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Rodrigues AM, Miguel C, Chaves I, António C. Mass spectrometry-based forest tree metabolomics. MASS SPECTROMETRY REVIEWS 2021; 40:126-157. [PMID: 31498921 DOI: 10.1002/mas.21603] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 08/05/2019] [Indexed: 05/24/2023]
Abstract
Research in forest tree species has advanced slowly when compared with other agricultural crops and model organisms, mainly due to the long-life cycles, large genome sizes, and lack of genomic tools. Additionally, trees are complex matrices, and the presence of interferents (e.g., oleoresins and cellulose) challenges the analysis of tree tissues with mass spectrometry (MS)-based analytical platforms. In this review, advances in MS-based forest tree metabolomics are discussed. Given their economic and ecological significance, particular focus is given to Pinus, Quercus, and Eucalyptus forest tree species to better understand their metabolite responses to abiotic and biotic stresses in the current climate change scenario. Furthermore, MS-based metabolomics technologies produce large and complex datasets that require expertize to adequately manage, process, analyze, and store the data in dedicated repositories. To ensure that the full potential of forest tree metabolomics data are translated into new knowledge, these data should comply with the FAIR principles (i.e., Findable, Accessible, Interoperable, and Re-usable). It is essential that adequate standards are implemented to annotate metadata from forest tree metabolomics studies as is already required by many science and governmental agencies and some major scientific publishers. © 2019 John Wiley & Sons Ltd. Mass Spec Rev 40:126-157, 2021.
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Affiliation(s)
- Ana Margarida Rodrigues
- Plant Metabolomics Laboratory, GreenIT-Bioresources for Sustainability, Instituto de Tecnologia Química e Biológica António Xavie, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, Oeiras, 2780-157, Portugal
| | - Célia Miguel
- Forest Genomics & Molecular Genetics Lab, BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Inês Chaves
- Forest Genomics & Molecular Genetics Lab, BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Carla António
- Plant Metabolomics Laboratory, GreenIT-Bioresources for Sustainability, Instituto de Tecnologia Química e Biológica António Xavie, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, Oeiras, 2780-157, Portugal
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Fukuda T, Takamatsu K, Bamba T, Fukusaki E. Potato tuber metabolomics-based prediction of chip color quality and application using gas chromatography/flame ionization detector. Biosci Biotechnol Biochem 2020; 84:2193-2198. [PMID: 32674667 DOI: 10.1080/09168451.2020.1793656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Potato (Solanum tuberosum L.) tubers are usually harvested once a year; thus, long-term storage is required to supply quality-assured tubers throughout the year. Further, an applicable method to predict tuber quality during storage is needed. In this study, gas chromatography-mass spectrometry (GC/MS) metabolomics was applied to identify applicable biomarkers for prediction of potato chip color based on 3 years' field-grown tubers. The projections to latent structures (PLS) prediction model, calculated from a metabolome data set obtained before storage, was consistent with actual measured chip color values. Additionally, GC with frame ionization detector (GC/FID) metabolite fingerprinting simultaneously re-constructed more reliable and relevant prediction models for chip color quality compared to GC/MS. Moreover, nine metabolites detected by GC/MS analysis were further validated as applicable prediction markers. This strategy will provide a practical and cost-effective quality-control tool for potato processing manufacturers on an industrial scale.
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Affiliation(s)
- Tomohiko Fukuda
- Agricultural Research Institute, Hokuren Federation of Agricultural Cooperatives , Sapporo, Japan
| | - Kiyofumi Takamatsu
- Agricultural Research Institute, Hokuren Federation of Agricultural Cooperatives , Sapporo, Japan
| | - Takeshi Bamba
- Department of Biotechnology, Graduate School of Engineering, Osaka University , Osaka, Japan.,Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University , Fukuoka, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University , Osaka, Japan
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Application of gas chromatography/flame ionization detector-based metabolite fingerprinting for authentication of Asian palm civet coffee (Kopi Luwak). J Biosci Bioeng 2015; 120:555-61. [PMID: 25912451 DOI: 10.1016/j.jbiosc.2015.03.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 02/15/2015] [Accepted: 03/03/2015] [Indexed: 01/13/2023]
Abstract
Development of authenticity screening for Asian palm civet coffee, the world-renowned priciest coffee, was previously reported using metabolite profiling through gas chromatography/mass spectrometry (GC/MS). However, a major drawback of this approach is the high cost of the instrument and maintenance. Therefore, an alternative method is needed for quality and authenticity evaluation of civet coffee. A rapid, reliable and cost-effective analysis employing a universal detector, GC coupled with flame ionization detector (FID), and metabolite fingerprinting has been established for discrimination analysis of 37 commercial and non-commercial coffee beans extracts. gas chromatography/flame ionization detector (GC/FID) provided higher sensitivity over a similar range of detected compounds than GC/MS. In combination with multivariate analysis, GC/FID could successfully reproduce quality prediction from GC/MS for differentiation of commercial civet coffee, regular coffee and coffee blend with 50 wt % civet coffee content without prior metabolite details. Our study demonstrated that GC/FID-based metabolite fingerprinting can be effectively actualized as an alternative method for coffee authenticity screening in industries.
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Cazacu G, Capraru M, Popa VI. Advances Concerning Lignin Utilization in New Materials. ADVANCES IN NATURAL POLYMERS 2013. [DOI: 10.1007/978-3-642-20940-6_8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Ochi H, Bamba T, Naito H, Iwatsuki K, Fukusaki E. Metabolic fingerprinting of hard and semi-hard natural cheeses using gas chromatography with flame ionization detector for practical sensory prediction modeling. J Biosci Bioeng 2012; 114:506-11. [DOI: 10.1016/j.jbiosc.2012.06.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Revised: 05/11/2012] [Accepted: 06/05/2012] [Indexed: 01/08/2023]
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Villalobos DP, Díaz-Moreno SM, Said ESS, Cañas RA, Osuna D, Van Kerckhoven SHE, Bautista R, Claros MG, Cánovas FM, Cantón FR. Reprogramming of gene expression during compression wood formation in pine: coordinated modulation of S-adenosylmethionine, lignin and lignan related genes. BMC PLANT BIOLOGY 2012; 12:100. [PMID: 22747794 PMCID: PMC3406974 DOI: 10.1186/1471-2229-12-100] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 06/29/2012] [Indexed: 05/02/2023]
Abstract
BACKGROUND Transcript profiling of differentiating secondary xylem has allowed us to draw a general picture of the genes involved in wood formation. However, our knowledge is still limited about the regulatory mechanisms that coordinate and modulate the different pathways providing substrates during xylogenesis. The development of compression wood in conifers constitutes an exceptional model for these studies. Although differential expression of a few genes in differentiating compression wood compared to normal or opposite wood has been reported, the broad range of features that distinguish this reaction wood suggest that the expression of a larger set of genes would be modified. RESULTS By combining the construction of different cDNA libraries with microarray analyses we have identified a total of 496 genes in maritime pine (Pinus pinaster, Ait.) that change in expression during differentiation of compression wood (331 up-regulated and 165 down-regulated compared to opposite wood). Samples from different provenances collected in different years and geographic locations were integrated into the analyses to mitigate the effects of multiple sources of variability. This strategy allowed us to define a group of genes that are consistently associated with compression wood formation. Correlating with the deposition of a thicker secondary cell wall that characterizes compression wood development, the expression of a number of genes involved in synthesis of cellulose, hemicellulose, lignin and lignans was up-regulated. Further analysis of a set of these genes involved in S-adenosylmethionine metabolism, ammonium recycling, and lignin and lignans biosynthesis showed changes in expression levels in parallel to the levels of lignin accumulation in cells undergoing xylogenesis in vivo and in vitro. CONCLUSIONS The comparative transcriptomic analysis reported here have revealed a broad spectrum of coordinated transcriptional modulation of genes involved in biosynthesis of different cell wall polymers associated with within-tree variations in pine wood structure and composition. In particular, we demonstrate the coordinated modulation at transcriptional level of a gene set involved in S-adenosylmethionine synthesis and ammonium assimilation with increased demand for coniferyl alcohol for lignin and lignan synthesis, enabling a better understanding of the metabolic requirements in cells undergoing lignification.
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Affiliation(s)
- David P Villalobos
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos, 29071, Málaga, Spain
- Department of Plant Molecular Biology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Sara M Díaz-Moreno
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos, 29071, Málaga, Spain
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology, AlbaNova University Centre, SE-10691, Stockholm, Sweden
| | - El-Sayed S Said
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos, 29071, Málaga, Spain
| | - Rafael A Cañas
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos, 29071, Málaga, Spain
| | - Daniel Osuna
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos, 29071, Málaga, Spain
- Departamento de Fisiología Vegetal, Centro Hispano-Luso de Investigaciones Agrarias, Facultad de Biología, Universidad de Salamanca, C/Río Duero 12, 37185, Salamanca, Spain
| | - Sonia H E Van Kerckhoven
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos, 29071, Málaga, Spain
| | - Rocío Bautista
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos, 29071, Málaga, Spain
| | - Manuel Gonzalo Claros
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos, 29071, Málaga, Spain
| | - Francisco M Cánovas
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos, 29071, Málaga, Spain
| | - Francisco R Cantón
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos, 29071, Málaga, Spain
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Jumtee K, Bamba T, Fukusaki E. Fast GC-FID based metabolic fingerprinting of Japanese green tea leaf for its quality ranking prediction. J Sep Sci 2009; 32:2296-304. [DOI: 10.1002/jssc.200900096] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Paiva JAP, Garnier-Géré PH, Rodrigues JC, Alves A, Santos S, Graça J, Le Provost G, Chaumeil P, Da Silva-Perez D, Bosc A, Fevereiro P, Plomion C. Plasticity of maritime pine (Pinus pinaster) wood-forming tissues during a growing season. THE NEW PHYTOLOGIST 2008; 179:1180-1194. [PMID: 18631295 DOI: 10.1111/j.1469-8137.2008.02536.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The seasonal effect is the most significant external source of variation affecting vascular cambial activity and the development of newly divided cells, and hence wood properties. Here, the effect of edapho-climatic conditions on the phenotypic and molecular plasticity of differentiating secondary xylem during a growing season was investigated. Wood-forming tissues of maritime pine (Pinus pinaster) were collected from the beginning to the end of the growing season in 2003. Data from examination of fibre morphology, Fourier-transform infrared spectroscopy (FTIR), analytical pyrolysis, and gas chromatography/mass spectrometry (GC/MS) were combined to characterize the samples. Strong variation was observed in response to changes in edapho-climatic conditions. A genomic approach was used to identify genes differentially expressed during this growing season. Out of 3512 studied genes, 19% showed a significant seasonal effect. These genes were clustered into five distinct groups, the largest two representing genes over-expressed in the early- or late-wood-forming tissues, respectively. The other three clusters were characterized by responses to specific edapho-climatic conditions. This work provides new insights into the plasticity of the molecular machinery involved in wood formation, and reveals candidate genes potentially responsible for the phenotypic differences found between early- and late-wood.
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Affiliation(s)
- J A P Paiva
- INRA, UMR1202, BIOGECO, Domaine de l'Hermitage, 69 route d'Arcachon, F-33612 Cestas Cedex, France
- Université de Bordeaux, UMR1202, BIOGECO, Bât B8 RdC, Av des Facultés, F-33405 Talence, France
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República-EAN, 2780-157 Oeiras, Portugal
- Tropical Research Institute of Portugal (IICT), Forestry and Forest Products Centre, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - P H Garnier-Géré
- INRA, UMR1202, BIOGECO, Domaine de l'Hermitage, 69 route d'Arcachon, F-33612 Cestas Cedex, France
- Université de Bordeaux, UMR1202, BIOGECO, Bât B8 RdC, Av des Facultés, F-33405 Talence, France
| | - J C Rodrigues
- Tropical Research Institute of Portugal (IICT), Forestry and Forest Products Centre, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - A Alves
- Tropical Research Institute of Portugal (IICT), Forestry and Forest Products Centre, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - S Santos
- Departamento de Engenharia Florestal, Instituto Superior de Agronomia, TULisbon, ISA-DEF, Tapada Ajuda, 1349-017 Lisboa, Portugal
| | - J Graça
- Departamento de Engenharia Florestal, Instituto Superior de Agronomia, TULisbon, ISA-DEF, Tapada Ajuda, 1349-017 Lisboa, Portugal
| | - G Le Provost
- INRA, UMR1202, BIOGECO, Domaine de l'Hermitage, 69 route d'Arcachon, F-33612 Cestas Cedex, France
- Université de Bordeaux, UMR1202, BIOGECO, Bât B8 RdC, Av des Facultés, F-33405 Talence, France
| | - P Chaumeil
- Université de Bordeaux, UMR1202, BIOGECO, Bât B8 RdC, Av des Facultés, F-33405 Talence, France
| | - D Da Silva-Perez
- Laboratoire Bois Process, FCBA InTechFibres, Domaine Universitaire, BP 251, 38044 Grenoble Cedex, France
| | - A Bosc
- INRA, UR Ecologie fonctionnelle et physique de l'Environnement, EPHYSE, 71 avenue Edouard Bourleaux, 33883 Villenave d'Ornon Cedex, France
| | - P Fevereiro
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República-EAN, 2780-157 Oeiras, Portugal
- Departamento de Biologia Vegetal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1700 Lisboa, Portugal
| | - C Plomion
- INRA, UMR1202, BIOGECO, Domaine de l'Hermitage, 69 route d'Arcachon, F-33612 Cestas Cedex, France
- Université de Bordeaux, UMR1202, BIOGECO, Bât B8 RdC, Av des Facultés, F-33405 Talence, France
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