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1. Temperature Shift Between Vineyards Modulates Berry Phenology and Primary Metabolism in a Varietal Collection of Wine Grapevine

Author

Kelem Gashu, Noga Sikron Persi, Elyashiv Drori, Eran Harcavi, Nurit Agam, Amnon Bustan, and Aaron Fait

Subjects
arid viticulture, climate change, organic acids, phenological phase, primary metabolism, sugars, Plant culture, SB1-1110
Abstract

Global climate change and the expected increase in temperature are altering the relationship between geography and grapevine (V. vinifera) varietal performance, and the implications of which are yet to be fully understood. We investigated berry phenology and biochemistry of 30 cultivars, 20 red and 10 white, across three seasons (2017–2019) in response to a consistent average temperature difference of 1.5°C during the growing season between two experimental sites. The experiments were conducted at Ramat Negev (RN) and Ramon (MR) vineyards, located in the Negev desert, Israel. A significant interaction between vineyard location, season, and variety affected phenology and berry indices. The warmer RN site was generally associated with an advanced phenological course for the white cultivars, which reached harvest up to 2 weeks earlier than at the MR site. The white cultivars also showed stronger correlation between non-consecutive phenological stages than did the red ones. In contrast, harvest time of red cultivars considerably varied according to seasons and sites. Warmer conditions extended fruit developmental phases, causing berry shriveling and cluster collapse in a few cultivars such as Pinot Noir, Ruby Cabernet, and Tempranillo. Analyses of organic acid content suggested differences between red and white cultivars in the content of malate, tartrate, and citrate in response to the temperature difference between sites. However, generally, cultivars at lower temperatures exhibited lower concentrations of pulp organic acids at véraison, but acid degradation until harvest was reduced, compared to the significant pace of acid decline at the warmer site. Sugars showed the greatest differences between sites in both white and red berries at véraison, but differences were seasonal dependent. At harvest, cultivars of both groups exhibited significant variation in hexose/sucrose ratio, and the averages of which varied from 1.6 to 2.9. Hexose/sucrose ratio was significantly higher among the red cultivars at the warmer RN, while this tendency was very slight among white cultivars. White cultivars seem to harbor a considerable degree of resilience due to a combination of earlier and shorter ripening phase, which avoids most of the summer heat. Taken together, our study demonstrates that the extensive genetic capacity of V. vinifera bears significant potential and plasticity to withstand the temperature increase associated with climate change.

Published
2020
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3. Metabolic Engineering Strategy Enables a Hundred-Fold Increase in Viniferin Levels in Vitis vinifera cv. Gamay Red Cell Culture

Author

Avichai Perl, Irena Dynkin, Sangram K. Lenka, Ru Wang, Noga Sikron-Persi, Michal Oren-Shamir, Varun Kumar, David Weiss, Aaron Fait, and Kelem Gashu

Subjects
0106 biological sciences, biology, Red Cell, Chemistry, 010401 analytical chemistry, food and beverages, DAHP synthase, Viniferin, Phenylalanine, Promoter, General Chemistry, Resveratrol, 01 natural sciences, 0104 chemical sciences, Metabolic engineering, chemistry.chemical_compound, Biochemistry, Cell culture, biology.protein, General Agricultural and Biological Sciences, 010606 plant biology & botany
Abstract

Stilbenes are phytoalexins with health-promoting benefits for humans. Here, we boost stilbenes' production, and in particular the resveratrol dehydrodimer viniferin, with significant pharmacological properties, by overexpressing stilbene synthase (STS) under unlimited phenylalanine (Phe) supply. Vitis vinifera cell cultures were co-transformed with a feedback-insensitive E. coli DAHP synthase (AroG*) and STS genes, under constitutive promoters. All transgenic lines had increased levels of Phe and stilbenes (74-fold higher viniferin reaching 0.74 mg/g DW). External Phe feeding of AroG* + STS lines caused a synergistic effect on resveratrol and viniferin accumulation, achieving a 26-fold (1.33 mg/g DW) increase in resveratrol and a 620-fold increase (6.2 mg/g DW) in viniferin, which to date is the highest viniferin accumulation reported in plant cultures. We suggest that this strategy of combining higher Phe availability and STS expression generates grape cell cultures as potential factories for sustainable production of stilbenes with a minor effect on the levels of flavonoids.

Published
2021

4. A Synchronized Increase of Stilbenes and Flavonoids in Metabolically Engineered

Author

Ru, Wang, Sangram Keshari, Lenka, Varun, Kumar, Noga, Sikron-Persi, Irena, Dynkin, David, Weiss, Avichai, Perl, Aaron, Fait, and Michal, Oren-Shamir

Subjects
Anthocyanins, Flavonoids, Gene Expression Regulation, Plant, Fruit, Stilbenes, Cell Culture Techniques, Escherichia coli, Vitis
Abstract

Stilbenes and flavonoids are two major health-promoting phenylpropanoid groups in grapes. Attempts to promote the accumulation of one group usually resulted in a decrease in the other. This study presents a unique strategy for simultaneously increasing metabolites in both groups in

Published
2021

5. Differential Response to Single and Combined Salt and Heat Stresses: Impact on Accumulation of Proteins and Metabolites in Dead Pericarps of Brassica juncea

Author

Jeevan R. Singiri, Bupur Swetha, Gideon Grafi, and Noga Sikron-Persi

Subjects
0106 biological sciences, 0301 basic medicine, QH301-705.5, Metabolite, Brassica juncea, reproductive phase, Brassica, 01 natural sciences, Catalysis, salinity, Inorganic Chemistry, 03 medical and health sciences, chemistry.chemical_compound, Metabolome, Food science, Proline, Biology (General), Physical and Theoretical Chemistry, QD1-999, Molecular Biology, Spectroscopy, chemistry.chemical_classification, biology, short episodes of high temperature, Organic Chemistry, food and beverages, General Medicine, stress response, biology.organism_classification, dead pericarps, Computer Science Applications, Amino acid, Citric acid cycle, Salinity, phytohormones, Chemistry, 030104 developmental biology, chemistry, Composition (visual arts), seed abortion, 010606 plant biology & botany
Abstract

Dead organs enclosing embryos, such as seed coats and pericarps, are emerging as important maternally-derived components of the dispersal unit that affect seed performance and fate. In the face of climate change and increased incidents of heatwaves, we sought to investigate the effect of salinity (S), short episodes of high temperature (HS), and combination of S + HS (SHS), at the reproductive phase, on the properties of dead pericarps of Brassica juncea. Proteome and metabolome analyses revealed multiple proteins and metabolites stored in dead pericarps whose levels and composition were altered under single and combined stress conditions. The protein profile of SHS showed a higher correlation with salt than with HS indicating the dominant effect of salt over heat stress. On the other hand, the analysis of metabolites showed that the profile of SHS has better correlation with HS than with salt. The integration of metabolic and proteomic data showed that changes in TCA cycle intermediates and certain amino acids (e.g., proline) under salt treatments (S and SHS) are highly correlated with changes in proteins involved in their biosynthetic pathways. Thus, accumulation of proteins and metabolites in dead pericarps is differently affected by single and combination of salt and heat stresses. Salinity appears to dominate plant response to combined stresses at the protein level, while heat appears to be the major factor affecting metabolite accumulation in dead pericarps.

Published
2021
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6. Accumulation of newly identified sulfur containing metabolites in Zygophyllum dumosum Boiss suggest for a role of secondary metabolism in petiole survival during the dry season

Author

Noga Sikron-Persi, Gila Granot, Aaron Fait, and Gideon Grafi

Subjects
Dry season, Botany, food and beverages, Plant Science, Zygophyllum, Biology, biology.organism_classification, Sulfur containing, Secondary metabolism, Agronomy and Crop Science, Ecology, Evolution, Behavior and Systematics, Petiole (botany)
Abstract

The biochemical composition of Zygophyllum dumosum Boiss (Zygophyllaceae) was analyzed in petioles collected in the summer and winter from plants growing in a natural ecosystem on a southeast-facing slope of the Negev desert. UPLC-QTOF MS based analysis identified season specific sulfur containing phenylpropanoids unreported in plants. Sulfuric-caffeic and -ferulic acid derivatives and isorhamnetin 3-O-(4-sulfate-rutinoside) were measured to accumulate specifically in the summer. The reported identification and accumulation of sulfate containing metabolites during the hot and dry summer can be related to the putative protective role reported for these compounds.

Published
2019

7. Algorithmic Learning for Auto-deconvolution of GC-MS Data to Enable Molecular Networking within GNPS

Author

Kelem Gashu, Madeleine Ernst, Mélissa Nothias Esposito, Kirill Veselkov, Michael M. Meijler, Robert A. Quinn, Gaud Dervilly, Audrey Poirier, Katherine N. Maloney, tzhak MizrahiI, Chao Song, Thomas O. Metz, Roman S. Borisov, Rob Knight, Mabel Gonzalez, Roxana Coras, Amina Bouslimani, Chiara Carazzone, Vasilis Vasiliou, Alexander A. Aksenov, Wout Bittremieux, Yann Guitton, Daniel Petras, Zheng Zhang, Larisa N. Kulikova, Robin Schmid, Ilaria Belluomo, James T. Morton, Sneha P. Couvillion, Brooke Anderson, Carrie D. Nicora, Kenneth L. Jones, S. Prévost, Sophie L. F. Doran, Louis-Félix Nothias, Dennis Veselkov, Erika M. Zink, Bruno Le Bizec, Andrea M. Smania, Chris Callewaert, Justin J. J. van der Hooft, Rachel Gregor, Pauline Le Boulch, Alexey V. Melnik, Adolfo Amézquita, Biswapriya B. Misra, Noga Sikron Persi, Mingxun Wang, Raphaël Lugan, Rachel Dutton, Morgan Panitchpakdi, Pieter C. Dorrestein, Meagan C. Burnet, Elizabeth Humston Fulmer, Ivan Laponogov, George B. Hanna, Viatcheslav B. Artaev, Kathleen Dorrestein, Aaron Fait, Andrea Georgina Albarracín Orio, Stav Eyal, Skaggs School of Pharmacy and Pharmaceutical Sciences [San Diego], University of California [San Diego] (UC San Diego), University of California-University of California, Collaborative Mass Spectrometry Innovation Center, Imperial College London, University of California, Wake Forest School of Medicine [Winston-Salem], Wake Forest Baptist Medical Center, Statens Serum Institut [Copenhagen], Wageningen University and Research [Wageningen] (WUR), Universidad de los Andes [Bogota] (UNIANDES), Center for Microbial Ecology and Technology (CMET), Universiteit Gent = Ghent University [Belgium] (UGENT), Michigan State University [East Lansing], Michigan State University System, Universidad Católica de Córdoba, Universidad Nacional de Córdoba [Argentina], Pacific Northwest National Laboratory (PNNL), LECO Corporation, Ben-Gurion University of the Negev (BGU), University of San Diego, Démarche intégrée pour l'obtention d'aliments de qualité (UMR QualiSud), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Laboratoire d'étude des Résidus et Contaminants dans les Aliments (LABERCA), Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), New York University School of Medicine (NYU), New York University School of Medicine, NYU System (NYU)-NYU System (NYU), West Coast Metabolomics Center, University of California [Davis] (UC Davis), Max Planck Institute for Molecular Plant Physiology, Center of Plant Systems Biology and Biotechnology [Plovdiv] (CPSBB), NHS Foundation Trust [London], The Royal Marsden, Yale School of Public Health (YSPH), Institute of Inorganic Chemistry and Analytical Chemistry, A.V. Topchiev Institute of Petrochemical Synthesis (TIPS), Russian Academy of Sciences [Moscow] (RAS), and Peoples Friendship University of Russia [RUDN University] (RUDN)

Subjects
0303 health sciences, 03 medical and health sciences, Computer science, [SDV]Life Sciences [q-bio], 010401 analytical chemistry, Molecular networking, Deconvolution, Gas chromatography–mass spectrometry, 01 natural sciences, Data science, 030304 developmental biology, 0104 chemical sciences
Abstract

Gas chromatography-mass spectrometry (GC-MS) represents an analytical technique with significant practical societal impact. Spectral deconvolution is an essential step for interpreting GC-MS data. No public GC-MS repositories that also enable repository-scale analysis exist, in part because deconvolution requires significant user input. We therefore engineered a scalable machine learning workflow for the Global Natural Product Social Molecular Networking (GNPS) analysis platform to enable the mass spectrometry community to store, process, share, annotate, compare, and perform molecular networking of GC-MS data. The workflow performs auto-deconvolution of compound fragmentation patterns via unsupervised non-negative matrix factorization, using a Fast Fourier Transform-based strategy to overcome scalability limitations. We introduce a “balance score” that quantifies the reproducibility of fragmentation patterns across all samples. We demonstrate the utility of the platform with breathomics analysis applied to the early detection of oesophago-gastric cancer, and by creating the first molecular spatial map of the human volatilome.

Published
2021

8. Metabolic Engineering Strategy Enables a Hundred-Fold Increase in Viniferin Levels in

Author

Ru, Wang, Sangram Keshari, Lenka, Varun, Kumar, Kelem, Gashu, Noga, Sikron-Persi, Irena, Dynkin, David, Weiss, Avichai, Perl, Aaron, Fait, and Michal, Oren-Shamir

Subjects
Metabolic Engineering, Stilbenes, Cell Culture Techniques, Escherichia coli, Humans, Vitis
Abstract

Stilbenes are phytoalexins with health-promoting benefits for humans. Here, we boost stilbenes' production, and in particular the resveratrol dehydrodimer viniferin, with significant pharmacological properties, by overexpressing

Published
2021

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

Author

Ilaria Belluomo, Morgan Panitchpakdi, Aleksandr Smirnov, Mélissa Nothias-Esposito, Alexey V. Melnik, Gaud Dervilly, Rachel J. Dutton, Adolfo Amézquita, Vasilis Vasiliou, Zheng Zhang, Daniel Petras, Carrie D. Nicora, Audrey Poirier, James T. Morton, Ivan Laponogov, George B. Hanna, Sneha P. Couvillion, Biswapriya B. Misra, Robin Schmid, Wout Bittremieux, Raphaël Lugan, Brooke A. Anderson, Yann Guitton, Chris Callewaert, Kenneth L. Jones, Robert A. Quinn, Rob Knight, Larisa N. Kulikova, Itzhak Mizrahi, Erika M. Zink, Mabel Gonzalez, Sophie L. F. Doran, Rachel Gregor, Pauline Le Boulch, Kelem Gashu, Xiuxia Du, Michael M. Meijler, Kirill Veselkov, Chao Song, Elizabeth Humston-Fulmer, Noga Sikron Persi, Justin J. J. van der Hooft, Dennis Veselkov, Monica Guma, Kathleen Dorrestein, Saleh Alseekh, Roxana Coras, Chiara Carazzone, Thomas O. Metz, Aaron Fait, Andrea Georgina Albarracín Orio, Alexander A. Aksenov, Jose U. Scher, Andrea M. Smania, Bruno Le Bizec, Stav Eyal, Dinesh Kumar Barupal, Pieter C. Dorrestein, Alisdair R. Fernie, Reza Mirnezami, S. Prévost, Louis-Félix Nothias, Meagan C. Burnet, Viatcheslav B. Artaev, Mingxun Wang, Katherine N. Maloney, Julia Manasson, Madeleine Ernst, Roman S. Borisov, Amina Bouslimani, The Vodafone Foundation, National Institutes of Health, Skaggs School of Pharmacy and Pharmaceutical Sciences [San Diego], University of California [San Diego] (UC San Diego), University of California-University of California, Collaborative Mass Spectrometry Innovation Center, Imperial College London, University of Antwerp (UA), Wake Forest School of Medicine [Winston-Salem], Wake Forest Baptist Medical Center, University of North Carolina [Charlotte] (UNC), University of North Carolina System (UNC), Statens Serum Institut [Copenhagen], Wageningen University and Research [Wageningen] (WUR), Universidad de los Andes [Bogota] (UNIANDES), Center for Microbial Ecology and Technology (CMET), Universiteit Gent = Ghent University [Belgium] (UGENT), University of California, Flatiron Institute, Simons Foundation, Michigan State University [East Lansing], Michigan State University System, Universidad Católica de Córdoba, Universidad Nacional de Córdoba [Argentina], Pacific Northwest National Laboratory (PNNL), LECO Corporation, Ben-Gurion University of the Negev (BGU), Démarche intégrée pour l'obtention d'aliments de qualité (UMR QualiSud), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Laboratoire d'étude des Résidus et Contaminants dans les Aliments (LABERCA), Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), New York University School of Medicine (NYU), New York University School of Medicine, NYU System (NYU)-NYU System (NYU), Icahn School of Medicine at Mount Sinai [New York] (MSSM), Center of Plant Systems Biology and Biotechnology [Plovdiv] (CPSBB), Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, NHS Foundation Trust [London], The Royal Marsden, Yale School of Public Health (YSPH), University of Münster, A.V. Topchiev Institute of Petrochemical Synthesis (TIPS), Russian Academy of Sciences [Moscow] (RAS), and Peoples Friendship University of Russia [RUDN University] (RUDN)

Subjects
Computer science, Bioinformatics, [SDV]Life Sciences [q-bio], Biomedical Engineering, MESH: Algorithms, Bioengineering, S Agricultura (General), Mass spectrometry, computer.software_genre, METABOLOMICS, Applied Microbiology and Biotechnology, Gas Chromatography-Mass Spectrometry, Article, Matrix decomposition, 03 medical and health sciences, 0302 clinical medicine, [STAT.ML]Statistics [stat]/Machine Learning [stat.ML], [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Bioinformatica, Metabolomics, Life Science, Animals, Humans, MESH: Metabolomics, Biology, 030304 developmental biology, Q Ciencia (General), 0303 health sciences, Science & Technology, MESH: Gas Chromatography-Mass Spectrometry, Workflow, Biotechnology & Applied Microbiology, Molecular networking, Molecular Medicine, Data mining, Deconvolution, Gas chromatography–mass spectrometry, Anura, computer, Engineering sciences. Technology, Life Sciences & Biomedicine, 030217 neurology & neurosurgery, Algorithms, Biotechnology, REPOSITORY, STANDARDS
Abstract

We engineered a machine learning approach, MSHub, to enable auto-deconvolution of gas chromatography–mass spectrometry (GC–MS) data. We then designed workflows to enable the community to store, process, share, annotate, compare and perform molecular networking of GC–MS data within the Global Natural Product Social (GNPS) Molecular Networking analysis platform. MSHub/GNPS performs auto-deconvolution of compound fragmentation patterns via unsupervised non-negative matrix factorization and quantifies the reproducibility of fragmentation patterns across samples., Fil: Aksenov, Alexander A. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos, Fil: Aksenov, Alexander A. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados Unidos, Fil: Laponogov, Ivan. South Kensington Campus. Imperial College London. Department of Surgery and Cancer; Reino Unido, Fil: Zhang, Zheng. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos, Fil: Doran, Sophie L. F. South Kensington Campus. Imperial College London. Department of Surgery and Cancer; Reino Unido, Fil: Belluomo, Ilaria. South Kensington Campus. Imperial College London. Department of Surgery and Cancer; Reino Unido, Fil: Veselkov, Dennis. Intelligify Limited. Reino Unido. South Kensington Campus. Imperial College. Department of Computing; Reino Unido, Fil: Bittremieux, Wout. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos, Fil: Bittremieux, Wout. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados Unidos, Fil: Bittremieux, Wout. University of Antwerp. Department of Computer Science; Belgica, Fil: Nothias, Louis Felix. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos, Fil: Nothias, Louis Felix. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados Unidos, Fil: Nothias-Esposito, Mélissa. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos, Fil: Nothias-Esposito, Mélissa. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados Unidos, Fil: Maloney, Katherine N. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos, Fil: Maloney, Katherine N. Point Loma Nazarene University. Department of Chemistry; Estados Unidos, Fil: Misra, Biswapriya B. Wake Forest School of Medicine. Section of Molecular Medicine. Department of Internal Medicine. Center for Precision Medicine; Estados Unidos, Fil: Melnik, Alexey V. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos, Fil: Smirnov, Aleksandr. University of North Carolina at Charlotte. Department of Bioinformatics and Genomics; Estados Unidos, Fil: Du, Xiuxia. University of North Carolina at Charlotte. Department of Bioinformatics and Genomics; Estados Unidos, Fil: Jones, Kenneth L. University of North Carolina at Charlotte. Department of Bioinformatics and Genomics; Estados Unidos, Fil: Dorrestein, Kathleen. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos, Fil: Dorrestein, Kathleen. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados Unidos, Fil: Panitchpakdi, Morgan. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos, Fil: Ernst, Madeleine. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos, Fil: Ernst, Madeleine. Statens Serum Institut. Danish Center for Neonatal Screening. Department of Congenital Disorders. Section for Clinical Mass Spectrometry; Dinamarca, Fil: van der Hooft, Justin J. J. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos, Fil: van der Hooft, Justin J. J. Wageningen University. Bioinformatics Group; Países Bajos, Fil: Gonzalez, Mabel. Universidad de los Andes. Department of Chemistry; Colombia, Fil: Carazzone, Chiara. Universidad de los Andes. Department of Chemistry; Colombia, Fil: Amézquita, Adolfo. Universidad de los Andes. Department of Biological Sciences; Colombia, Fil: Callewaert, Chris. Center for Microbial Ecology and Technology; Belgica, Fil: Callewaert, Chris. University of California. Department of Pediatrics; Estados Unidos, Fil: Morton, James T. University of California. Department of Pediatrics; Estados Unidos, Fil: Morton, James T. Simons Foundation. Flatiron Institute. Center for Computational Biology; Estados Unidos, Fil: Quinn, Robert A. Michigan State University. Department of Biochemistry and Molecular Biology; Estados Unidos, Fil: Bouslimani, Amina. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos, Fil: Bouslimani, Amina. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados Unidos, Fil: Orio, Andrea Albarracín. Universidad Católica de Córdoba. IRNASUS. CONICET. Facultad de Ciencias Agropecuarias; Argentina, Fil: Petras, Daniel. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos, Fil: Petras, Daniel. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados Unidos, Fil: Smania, Andrea M. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Química Biológica Ranwel Caputto; Argentina, Fil: Smania, Andrea M. Centro de Investigaciones en Química Biológica de Córdoba. Universidad Nacional de Córdoba. CONICET; Argentina, Fil: Couvillion, Sneha P. Pacific Northwest National Laboratory. Biological Sciences Division; Estados Unidos, Fil: Burnet, Meagan C. Pacific Northwest National Laboratory. Biological Sciences Division; Estados Unidos, Fil: Nicora, Carrie D. Pacific Northwest National Laboratory. Biological Sciences Division; Estados Unidos, Fil: Zink, Erika. Pacific Northwest National Laboratory. Biological Sciences Division; Estados Unidos, Fil: Metz, Thomas O. Pacific Northwest National Laboratory. Biological Sciences Division; Estados Unidos, Fil: Artaev, Viatcheslav. LECO Corporation; Estados Unidos, Fil: Humston-Fulmer, Elizabeth. LECO Corporation; Estados Unidos, Fil: Gregor, Rachel. Ben-Gurion University of the Negev. Department of Chemistry and the National Institute for Biotechnology in the Negev; Israel, Fil: Meijler, Michael M. Ben-Gurion University of the Negev. Department of Chemistry and the National Institute for Biotechnology in the Negev; Israel, Fil: Mizrahi, Itzhak. Ben-Gurion University of the Negev. Department of Life Sciences and the National Institute for Biotechnology in the Negev; Israel, Fil: Eyal, Stav. Ben-Gurion University of the Negev. Department of Life Sciences and the National Institute for Biotechnology in the Negev; Israel, Fil: Anderson, Brooke. University of California. Division of Biological Sciences; Estados Unidos, Fil: Dutton, Rachel. University of California. Division of Biological Sciences; Estados Unidos, Fil: Lugan, Raphaël. Université d’Avignon et des Pays du Vaucluse, Agrosciences. UMR Qualisud; Francia, Fil: Boulch, Pauline Le. Université d’Avignon et des Pays du Vaucluse, Agrosciences. UMR Qualisud; Francia, Fil: Guitton, Yann. INRAe. Oniris. Laboratoire d’Etude des Résidus et Contaminants dans les Aliments (LABERCA); Francia, Fil: Prevost, Stephanie. INRAe. Oniris. Laboratoire d’Etude des Résidus et Contaminants dans les Aliments (LABERCA); Francia, Fil: Poirier, Audrey. INRAe. Oniris. Laboratoire d’Etude des Résidus et Contaminants dans les Aliments (LABERCA); Francia, Fil: Dervilly, Gaud. INRAe. Oniris. Laboratoire d’Etude des Résidus et Contaminants dans les Aliments (LABERCA); Francia, Fil: Le Bizec, Bruno. Oniris. Laboratoire d’Etude des Résidus et Contaminants dans les Aliments (LABERCA); Francia, Fil: Fait, Aaron. Ben Gurion University of the Negev. Sede Boqer Campus. The Jacob Blaustein Institutes for Desert Research. The French Associates Institute for Agriculture and Biotechnology of Dryland; Israel, Fil: Persi, Noga Sikron. Ben Gurion University of the Negev. Sede Boqer Campus. The Jacob Blaustein Institutes for Desert Research. The French Associates Institute for Agriculture and Biotechnology of Dryland; Israel, Fil: Song, Chao. Ben Gurion University of the Negev. Sede Boqer Campus. The Jacob Blaustein Institutes for Desert Research. The French Associates Institute for Agriculture and Biotechnology of Dryland; Israel, Fil: Gashu, Kelem. Ben Gurion University of the Negev. Sede Boqer Campus. The Jacob Blaustein Institutes for Desert Research. The French Associates Institute for Agriculture and Biotechnology of Dryland; Israel, Fil: Coras, Roxana. University of California. Department of Medicine. Division of Rheumatology; Estados Unidos, Fil: Guma, Monica. University of California. Department of Medicine. Division of Rheumatology; Estados Unidos, Fil: Manasson, Julia. New York University School of Medicine. Department of Medicine. Division of Rheumatology; Estados Unidos, Fil: Scher, Jose U. New York University School of Medicine. Department of Medicine. Division of Rheumatology; Estados Unidos, Fil: Barupal, Dinesh Kumar. Icahn School of Medicine at Mount Sinai. Department of Environmental Medicine and Public Health; Estados Unidos, Fil: Alseekh, Saleh. Max Planck Institute for Molecular Plant Physiology; Alemania, Fil: Alseekh, Saleh. Center of Plant Systems Biology and Biotechnology (CPSBB); Bulgaria, Fil: Fernie, Alisdair R. Max Planck Institute for Molecular Plant Physiology; Alemania, Fil: Fernie, Alisdair R. Center of Plant Systems Biology and Biotechnology (CPSBB); Bulgaria, Fil: Mirnezami, Reza. Royal Free Hospital NHS Foundation Trust. Department of Colorectal Surgery; Reino Unido, Fil: Vasiliou, Vasilis. Yale University. Yale School of Public Health. Department of Environmental Health Sciences; Estados Unidos, Fil: Schmid, Robin. University of Münster. Institute of Inorganic and Analytical Chemistry; Alemania, Fil: Borisov, Roman S. A.V. Topchiev Institute of Petrochemical Synthesis RAS; Rusia, Fil: Kulikova, Larisa N. Рeoples’ Friendship University of Russia (RUDN University); Rusia, Fil: Knight, Rob. University of California. Department of Pediatrics; Estados Unidos, Fil: Knight, Rob. University of California. UCSD Center for Microbiome Innovation; Estados Unidos, Fil: Knight, Rob. University of California. Department of Bioengineering; Estados Unidos, Fil: Wang, Mingxun. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos, Fil: Wang, Mingxun. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados Unidos, Fil: Hanna, George B. South Kensington Campus. Imperial College London. Department of Surgery and Cancer; Reino Unido, Fil: Dorrestein, Pieter C. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos, Fil: Dorrestein, Pieter C. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados Unidos, Fil: Dorrestein, Pieter C. University of California. Department of Pediatrics; Estados Unidos, Fil: Veselkov, Kirill. South Kensington Campus. Imperial College London. Department of Surgery and Cancer; Reino Unido

Published
2020

10. Histone modifications associated with drought tolerance in the desert plant Zygophyllum dumosum Boiss

Author

Susheela Talwara, Ofer Gaspan, Noga Sikron-Persi, Assa Florentin, Yigal Granot, Laju K. Paul, Gideon Grafi, Yaakov Morgenstern, and Gila Granot

Subjects
Wet season, Perennial plant, Zygophyllum, Drought tolerance, ved/biology.organism_classification_rank.species, Plant Science, Genes, Plant, Methylation, Shrub, Histones, Xerophyte, Dry season, Botany, Genetics, Humans, Plant Proteins, biology, ved/biology, Lysine, fungi, Anabasis articulata, Methyltransferases, biology.organism_classification, Adaptation, Physiological, Droughts, Plant Leaves, Repressor Proteins, Cell Nucleus Size, Seasons, Desert Climate, Protein Processing, Post-Translational
Abstract

Zygophyllum dumosum Boiss. is a perennial Saharo-Arabian phytogeographical element and a dominant shrub on the rocky limestone southeast-facing slopes of the Negev desert. The plant is highly active during the winter, and semideciduous during the dry summer, i.e., it sheds its leaflets, while leaving the thick, fleshy petiole green and rather active during the dry season. Being resistant to extreme perennial drought, Z. dumosum appears to provide an intriguing model plant for studying epigenetic mechanisms associated with drought tolerance in natural habitats. The transition from the wet to the dry season was accompanied by a significant decrease in nuclear size and with posttranslational modifications of histone H3 N-terminal tail. Dimethylation of H3 at lysine 4 (H3K4)--a modification associated with active gene expression--was found to be high during the wet season but gradually diminished on progression to the dry season. Unexpectedly, H3K9 di- and trimethylation as well as H3K27 di- and trimethylation could not be detected in Z. dumosum; H3K9 monomethylation appears to be prominent in Z. dumosum during the wet but not during the dry season. Contrary to Z. dumosum, H3K9 dimethylation was detected in other desert plants, including Artemisia sieberi, Anabasis articulata and Haloxylon scoparium. Taken together, our results demonstrate dynamic genome organization and unique pattern of histone H3 methylation displayed by Z. dumosum, which could have an adaptive value in variable environments of the Negev desert.

Published
2009

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