe the development of a quantitative real-time PCR platform that allows accurate quantification of the expression level of approximately 1000 tomato transcription factors. In addition to utilizing this novel approach, we performed cDNA microarray analysis and metabolite profiling of primary and secondary metabolites using GC-MS and LC-MS, respectively. We applied these platforms to pericarp material harvested throughout fruit development, studying both wild-type Solanum lycopersicum cv. Ailsa Craig and the hp1 mutant. This mutant is functionally deficient in the tomato homologue of the negative regulator of the light signal transduction gene DDB1 from Arabidopsis, and is furthermore characterized by dramatically increased pigment and phenolic contents. We choose this particular mutant as it had previously been shown to have dramatic alterations in the content of several important fruit metabolites but relatively little impact on other ripening phenotypes. The combined dataset was mined in order to identify metabolites that were under the control of these transcription factors, and, where possible, the respective transcriptional regulation underlying this control. The results are discussed in terms of both programmed fruit ripening and development and the transcriptional and metabolic shifts that occur in parallel during these processes.
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Affiliation(s)
- Johannes Rohrmann
- Max-Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Potsdam, Germany
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68
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Vallverdú-Queralt A, Medina-Remón A, Casals-Ribes I, Amat M, Lamuela-Raventós RM. A metabolomic approach differentiates between conventional and organic ketchups. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2011; 59:11703-11710. [PMID: 21958116 DOI: 10.1021/jf202822s] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The agronomic environments in which tomatoes are cultivated potentially affect the levels of antioxidants and other metabolites in commercial products. In this study, biochemical and metabolomic techniques were used to assess the differences between ketchups produced by organic and conventional systems. An untargeted metabolomic approach using QToF-MS was used to identify those nutrients that have the greatest impact on the overall metabolomic profile of organic ketchups as compared to conventional ones. Individual polyphenols were quantified using LC-ESI-QqQ. This multifaceted approach revealed that the agronomic environment in which tomatoes are grown induces alterations in the content of antioxidant capacity, phenolics, and other metabolites in ketchups. Organic cultivation was found to provide tomatoes and tomato-derived products with a significantly higher content of antioxidant microconstituents, whereas glutamylphenylalanine and N-malonyltryptophan were detected only in conventional ketchups.
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Affiliation(s)
- Anna Vallverdú-Queralt
- Nutrition and Food Science Department, XaRTA, INSA, Pharmacy School, University of Barcelona, 08028 Barcelona, Spain
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69
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Matas AJ, Yeats TH, Buda GJ, Zheng Y, Chatterjee S, Tohge T, Ponnala L, Adato A, Aharoni A, Stark R, Fernie AR, Fei Z, Giovannoni JJ, Rose JK. Tissue- and cell-type specific transcriptome profiling of expanding tomato fruit provides insights into metabolic and regulatory specialization and cuticle formation. THE PLANT CELL 2011; 23:3893-910. [PMID: 22045915 PMCID: PMC3246317 DOI: 10.1105/tpc.111.091173] [Citation(s) in RCA: 156] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 10/13/2011] [Accepted: 10/18/2011] [Indexed: 05/18/2023]
Abstract
Tomato (Solanum lycopersicum) is the primary model for the study of fleshy fruits, and research in this species has elucidated many aspects of fruit physiology, development, and metabolism. However, most of these studies have involved homogenization of the fruit pericarp, with its many constituent cell types. Here, we describe the coupling of pyrosequencing technology with laser capture microdissection to characterize the transcriptomes of the five principal tissues of the pericarp from tomato fruits (outer and inner epidermal layers, collenchyma, parenchyma, and vascular tissues) at their maximal growth phase. A total of 20,976 high-quality expressed unigenes were identified, of which more than half were ubiquitous in their expression, while others were cell type specific or showed distinct expression patterns in specific tissues. The data provide new insights into the spatial distribution of many classes of regulatory and structural genes, including those involved in energy metabolism, source-sink relationships, secondary metabolite production, cell wall biology, and cuticle biogenesis. Finally, patterns of similar gene expression between tissues led to the characterization of a cuticle on the inner surface of the pericarp, demonstrating the utility of this approach as a platform for biological discovery.
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Affiliation(s)
- Antonio J. Matas
- Department of Plant Biology, Cornell University, Ithaca, New York 14853
| | - Trevor H. Yeats
- Department of Plant Biology, Cornell University, Ithaca, New York 14853
| | - Gregory J. Buda
- Department of Plant Biology, Cornell University, Ithaca, New York 14853
| | - Yi Zheng
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853
| | - Subhasish Chatterjee
- Department of Chemistry, City College of New York, City University of New York Graduate Center and Institute for Macromolecular Assemblies, New York, New York 10031
| | - Takayuki Tohge
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
| | - Lalit Ponnala
- Computational Biology Service Unit, Cornell University, Ithaca, New York 14853
| | - Avital Adato
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ruth Stark
- Department of Chemistry, City College of New York, City University of New York Graduate Center and Institute for Macromolecular Assemblies, New York, New York 10031
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853
- U.S. Department of Agriculture–Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, New York 14853
| | - James J. Giovannoni
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853
- U.S. Department of Agriculture–Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, New York 14853
| | - Jocelyn K.C. Rose
- Department of Plant Biology, Cornell University, Ithaca, New York 14853
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70
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Wahyuni Y, Ballester AR, Sudarmonowati E, Bino RJ, Bovy AG. Metabolite biodiversity in pepper (Capsicum) fruits of thirty-two diverse accessions: variation in health-related compounds and implications for breeding. PHYTOCHEMISTRY 2011; 72:1358-70. [PMID: 21514607 DOI: 10.1016/j.phytochem.2011.03.016] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 03/17/2011] [Accepted: 03/18/2011] [Indexed: 05/20/2023]
Abstract
A comprehensive study on morphology and biochemical compounds of 32 Capsicum spp. accessions has been performed. Accessions represented four pepper species, Capsicum annuum, Capsicum frutescens, Capsicum chinense and Capsicum baccatum which were selected by their variation in morphological characters such as fruit color, pungency and origin. Major metabolites in fruits of pepper, carotenoids, capsaicinoids (pungency), flavonoid glycosides, and vitamins C and E were analyzed and quantified by high performance liquid chromatography. The results showed that composition and level of metabolites in fruits varied greatly between accessions and was independent of species and geographical location. Fruit color was determined by the accumulation of specific carotenoids leading to salmon, yellow, orange, red and brown colored fruits. Levels of both O- and C-glycosides of quercetin, luteolin and apigenin varied strongly between accessions. All non-pungent accessions were devoid of capsaicins, whereas capsaicinoid levels ranged from 0.07 up to 80 mg/100g fr. wt. in fruit pericarp. In general, pungent accessions accumulated the highest capsaicinoid levels in placenta plus seed tissue compared to pericarp. The non-pungent capsaicinoid analogs, capsiates, could be detected at low levels in some pungent accessions. All accessions accumulated high levels of vitamin C, up to 200 mg/100g fr. wt. The highest vitamin E concentration found was 16 mg/100g fr. wt. Based on these metabolic data, five accessions were selected for further metabolic and molecular analysis, in order to isolate key genes involved in the production of these compounds and to assist future breeding programs aimed at optimizing the levels of health-related compounds in pepper fruit.
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Affiliation(s)
- Yuni Wahyuni
- Plant Research International, 6700 AA Wageningen, The Netherlands
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71
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Abstract
With the advent of the -omics era, classical technology platforms, such as hyphenated mass spectrometry, are currently undergoing a transformation toward high-throughput application. These novel platforms yield highly detailed metabolite profiles in large numbers of samples. Such profiles can be used as fingerprints for the accurate identification and classification of samples as well as for the study of effects of experimental conditions on the concentrations of specific metabolites. Challenges for the application of these methods lie in the acquisition of high-quality data, data normalization, and data mining. Here, a high-throughput fingerprinting approach based on analysis of headspace volatiles using ultrafast gas chromatography coupled to time of flight mass spectrometry (ultrafast GC/TOF-MS) was developed and evaluated for classification and screening purposes in food fermentation. GC-MS mass spectra of headspace samples of milk fermented by different mixed cultures of lactic acid bacteria (LAB) were collected and preprocessed in MetAlign, a dedicated software package for the preprocessing and comparison of liquid chromatography (LC)-MS and GC-MS data. The Random Forest algorithm was used to detect mass peaks that discriminated combinations of species or strains used in fermentations. Many of these mass peaks originated from key flavor compounds, indicating that the presence or absence of individual strains or combinations of strains significantly influenced the concentrations of these components. We demonstrate that the approach can be used for purposes like the selection of strains from collections based on flavor characteristics and the screening of (mixed) cultures for the presence or absence of strains. In addition, we show that strain-specific flavor characteristics can be traced back to genetic markers when comparative genome hybridization (CGH) data are available.
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72
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Romero I, Tikunov Y, Bovy A. Virus-induced gene silencing in detached tomatoes and biochemical effects of phytoene desaturase gene silencing. JOURNAL OF PLANT PHYSIOLOGY 2011; 168:1129-35. [PMID: 21377758 DOI: 10.1016/j.jplph.2010.12.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 12/27/2010] [Accepted: 12/29/2010] [Indexed: 05/07/2023]
Abstract
Virus-induced gene silencing (VIGS) is a technology that has rapidly emerged for gene function studies in plants. Many advances have been made in applying this technique in an increasing number of crops. Recently, VIGS has been successfully used to silence genes in tomato fruit through agroinfiltration of fruit attached to the plant. The phytoene desaturase (Pds) gene has been widely used as a reporter gene in VIGS experiments, although little is known about the changes that occur due to its silencing in plants. In this paper, we describe the efficient silencing of the Pds gene through the VIGS approach in detached tomato fruits, which makes the VIGS procedure even more versatile and applicable. After 16 days of agroinfiltration, approximately 75% of the tomatoes showed Pds silencing symptoms, although the distribution of silenced areas was variable among fruits. To study the potential effects caused by Pds silencing in detached tomatoes, carotenoids and other semi-polar secondary metabolites were analyzed using Liquid Chromatography-Mass Spectrometry. In addition, potential differences in primary metabolites were analyzed using Gas Chromatography-Mass Spectrometry. The results indicated that the yellow phenotype observed in Pds-silenced fruit was mainly due to the lack of the red-colored lycopene and therefore to a more pronounced contribution of the yellow-orange carotenoids (lutein, violaxanthin, and zeaxanthin) to the final color of the fruits. Furthermore, the biochemical changes observed in Pds-silenced detached tomatoes suggested that carotenoid and other pathways, e.g. leading to alkaloids and flavonoids, might be affected by the silencing of this reporter gene, and this should be taken into consideration for future experimental designs.
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Affiliation(s)
- Irene Romero
- Plant Research International, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
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73
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Accelerating analysis for metabolomics, drugs and their metabolites in biological samples using multidimensional gas chromatography. Bioanalysis 2011; 1:367-91. [PMID: 21083173 DOI: 10.4155/bio.09.28] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Gas chromatography (GC) with mass spectrometry (MS) is one of the great enabling analytical tools available to the chemical and biochemical analyst for the measurement of volatile and semi-volatile compounds. From the analysis result, it is possible to assess progress in chemical reactions, to monitor environmental pollutants in a wide range of soil, water or air samples, to determine if an athlete or horse trainer has contravened doping laws, or if crude oil has migrated through subsurface rock to a reservoir. Each of these scenarios and samples has an associated implementation method for GC-MS. However, few samples and the associated interpretation of data is as complex or important as biochemical sample analysis for trace drugs or metabolites. Improving the analysis in both the GC and MS domains is a continual search for better separation, selectivity and sensitivity. Multidimensional methods are playing important roles in providing quality data to address the needs of analysts.
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74
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Pino Del Carpio D, Basnet RK, De Vos RCH, Maliepaard C, Paulo MJ, Bonnema G. Comparative methods for association studies: a case study on metabolite variation in a Brassica rapa core collection. PLoS One 2011; 6:e19624. [PMID: 21602927 PMCID: PMC3094343 DOI: 10.1371/journal.pone.0019624] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Accepted: 04/13/2011] [Indexed: 11/20/2022] Open
Abstract
Background Association mapping is a statistical approach combining phenotypic traits and
genetic diversity in natural populations with the goal of correlating the
variation present at phenotypic and allelic levels. It is essential to
separate the true effect of genetic variation from other confounding
factors, such as adaptation to different uses and geographical locations.
The rapid availability of large datasets makes it necessary to explore
statistical methods that can be computationally less intensive and more
flexible for data exploration. Methodology/Principal Findings A core collection of 168 Brassica rapa accessions of
different morphotypes and origins was explored to find genetic association
between markers and metabolites: tocopherols, carotenoids, chlorophylls and
folate. A widely used linear model with modifications to account for
population structure and kinship was followed for association mapping. In
addition, a machine learning algorithm called Random Forest (RF) was used as
a comparison. Comparison of results across methods resulted in the selection
of a set of significant markers as promising candidates for further work.
This set of markers associated to the metabolites can potentially be applied
for the selection of genotypes with elevated levels of these
metabolites. Conclusions/Significance The incorporation of the kinship correction into the association model did
not reduce the number of significantly associated markers. However
incorporation of the STRUCTURE correction (Q matrix) in the linear
regression model greatly reduced the number of significantly associated
markers. Additionally, our results demonstrate that RF is an interesting
complementary method with added value in association studies in plants,
which is illustrated by the overlap in markers identified using RF and a
linear mixed model with correction for kinship and population structure.
Several markers that were selected in RF and in the models with correction
for kinship, but not for population structure, were also identified as QTLs
in two bi-parental DH populations.
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Affiliation(s)
| | - Ram Kumar Basnet
- Laboratory of Plant Breeding, Wageningen
University, Wageningen, The Netherlands
- Centre for BioSystems Genomics, Wageningen,
The Netherlands
| | - Ric C. H. De Vos
- Plant Research International, Wageningen
University and Research Centre (Wageningen-UR), Wageningen, The
Netherlands
- Centre for BioSystems Genomics, Wageningen,
The Netherlands
| | - Chris Maliepaard
- Laboratory of Plant Breeding, Wageningen
University, Wageningen, The Netherlands
| | - Maria João Paulo
- Biometris-Applied Statistics, Wageningen
University and Research Center, Wageningen, The Netherlands
| | - Guusje Bonnema
- Laboratory of Plant Breeding, Wageningen
University, Wageningen, The Netherlands
- Centre for BioSystems Genomics, Wageningen,
The Netherlands
- * E-mail:
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75
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Moing A, Aharoni A, Biais B, Rogachev I, Meir S, Brodsky L, Allwood JW, Erban A, Dunn WB, Kay L, de Koning S, de Vos RCH, Jonker H, Mumm R, Deborde C, Maucourt M, Bernillon S, Gibon Y, Hansen TH, Husted S, Goodacre R, Kopka J, Schjoerring JK, Rolin D, Hall RD. Extensive metabolic cross-talk in melon fruit revealed by spatial and developmental combinatorial metabolomics. THE NEW PHYTOLOGIST 2011; 190:683-96. [PMID: 21275993 DOI: 10.1111/j.1469-8137.2010.03626.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
• Variations in tissue development and spatial composition have a major impact on the nutritional and organoleptic qualities of ripe fleshy fruit, including melon (Cucumis melo). To gain a deeper insight into the mechanisms involved in these changes, we identified key metabolites for rational food quality design. • The metabolome, volatiles and mineral elements were profiled employing an unprecedented range of complementary analytical technologies. Fruits were followed at a number of time points during the final ripening process and tissues were collected across the fruit flesh from rind to seed cavity. Approximately 2000 metabolite signatures and 15 mineral elements were determined in an assessment of temporal and spatial melon fruit development. • This study design enabled the identification of: coregulated hubs (including aspartic acid, 2-isopropylmalic acid, β-carotene, phytoene and dihydropseudoionone) in metabolic association networks; global patterns of coordinated compositional changes; and links of primary and secondary metabolism to key mineral and volatile fruit complements. • The results reveal the extent of metabolic interactions relevant to ripe fruit quality and thus have enabled the identification of essential candidate metabolites for the high-throughput screening of melon breeding populations for targeted breeding programmes aimed at nutrition and flavour improvement.
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Affiliation(s)
- Annick Moing
- INRA-UMR 619 Biologie du Fruit, Centre INRA de Bordeaux, Villenave d'Ornon, France.
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76
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Abstract
The combined factors of financial and food security, a rapidly increasing population and the associated requirement for food generated sustainably in a changing environment have brought food swiftly to the top of most government agendas. The consequence of this is that we need to produce more food at an equivalent or higher quality with lower inputs. These aims are achievable using conventional breeding, but not in the required timelines, and thus state-of-the-art genetic and analytical technologies are coming to the forefront. The concept of metabolomics, underpinned by mainstream (GC–MS, LC–MS, NMR) and specialist (MALDI-TOF-MS) analytical technologies addressing broad chemical (class) targets and dynamic ranges, offers significant potential to add significant value to crop and food science and deliver on future food demands. Metabolomics has now found a home in the food analytical toolbox with raw material quality and safety the major quality areas, although, as we will show, it is translating beyond this into food storage, shelf-life and post-harvest processing.
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77
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Carvalho RF, Aidar ST, Azevedo RA, Dodd IC, Peres LEP. Enhanced transpiration rate in the high pigment 1 tomato mutant and its physiological significance. PLANT BIOLOGY (STUTTGART, GERMANY) 2011; 13:546-550. [PMID: 21489107 DOI: 10.1111/j.1438-8677.2010.00438.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Tomato high pigment (hp) mutants represent an interesting horticultural resource due to their enhanced accumulation of carotenoids, flavonoids and vitamin C. Since hp mutants are known for their exaggerated light responses, the molecules accumulated are likely to be antioxidants, recruited to deal with light and others stresses. Further phenotypes displayed by hp mutations are reduced growth and an apparent disturbance in water loss. Here, we examined the impact of the hp1 mutation and its near isogenic line cv Micro-Tom (MT) on stomatal conductance (gs), transpiration (E), CO(2) assimilation (A) and water use efficiency (WUE). Detached hp1 leaves lost water more rapidly than control leaves, but this behaviour was reversed by exogenous abscisic acid (ABA), indicating the ability of hp1 to respond to this hormone. Although attached hp1 leaves had enhanced gs, E and A compared to control leaves, genotypic differences were lost when water was withheld. Both instantaneous leaf-level WUE and long-term whole plant WUE did not differ between hp1 and MT. Our results indicate a link between exaggerated light response and water loss in hp1, which has important implications for the use of this mutant in both basic and horticultural research.
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Affiliation(s)
- R F Carvalho
- Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, São Paulo, Brazil
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78
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Capanoglu E, Beekwilder J, Boyacioglu D, De Vos RCH, Hall RD. The effect of industrial food processing on potentially health-beneficial tomato antioxidants. Crit Rev Food Sci Nutr 2011; 50:919-30. [PMID: 21108072 DOI: 10.1080/10408390903001503] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Increasing desires from both consumers and producers to understand better which nutritive components are present in our food and how these are influenced by industrial processing strategies is resulting in extra research involving the use of state-of-the-art technologies to generate novel biochemical information. In this review, attention has been focused on tomato as this is a product eaten right across the world both as fresh produce and after having been processed in a wide variety of ways. There is a particular interest in tomato as it is a major component in the so-called "Mediterranean diet" which has recently been associated with a healthier lifestyle. Tomatoes are rich sources of a variety of nutritional compounds and especially some key antioxidant components such as the carotenoid lycopene, vitamin C, and a range of polyphenols. The potentially protective properties of these antioxidants are of great interest and the consumer has already become aware of their potential importance. Surveying the literature has revealed that much research has been done on the biochemical composition of tomato and its products. However, it remains difficult to make clear conclusions on optimizing the processing strategy. Many, apparently conflicting, findings have been reported and consequently, in this review, we have drawn attention to these and have attempted to clarify their cause. Finally, a range of recommendations has been made as to how future research might be performed in order to generate more concrete conclusions enabling recommendations towards more optimized processing strategies.
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Affiliation(s)
- Esra Capanoglu
- Istanbul Technical University, Food Engineering Department, Turkey
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79
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Allwood JW, De Vos RC, Moing A, Deborde C, Erban A, Kopka J, Goodacre R, Hall RD. Plant Metabolomics and Its Potential for Systems Biology Research. Methods Enzymol 2011; 500:299-336. [DOI: 10.1016/b978-0-12-385118-5.00016-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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De Vos RCH, Schipper B, Hall RD. High-performance liquid chromatography-mass spectrometry analysis of plant metabolites in brassicaceae. Methods Mol Biol 2011; 860:111-28. [PMID: 22351174 DOI: 10.1007/978-1-61779-594-7_8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The Brassicaceae family comprises a variety of plant species that are of high economic importance as -vegetables or industrial crops. This includes crops such as Brassica rapa (turnip, Bok Choi), B. oleracea (cabbages, broccoli, cauliflower, etc.), and B. napus (oil seed rape), and also includes the famous genetic model of plant research, Arabidopsis thaliana (thale cress). Brassicaceae plants contain a large variety of interesting secondary metabolites, including glucosinolates, hydroxycinnamic acids, and flavonoids. These metabolites are also of particular importance due to their proposed positive effects on human health. Next to these well-known groups of phytochemicals, many more metabolites are of course also present in crude extracts prepared from Brassica and Arabidopsis plant material.High-pressure liquid chromatography coupled to mass spectrometry (HPLC-MS), especially if combined with a high mass resolution instrument such as a QTOF MS, is a powerful approach to separate, detect, and annotate metabolites present in crude aqueous-alcohol plant extracts. Using an essentially unbiased procedure that takes into account all metabolite mass signals from the raw data files, detailed information on the relative abundance of hundreds of both known and, as yet, unknown semipolar metabolites can be obtained. These comprehensive metabolomics data can then be used to, for instance, identify genetic markers regulating metabolic composition, determine effects of (a)biotic stress or specific growth conditions, or establish metabolite changes occurring upon food processing or storage.This chapter describes in detail a procedure for preparing crude extracts and performing comprehensive HPLC-QTOF MS-based profiling of semi-polar metabolites in Brassicaceae plant material. Compounds present in the extract can be (partially or completely) annotated based on their accurate mass, their MS/MS fragments and on other specific chemical characteristics such as retention time and UV-absorbance spectrum.
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Affiliation(s)
- Ric C H De Vos
- Plant Research International, Wageningen, The Netherlands.
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81
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McGloughlin MN. Modifying agricultural crops for improved nutrition. N Biotechnol 2010; 27:494-504. [DOI: 10.1016/j.nbt.2010.07.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2010] [Accepted: 07/08/2010] [Indexed: 01/17/2023]
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82
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Gómez-Romero M, Segura-Carretero A, Fernández-Gutiérrez A. Metabolite profiling and quantification of phenolic compounds in methanol extracts of tomato fruit. PHYTOCHEMISTRY 2010; 71:1848-64. [PMID: 20810136 DOI: 10.1016/j.phytochem.2010.08.002] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 07/30/2010] [Accepted: 08/02/2010] [Indexed: 05/09/2023]
Abstract
The consumption of tomatoes and tomato products has been associated with a reduction in the risk of contracting some types of cancer and other chronic diseases. These beneficial properties may be attributed to the presence of key metabolites and the interactions among them. We have developed and validated an analytical method for the comprehensive profiling of semi-polar metabolites in the methanol extract of three cultivars of raw tomatoes (Daniela, Raf and Rambo) grown in Almería, in south-east Spain. Diode-array and time-of-flight/ion-trap mass spectrometry detectors were used to ensure the wide detection of metabolites with highly divergent properties. The masses thus detected were assigned by matching their accurate mass-signals with tomato compounds reported in the literature, and supplemented by UV and MS/MS information, reference compounds and existing metabolite databases. In this way we were able to identify tentatively 135 compounds belonging to various structural classes, 21 of which are to our knowledge reported for the first time in the tomato fruit. Among the metabolites identified, the most abundant were phenolic compounds. This class of secondary metabolites is attracting considerable attention from producers and consumers due to their antioxidant activity and nutritional properties. Their quantitative analysis was achieved by using closely related derivatives for each family.
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Affiliation(s)
- María Gómez-Romero
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, c/Fuentenueva s/n, 18071 Granada, Spain.
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83
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Lamers PP, van de Laak CCW, Kaasenbrood PS, Lorier J, Janssen M, De Vos RCH, Bino RJ, Wijffels RH. Carotenoid and fatty acid metabolism in light-stressed Dunaliella salina. Biotechnol Bioeng 2010; 106:638-48. [PMID: 20229508 DOI: 10.1002/bit.22725] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
beta-Carotene is overproduced in the alga Dunaliella salina in response to high light intensities. We have studied the effects of a sudden light increase on carotenoid and fatty acid metabolism using a flat panel photobioreactor that was run in turbidostat mode to ensure a constant light regime throughout the experiments. Upon the shift to an increased light intensity, beta-carotene production commenced immediately. The first 4 h after induction were marked by constant intracellular levels of beta-carotene (2.2 g LCV(-1)), which resulted from identical increases in the production rates of cell volume and beta-carotene. Following this initial phase, beta-carotene productivity continued to increase while the cell volume productivity dropped. As a result, the intracellular beta-carotene concentration increased reaching a maximum of 17 g LCV(-1) after 2 days of light stress. Approximately 1 day before that, the maximum beta-carotene productivity of 30 pg cell(-1) day(-1) (equivalent to 37 mg LRV(-1) day(-1)) was obtained, which was about one order of magnitude larger than the average productivity reported for a commercial beta-carotene production facility, indicating a vast potential for improvement. Furthermore, by studying the light-induced changes in both beta-carotene and fatty acid metabolism, it appeared that carotenoid overproduction was associated with oil globule formation and a decrease in the degree of fatty acid unsaturation. Our results indicate that cellular beta-carotene accumulation in D. salina correlates with accumulation of specific fatty acid species (C16:0 and C18:1) rather than with total fatty acid content.
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Affiliation(s)
- Packo P Lamers
- Wageningen University, Bioprocess Engineering, P.O. Box 8129, 6700 EV Wageningen, the Netherlands.
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84
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Azari R, Reuveni M, Evenor D, Nahon S, Shlomo H, Chen L, Levin I. Overexpression of UV-DAMAGED DNA BINDING PROTEIN 1 links plant development and phytonutrient accumulation in high pigment-1 tomato. JOURNAL OF EXPERIMENTAL BOTANY 2010; 61:3627-37. [PMID: 20566564 PMCID: PMC2921201 DOI: 10.1093/jxb/erq176] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Revised: 05/07/2010] [Accepted: 05/26/2010] [Indexed: 05/19/2023]
Abstract
Fruits of tomato plants carrying the high pigment-1 mutations hp-1 and hp-1(w) are characterized by an increased number of plastids coupled with enhanced levels of functional metabolites. Unfortunately, hp-1 mutant plants are also typified by light-dependent retardation in seedling and whole-plant growth and development, which limits their cultivation. These mutations were mapped to the gene encoding UV-DAMAGED DNA BINDING PROTEIN 1 (DDB1) and, recently, fruit-specific RNA interference studies have demonstrated an increased number of plastids and enhanced carotenoid accumulation in the transgenic tomato fruits. However, whole-plant overexpression of DDB1, required to substantiate its effects on seedling and plant development and to couple them with fruit phenotypes, has heretofore been unsuccessful. In this study, five transgenic lines constitutively overexpressing normal DDB1 in hp-1 mutant plants were analysed. Eleven-day-old seedlings, representing these lines, displayed up to approximately 73- and approximately 221-fold overexpression of the gene in hypocotyls and cotyledons, respectively. This overexpression resulted in statistically significant reversion to the non-mutant developmental phenotypes, including more than a full quantitative reversion. This reversion of phenotypes was generally accompanied by correlated responses in chlorophyll accumulation and altered expression of selected light signalling genes: PHYTOCHROME A, CRYPTOCHROME 1, ELONGATED HYPOCOTYL 5, and the gene encoding CHLOROPHYLL A/B-BINDING PROTEIN 4. Cumulatively, these results provide the missing link between DDB1 and its effects on tomato plant development.
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Affiliation(s)
| | | | | | | | | | | | - Ilan Levin
- To whom correspondence should be addressed. E-mail:
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85
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Wolters AMA, Uitdewilligen JGAML, Kloosterman BA, Hutten RCB, Visser RGF, van Eck HJ. Identification of alleles of carotenoid pathway genes important for zeaxanthin accumulation in potato tubers. PLANT MOLECULAR BIOLOGY 2010; 73:659-71. [PMID: 20490894 PMCID: PMC2898108 DOI: 10.1007/s11103-010-9647-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Accepted: 04/30/2010] [Indexed: 05/04/2023]
Abstract
We have investigated the genetics and molecular biology of orange flesh colour in potato (Solanum tuberosum L.). To this end the natural diversity in three genes of the carotenoid pathway was assessed by SNP analyses. Association analysis was performed between SNP haplotypes and flesh colour phenotypes in diploid and tetraploid potato genotypes. We observed that among eleven beta-carotene hydroxylase 2 (Chy2) alleles only one dominant allele has a major effect, changing white into yellow flesh colour. In contrast, none of the lycopene epsilon cyclase (Lcye) alleles seemed to have a large effect on flesh colour. Analysis of zeaxanthin epoxidase (Zep) alleles showed that all (diploid) genotypes with orange tuber flesh were homozygous for one specific Zep allele. This Zep allele showed a reduced level of expression. The complete genomic sequence of the recessive Zep allele, including the promoter, was determined, and compared with the sequence of other Zep alleles. The most striking difference was the presence of a non-LTR retrotransposon sequence in intron 1 of the recessive Zep allele, which was absent in all other Zep alleles investigated. We hypothesise that the presence of this large sequence in intron 1 caused the lower expression level, resulting in reduced Zep activity and accumulation of zeaxanthin. Only genotypes combining presence of the dominant Chy2 allele with homozygosity for the recessive Zep allele produced orange-fleshed tubers that accumulated large amounts of zeaxanthin.
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Affiliation(s)
- Anne-Marie A Wolters
- Laboratory of Plant Breeding, Wageningen University, PO Box 386, 6700 AJ Wageningen, The Netherlands.
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86
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Nashilevitz S, Melamed-Bessudo C, Izkovich Y, Rogachev I, Osorio S, Itkin M, Adato A, Pankratov I, Hirschberg J, Fernie AR, Wolf S, Usadel B, Levy AA, Rumeau D, Aharoni A. An orange ripening mutant links plastid NAD(P)H dehydrogenase complex activity to central and specialized metabolism during tomato fruit maturation. THE PLANT CELL 2010; 22:1977-97. [PMID: 20571113 PMCID: PMC2910969 DOI: 10.1105/tpc.110.074716] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2010] [Revised: 05/14/2010] [Accepted: 06/07/2010] [Indexed: 05/18/2023]
Abstract
In higher plants, the plastidial NADH dehydrogenase (Ndh) complex supports nonphotochemical electron fluxes from stromal electron donors to plastoquinones. Ndh functions in chloroplasts are not clearly established; however, its activity was linked to the prevention of the overreduction of stroma, especially under stress conditions. Here, we show by the characterization of Orr(Ds), a dominant transposon-tagged tomato (Solanum lycopersicum) mutant deficient in the NDH-M subunit, that this complex is also essential for the fruit ripening process. Alteration to the NDH complex in fruit changed the climacteric, ripening-associated metabolites and transcripts as well as fruit shelf life. Metabolic processes in chromoplasts of ripening tomato fruit were affected in Orr(Ds), as mutant fruit were yellow-orange and accumulated substantially less total carotenoids, mainly beta-carotene and lutein. The changes in carotenoids were largely influenced by environmental conditions and accompanied by modifications in levels of other fruit antioxidants, namely, flavonoids and tocopherols. In contrast with the pigmentation phenotype in mature mutant fruit, Orr(Ds) leaves and green fruits did not display a visible phenotype but exhibited reduced Ndh complex quantity and activity. This study therefore paves the way for further studies on the role of electron transport and redox reactions in the regulation of fruit ripening and its associated metabolism.
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Affiliation(s)
- Shai Nashilevitz
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
- Faculty of Agricultural, Food, and Environmental Quality Sciences, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | | | - Yinon Izkovich
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ilana Rogachev
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sonia Osorio
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Maxim Itkin
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Avital Adato
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ilya Pankratov
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Joseph Hirschberg
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Alisdair R. Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Shmuel Wolf
- Faculty of Agricultural, Food, and Environmental Quality Sciences, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Björn Usadel
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Avraham A. Levy
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dominique Rumeau
- Commissariat à l'Energie Atomique Cadarache, Direction des Sciences du Vivant, Institut de Biologie Environnementale et Biotechnologie, Service de Biologie Végétale et de Microbiologie Environnementale, Laboratoire d'Ecophysiologie Moléculaire des Plantes, Unité Mixte de Recherche 6191, Centre National de la Recherche Scientifique/Commissariat à l'Energie Atomique/Université de la Méditerranée, F-13108 Saint-Paul-lez-Durance, France
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
- Address correspondence to
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87
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From QTL to candidate gene: genetical genomics of simple and complex traits in potato using a pooling strategy. BMC Genomics 2010; 11:158. [PMID: 20210995 PMCID: PMC2843620 DOI: 10.1186/1471-2164-11-158] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Accepted: 03/08/2010] [Indexed: 11/10/2022] Open
Abstract
Background Utilization of the natural genetic variation in traditional breeding programs remains a major challenge in crop plants. The identification of candidate genes underlying, or associated with, phenotypic trait QTLs is desired for effective marker assisted breeding. With the advent of high throughput -omics technologies, screening of entire populations for association of gene expression with targeted traits is becoming feasible but remains costly. Here we present the identification of novel candidate genes for different potato tuber quality traits by employing a pooling approach reducing the number of hybridizations needed. Extreme genotypes for a quantitative trait are collected and the RNA from contrasting bulks is then profiled with the aim of finding differentially expressed genes. Results We have successfully implemented the pooling strategy for potato quality traits and identified candidate genes associated with potato tuber flesh color and tuber cooking type. Elevated expression level of a dominant allele of the β-carotene hydroxylase (bch) gene was associated with yellow flesh color through mapping of the gene under a major QTL for flesh color on chromosome 3. For a second trait, a candidate gene with homology to a tyrosine-lysine rich protein (TLRP) was identified based on allele specificity of the probe on the microarray. TLRP was mapped on chromosome 9 in close proximity to a QTL for potato cooking type strengthening its significance as a candidate gene. Furthermore, we have performed a profiling experiment targeting a polygenic trait, by pooling individual genotypes based both on phenotypic and marker data, allowing the identification of candidate genes associated with the two different linkage groups. Conclusions A pooling approach for RNA-profiling with the aim of identifying novel candidate genes associated with tuber quality traits was successfully implemented. The identified candidate genes for tuber flesh color (bch) and cooking type (tlrp) can provide useful markers for breeding schemes in the future. Strengths and limitations of the approach are discussed.
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88
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Ohta D, Kanaya S, Suzuki H. Application of Fourier-transform ion cyclotron resonance mass spectrometry to metabolic profiling and metabolite identification. Curr Opin Biotechnol 2010; 21:35-44. [DOI: 10.1016/j.copbio.2010.01.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Revised: 01/15/2010] [Accepted: 01/20/2010] [Indexed: 12/23/2022]
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Kleinegris DMM, Janssen M, Brandenburg WA, Wijffels RH. The selectivity of milking of Dunaliella salina. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2010; 12:14-23. [PMID: 19475448 PMCID: PMC2816252 DOI: 10.1007/s10126-009-9195-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Accepted: 05/02/2009] [Indexed: 05/07/2023]
Abstract
The process of the simultaneous production and extraction of carotenoids, milking, of Dunaliella salina was studied. We would like to know the selectivity of this process. Could all the carotenoids produced be extracted? And would it be possible to vary the profile of the produced carotenoids and, consequently, influence the type of carotenoids extracted? By using three different D. salina strains and three different stress conditions, we varied the profiles of the carotenoids produced. Between Dunaliella bardawil and D. salina 19/18, no remarkable differences were seen in the extraction profiles, although D. salina 19/18 seemed to be better extractable. D. salina 19/25 was not "milkable" at all. The milking process could only be called selective for secondary carotenoids in case gentle mixing was used. In aerated flat-panel photobioreactors, extraction was much better, but selectiveness decreased and also chlorophyll and primary carotenoids were extracted. This was possibly related to cell damage due to shear stress.
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Affiliation(s)
- Dorinde M M Kleinegris
- Agrotechnology and Food Science, Bioprocess Engineering Group, Wageningen University and Research Centre, P.O. Box 8129, 6700 EV Wageningen, The Netherlands.
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90
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Azari R, Tadmor Y, Meir A, Reuveni M, Evenor D, Nahon S, Shlomo H, Chen L, Levin I. Light signaling genes and their manipulation towards modulation of phytonutrient content in tomato fruits. Biotechnol Adv 2010; 28:108-18. [DOI: 10.1016/j.biotechadv.2009.10.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 09/01/2009] [Accepted: 09/01/2009] [Indexed: 12/26/2022]
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91
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Ballester AR, Molthoff J, de Vos R, Hekkert BTL, Orzaez D, Fernández-Moreno JP, Tripodi P, Grandillo S, Martin C, Heldens J, Ykema M, Granell A, Bovy A. Biochemical and molecular analysis of pink tomatoes: deregulated expression of the gene encoding transcription factor SlMYB12 leads to pink tomato fruit color. PLANT PHYSIOLOGY 2010; 152:71-84. [PMID: 19906891 PMCID: PMC2799347 DOI: 10.1104/pp.109.147322] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Accepted: 11/03/2009] [Indexed: 05/18/2023]
Abstract
The color of tomato fruit is mainly determined by carotenoids and flavonoids. Phenotypic analysis of an introgression line (IL) population derived from a cross between Solanum lycopersicum 'Moneyberg' and the wild species Solanum chmielewskii revealed three ILs with a pink fruit color. These lines had a homozygous S. chmielewskii introgression on the short arm of chromosome 1, consistent with the position of the y (yellow) mutation known to result in colorless epidermis, and hence pink-colored fruit, when combined with a red flesh. Metabolic analysis showed that pink fruit lack the ripening-dependent accumulation of the yellow-colored flavonoid naringenin chalcone in the fruit peel, while carotenoid levels are not affected. The expression of all genes encoding biosynthetic enzymes involved in the production of the flavonol rutin from naringenin chalcone was down-regulated in pink fruit, suggesting that the candidate gene underlying the pink phenotype encodes a regulatory protein such as a transcription factor rather than a biosynthetic enzyme. Of 26 MYB and basic helix-loop-helix transcription factors putatively involved in regulating transcription of genes in the phenylpropanoid and/or flavonoid pathway, only the expression level of the MYB12 gene correlated well with the decrease in the expression of structural flavonoid genes in peel samples of pink- and red-fruited genotypes during ripening. Genetic mapping and segregation analysis showed that MYB12 is located on chromosome 1 and segregates perfectly with the characteristic pink fruit color. Virus-induced gene silencing of SlMYB12 resulted in a decrease in the accumulation of naringenin chalcone, a phenotype consistent with the pink-colored tomato fruit of IL1b. In conclusion, biochemical and molecular data, gene mapping, segregation analysis, and virus-induced gene silencing experiments demonstrate that the MYB12 transcription factor plays an important role in regulating the flavonoid pathway in tomato fruit and suggest strongly that SlMYB12 is a likely candidate for the y mutation.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Arnaud Bovy
- Plant Research International, 6700 AA Wageningen, The Netherlands (A.-R.B., J.M., R.d.V., B.t.L.H., A.B.); Centre for Biosystems Genomics, 6700 PB Wageningen, The Netherlands (A.-R.B., R.d.V., A.B.); Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, 46022 Valencia, Spain (D.O., J.-P.F.-M., A.G.); Consiglio Nazionale delle Ricerche-Istituto di Genetica Vegetale, I–80055 Portici, Italy (P.T., S.G.); John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, United Kingdom (C.M.); and Enza Zaden Research and Development, 1600 AA Enkhuizen, The Netherlands (J.H., M.Y.)
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92
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Adato A, Mandel T, Mintz-Oron S, Venger I, Levy D, Yativ M, Domínguez E, Wang Z, De Vos RCH, Jetter R, Schreiber L, Heredia A, Rogachev I, Aharoni A. Fruit-surface flavonoid accumulation in tomato is controlled by a SlMYB12-regulated transcriptional network. PLoS Genet 2009; 5:e1000777. [PMID: 20019811 PMCID: PMC2788616 DOI: 10.1371/journal.pgen.1000777] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Accepted: 11/18/2009] [Indexed: 12/22/2022] Open
Abstract
The cuticle covering plants' aerial surfaces is a unique structure that plays a key role in organ development and protection against diverse stress conditions. A detailed analysis of the tomato colorless-peel y mutant was carried out in the framework of studying the outer surface of reproductive organs. The y mutant peel lacks the yellow flavonoid pigment naringenin chalcone, which has been suggested to influence the characteristics and function of the cuticular layer. Large-scale metabolic and transcript profiling revealed broad effects on both primary and secondary metabolism, related mostly to the biosynthesis of phenylpropanoids, particularly flavonoids. These were not restricted to the fruit or to a specific stage of its development and indicated that the y mutant phenotype is due to a mutation in a regulatory gene. Indeed, expression analyses specified three R2R3-MYB-type transcription factors that were significantly down-regulated in the y mutant fruit peel. One of these, SlMYB12, was mapped to the genomic region on tomato chromosome 1 previously shown to harbor the y mutation. Identification of an additional mutant allele that co-segregates with the colorless-peel trait, specific down-regulation of SlMYB12 and rescue of the y phenotype by overexpression of SlMYB12 on the mutant background, confirmed that a lesion in this regulator underlies the y phenotype. Hence, this work provides novel insight to the study of fleshy fruit cuticular structure and paves the way for the elucidation of the regulatory network that controls flavonoid accumulation in tomato fruit cuticle.
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Affiliation(s)
- Avital Adato
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Tali Mandel
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Shira Mintz-Oron
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ilya Venger
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Dorit Levy
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Merav Yativ
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Eva Domínguez
- Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Spain
| | - Zhonghua Wang
- Department of Botany and Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ric C. H. De Vos
- Business Unit Bioscience, Plant Research International, and Centre for BioSystems Genomics, Wageningen, The Netherlands
| | - Reinhard Jetter
- Department of Botany and Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lukas Schreiber
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
| | - Antonio Heredia
- Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Spain
| | - Ilana Rogachev
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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93
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Itkin M, Seybold H, Breitel D, Rogachev I, Meir S, Aharoni A. TOMATO AGAMOUS-LIKE 1 is a component of the fruit ripening regulatory network. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 60:1081-95. [PMID: 19891701 DOI: 10.1111/j.1365-313x.2009.04064.x] [Citation(s) in RCA: 204] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
After fertilization, the expanding carpel of fleshy fruit goes through a phase change to ripening. Although the role of ethylene signalling in mediating climacteric ripening has been established, knowledge regarding the regulation of ethylene biosynthesis and its association with fruit developmental programs is still lacking. A functional screen of tomato transcription factors showed that silencing of the TOMATO AGAMOUS-LIKE 1 (TAGL1) MADS box gene results in altered fruit pigmentation. Over-expressing TAGL1 as a chimeric repressor suggested a role in controlling ripening, as transgenic tomato fruit showed reduced carotenoid and ethylene levels, suppressed chlorophyll breakdown, and down-regulation of ripening-associated genes. Moreover, fruits over-expressing TAGL1 accumulated more lycopene, and their sepals were swollen, accumulated high levels of the yellow flavonoid naringenin chalcone and contained lycopene. Transient promoter-binding assays indicated that part of the TAGL1 activity in ripening is executed through direct activation of ACS2, an ethylene biosynthesis gene that has recently been reported to be a target of the RIN MADS box factor. Examination of the TAGL1 transcript and its over-expression in the rin mutant background suggested that RIN does not regulate TAGL1 or vice versa. The results also indicated RIN-dependent and -independent processes that are regulated by TAGL1. We also noted that fruit of TAGL1 loss-of-function lines had a thin pericarp layer, indicating an additional role for TAGL1 in carpel expansion prior to ripening. The results add a new component to the current model of the regulatory network that controls fleshy fruit ripening and its association with the ethylene biosynthesis pathway.
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Affiliation(s)
- Maxim Itkin
- Department of Plant Sciences, Weizmann Institute of Science, PO Box 26, Rehovot 76100, Israel
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Wolfender JL, Glauser G, Boccard J, Rudaz S. MS-based Plant Metabolomic Approaches for Biomarker Discovery. Nat Prod Commun 2009. [DOI: 10.1177/1934578x0900401019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Metabolomics, which aims at the comprehensive and quantitative analysis of wide arrays of metabolites in biological samples, is playing an increasingly important role in plant science. Various biological issues have been successfully studied by this holistic approach that includes global metabolite composition assessment, mutant characterization, taxonomy, developmental processes, stress response, interaction with environment, quality control assessment and mode of action of herbal medicine. This review summarizes the main mass spectrometry methods used for performing these studies and discusses the potential, but also the current limitations of the various approaches. The intention is not to cover exhaustively the field, which has considerably grown over about one decade, but to give a brief insight into the methods commonly employed and discuss some applications that reveal the potential of metabolomics in phytochemistry and systems biology.
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Affiliation(s)
- Jean-Luc Wolfender
- Laboratory of Pharmacognosy and Phytochemistry, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 30, quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Gaetan Glauser
- Laboratory of Pharmacognosy and Phytochemistry, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 30, quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
- Laboratory of Pharmaceutical Analytical Chemistry, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 20, Bd d'Yvoy, CH-1211 Geneva 4, Switzerland
| | - Julien Boccard
- Laboratory of Pharmaceutical Analytical Chemistry, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 20, Bd d'Yvoy, CH-1211 Geneva 4, Switzerland
| | - Serge Rudaz
- Laboratory of Pharmaceutical Analytical Chemistry, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 20, Bd d'Yvoy, CH-1211 Geneva 4, Switzerland
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95
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Tzin V, Malitsky S, Aharoni A, Galili G. Expression of a bacterial bi-functional chorismate mutase/prephenate dehydratase modulates primary and secondary metabolism associated with aromatic amino acids in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 60:156-167. [PMID: 19508381 DOI: 10.1111/j.1365-313x.2009.03945.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Plants can synthesize the aromatic amino acid Phe via arogenate, but it is still not known whether they also use an alternative route for Phe biosynthesis via phenylpyruvate, like many micro-organisms. To examine this possibility, we expressed a bacterial bi-functional PheA (chorismate mutase/prephenate dehydratase) gene in Arabidopsis thaliana that converts chorismate via prephenate into phenylpyruvate. The PheA-expressing plants showed a large increase in the level of Phe, implying that they can convert phenylpyruvate into Phe. In addition, PheA expression rendered the plants more sensitive than wild-type plants to the Trp biosynthesis inhibitor 5-methyl-Trp, implying that Phe biosynthesis competes with Trp biosynthesis from their common precursor chorismate. Surprisingly, GC-MS, LC-MS and microarray analyses showed that this increase in Phe accumulation only had a very minor effect on the levels of other primary metabolites as well as on the transcriptome profile, implying little regulatory cross-interaction between the aromatic amino acid biosynthesis network and the bulk of the Arabidopsis transcriptome and primary metabolism. However, the levels of a number of secondary metabolites derived from all three aromatic amino acids (Phe, Trp and Tyr) were altered in the PheA plants, implying regulatory cross-interactions between the flux of aromatic amino acid biosynthesis from chorismate and their further metabolism into various secondary metabolites. Taken together, our results provide insights into the regulatory mechanisms of aromatic amino acid biosynthesis and their interaction with central primary metabolism, as well as the regulatory interface between primary and secondary metabolism.
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Affiliation(s)
- Vered Tzin
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
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96
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Gupta V, Mathur S, Solanke AU, Sharma MK, Kumar R, Vyas S, Khurana P, Khurana JP, Tyagi AK, Sharma AK. Genome analysis and genetic enhancement of tomato. Crit Rev Biotechnol 2009; 29:152-81. [PMID: 19319709 DOI: 10.1080/07388550802688870] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Solanaceae is an important family of vegetable crops, ornamentals and medicinal plants. Tomato has served as a model member of this family largely because of its enriched cytogenetic, genetic, as well as physical, maps. Mapping has helped in cloning several genes of importance such as Pto, responsible for resistance against bacterial speck disease, Mi-1.2 for resistance against nematodes, and fw2.2 QTL for fruit weight. A high-throughput genome-sequencing program has been initiated by an international consortium of 10 countries. Since heterochromatin has been found to be concentrated near centromeres, the consortium is focusing on sequencing only the gene-rich euchromatic region. Genomes of the members of Solanaceae show a significant degree of synteny, suggesting that the tomato genome sequence would help in the cloning of genes for important traits from other Solanaceae members as well. ESTs from a large number of cDNA libraries have been sequenced, and microarray chips, in conjunction with wide array of ripening mutants, have contributed immensely to the understanding of the fruit-ripening phenomenon. Work on the analysis of the tomato proteome has also been initiated. Transgenic tomato plants with improved abiotic stress tolerance, disease resistance and insect resistance, have been developed. Attempts have also been made to develop tomato as a bioreactor for various pharmaceutical proteins. However, control of fruit quality and ripening remains an active and challenging area of research. Such efforts should pave the way to improve not only tomato, but also other solanaceous crops.
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Affiliation(s)
- Vikrant Gupta
- Interdisciplinary Centre for Plant Genomics, Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
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97
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Krall L, Huege J, Catchpole G, Steinhauser D, Willmitzer L. Assessment of sampling strategies for gas chromatography-mass spectrometry (GC-MS) based metabolomics of cyanobacteria. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:2952-60. [PMID: 19631594 DOI: 10.1016/j.jchromb.2009.07.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Revised: 06/29/2009] [Accepted: 07/05/2009] [Indexed: 12/13/2022]
Abstract
Metabolomics is the comprehensive analysis of the small molecules that compose an organism's metabolism. The main limiting step in microbial metabolomics is the requirement for fast and efficient separation of microbes from the culture medium under conditions in which metabolism is rapidly halted. In this article we compare three different sampling strategies, quenching, filtering, and centrifugation, for arresting the metabolic activities of two morphologically diverse cyanobacteria, the unicellular Synechocystis sp. PCC 6803 and the filamentous Nostoc sp. PCC 7120 for GC-MS analysis. We demonstrate that each sampling technique produces internally consistent and reproducible data, however, cold methanol-water quenching caused leakage and substantial loss of metabolites from various compound classes, while fast filtering and centrifugation produced quite similar metabolite pool sizes, even for metabolites with predicted high turnover. This indicates that cyanobacterial metabolic pools, as measured by GC-MS, do not show high turnover under standard growing conditions. As well, using stable (13)C labeling we show the biological origin of some of the consistently observed unknown analytes. With the development of these techniques, we establish the basis for broad scale comparative metabolite profiling of cyanobacteria.
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Affiliation(s)
- Leonard Krall
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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98
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Lavi N, Tadmor Y, Meir A, Bechar A, Oren-Shamir M, Ovadia R, Reuveni M, Nahon S, Shlomo H, Chen L, Levin I. Characterization of the intense pigment tomato genotype emphasizing targeted fruit metabolites and chloroplast biogenesis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2009; 57:4818-4826. [PMID: 19391624 DOI: 10.1021/jf900190r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The tomato INTENSE PIGMENT (IP) genotype is characterized by intense visual pigmentation of unripe and ripe fruits, not thoroughly analyzed thus far. This study was therefore designed to analyze key morphologic, metabolomic, and photomorphogenic phenotypes of this genotype in comparison to its near-isogenic normal counterpart and to evaluate its significance relative to other tomato mutants known for increased fruit pigmentation. The IP genotype produced smaller and darker red fruits, and a substantially increased chloroplast biogenesis was found in its green fruit and leaf tissues. Ripe-red fruits of the IP genotype produced 34-38% more soluble solids and up to 62.6% more carotenoids, but no differences were found in the concentration of flavonoid compounds in its peel tissue. The IP genotype was found to display a greater hypocotyl inhibition response to blue and yellow light, but a more prominent and novel response to total darkness. As a whole, the IP genotype exhibited highly desirable traits, making it a valuable genotype for tomato breeders attempting to introduce functional and taste qualities into tomato fruits.
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Affiliation(s)
- Noga Lavi
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel
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99
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Kovács K, Fray RG, Tikunov Y, Graham N, Bradley G, Seymour GB, Bovy AG, Grierson D. Effect of tomato pleiotropic ripening mutations on flavour volatile biosynthesis. PHYTOCHEMISTRY 2009; 70:1003-8. [PMID: 19539963 DOI: 10.1016/j.phytochem.2009.05.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Revised: 04/28/2009] [Accepted: 05/01/2009] [Indexed: 05/19/2023]
Abstract
Ripening is a tightly controlled and developmentally regulated process involving networks of genes, and metabolites that result in dramatic changes in fruit colour, texture and flavour. Molecular and genetic analysis in tomato has revealed a series of regulatory genes involved in fruit development and ripening, including MADS box and SPB box transcription factors and genes involved in ethylene synthesis, signalling and response. Volatile metabolites represent a significant part of the plant metabolome, playing an important role in plant signalling, defence strategies and probably in regulatory mechanisms. They also play an important role in fruit quality. In order to acquire a better insight into the biochemical and genetic control of flavour compound generation and links between these metabolites and the central regulators of ripening, five pleiotropic mutant tomato lines were subjected to volatile metabolite profiling in comparison with wild-type Ailsa Craig. One hundred and seventeen volatile compounds were identified and quantified using SPME (Solid Phase Microextraction) headspace extraction followed by Gas Chromatography-Mass Spectrometry (GC-MS) and the data were subjected to multivariate comparative analysis. We find that the different mutants each produce distinct volatile profiles during ripening. Through principal component analysis the volatiles most dramatically affected are those derived from fatty-acids. The results are consistent with the suggestion that specific isoforms of lipoxygenase located in the plastids and the enzymes that provide precursors and downstream metabolites play a key role in determining volatile composition.
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Affiliation(s)
- Katalin Kovács
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
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100
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Iijima Y, Aoki K. Application of Metabolomics to Improve Tomato Fruit Productivity and Quality. ACTA ACUST UNITED AC 2009. [DOI: 10.2503/jjshs1.78.14] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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