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Zhang J, Aroca A, Hervás M, Navarro JA, Moreno I, Xie Y, Romero LC, Gotor C. Analysis of sulfide signaling in rice highlights specific drought responses. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5130-5145. [PMID: 38808567 PMCID: PMC11349868 DOI: 10.1093/jxb/erae249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/26/2024] [Indexed: 05/30/2024]
Abstract
Hydrogen sulfide regulates essential plant processes, including adaptation responses to stress situations, and the best characterized mechanism of action of sulfide consists of the post-translational modification of persulfidation. In this study, we reveal the first persulfidation proteome described in rice including 3443 different persulfidated proteins that participate in a broad range of biological processes and metabolic pathways. In addition, comparative proteomics revealed specific proteins involved in sulfide signaling during drought responses. Several proteins are involved in the maintenance of cellular redox homeostasis, the tricarboxylic acid cycle and energy-related pathways, and ion transmembrane transport and cellular water homeostasis, with the aquaporin family showing the highest differential levels of persulfidation. We revealed that water transport activity is regulated by sulfide which correlates with an increasing level of persulfidation of aquaporins. Our findings emphasize the impact of persulfidation on total ATP levels, fatty acid composition, levels of reactive oxygen species, antioxidant enzymatic activities, and relative water content. Interestingly, the role of persulfidation in aquaporin transport activity as an adaptation response in rice differs from current knowledge of Arabidopsis, which highlights the distinct role of sulfide in improving rice tolerance to drought.
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Affiliation(s)
- Jing Zhang
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, 49, 41092 Seville, Spain
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Angeles Aroca
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, 49, 41092 Seville, Spain
| | - Manuel Hervás
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, 49, 41092 Seville, Spain
| | - José A Navarro
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, 49, 41092 Seville, Spain
| | - Inmaculada Moreno
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, 49, 41092 Seville, Spain
| | - Yanjie Xie
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Luis C Romero
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, 49, 41092 Seville, Spain
| | - Cecilia Gotor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, 49, 41092 Seville, Spain
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2
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Zhu F, Ahchige MW, Wen W, Cheng Y, Alseekh S, Fernie AR. The natural variance of Arabidopsis secondary metabolism on extended darkness. Sci Data 2024; 11:841. [PMID: 39097666 PMCID: PMC11297995 DOI: 10.1038/s41597-024-03694-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 07/29/2024] [Indexed: 08/05/2024] Open
Abstract
In plants due to their sessile nature, secondary metabolites are important components against different abiotic and biotic stress, such as extended darkness. For this reason, the variation of secondary metabolite content of the Arabidopsis thaliana HapMap natural population following 0-and 6-d darkness treatment were detected and the raw data of different accessions at two timepoints were deposited in the Zenodo database. Moreover, the annotated secondary metabolites of these samples are presented in this data descriptor, which we believe will be a usefully re-usable resource for future integrative analysis with dark-treated transcripts, proteins or other phenotypic data in order to comprehensively illustrate the multiomic landscape of Arabidopsis in response to the stresses exerted by extended darkness.
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Affiliation(s)
- Feng Zhu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, National R&D Center for Citrus Preservation, Huazhong Agricultural University, 430070, Wuhan, China
- Hubei Hongshan Laboratory, 430070, Wuhan, China
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Micha Wijesingha Ahchige
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Weiwei Wen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, National R&D Center for Citrus Preservation, Huazhong Agricultural University, 430070, Wuhan, China
- Hubei Hongshan Laboratory, 430070, Wuhan, China
| | - Yunjiang Cheng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, National R&D Center for Citrus Preservation, Huazhong Agricultural University, 430070, Wuhan, China
- Hubei Hongshan Laboratory, 430070, Wuhan, China
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
- Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria.
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
- Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria.
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3
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Stavrakeva K, Metodieva K, Benina M, Bivolarska A, Dimov I, Choneva M, Kokova V, Alseekh S, Ivanova V, Vatov E, Gechev T, Mladenova T, Mladenov R, Todorov K, Stoyanov P, Gyuzeleva D, Popova M, Apostolova E. Metabolic Composition of Methanolic Extract of the Balkan Endemic Species Micromeria frivaldszkyana (Degen) Velen and Its Anti-Inflammatory Effect on Male Wistar Rats. Int J Mol Sci 2024; 25:5396. [PMID: 38791434 PMCID: PMC11121417 DOI: 10.3390/ijms25105396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/30/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Extracts from medicinal plants are widely used in the treatment and prevention of different diseases. Micromeria frivaldszkyana is a Balkan endemic species with reported antioxidant and antimicrobial characteristics; however, its phytochemical composition is not well defined. Here, we examined the metabolome of M. frivaldszkyana by chromatography-mass spectrometry (GC-MS), ultra-performance liquid chromatography-mass spectrometry (UPLC-MS-MS), and inductively coupled plasma mass spectrometry (ICP-MS). Amino acids, organic acids, sugars, and sugar alcohols were the primary metabolites with the highest levels in the plant extract. Detailed analysis of the sugar content identified high levels of sucrose, glucose, mannose, and fructose. Lipids are primary plant metabolites, and the analysis revealed triacylglycerols as the most abundant lipid group. Potassium (K), magnesium (Mg), zinc (Zn), and calcium (Ca) were the elements with the highest content. The results showed linarin, 3-caffeoil-quinic acid, and rosmarinic acid, as well as a number of polyphenols, as the most abundant secondary metabolites. Among the flavonoids and polyphenols with a high presence were eupatorin, kaempferol, and apigenin-compounds widely known for their bioactive properties. Further, the acute toxicity and potential anti-inflammatory activity of the methanolic extract were evaluated in Wistar rats. No toxic effects were registered after a single oral application of the extract in doses of between 200 and 5000 mg/kg bw. A fourteen-day pre-treatment with methanolic extract of M. frivaldszkyana in doses of 250, 400, and 500 mg/kg bw induced anti-inflammatory activity in the 1st, 2nd, and 3rd hours after carrageenan injection in a model of rat paw edema. This effect was also present in the 4th hour only in the group treated with a dose of 500 mg/kg. In conclusion, M. frivaldszkyana extract is particularly rich in linarin, rosmarinic acid, and flavonoids (eupatorin, kaempferol, and apigenin). Its methanolic extract induced no toxicity in male Wistar rats after oral application in doses of up to 5000 mg/kg bw. Additionally, treatment with the methanolic extract for 14 days revealed anti-inflammatory potential in a model of rat paw edema on the 1st, 2nd, and 3rd hours after the carrageenan injection. These results show the anti-inflammatory potential of the plant, which might be considered for further exploration and eventual application as a phytotherapeutic agent.
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Affiliation(s)
- Kristina Stavrakeva
- Department of Pharmacology, Toxicology, and Pharmacotherapy, Faculty of Pharmacy, Medical University of Plovdiv, Vasil Aprilov Str. 15A, 4002 Plovdiv, Bulgaria; (K.S.); (V.K.)
| | - Kalina Metodieva
- Department of Medical Biochemistry, Faculty of Pharmacy, Medical University of Plovdiv, Vasil Aprilov Str. 15A, 4002 Plovdiv, Bulgaria; (K.M.); (A.B.); (I.D.); (M.C.)
| | - Maria Benina
- Center of Plant Systems Biology and Biotechnology, 14, Sveti Knyaz Boris I Pokrastitel, Str., 4023 Plovdiv, Bulgaria; (M.B.); (S.A.); (V.I.); (E.V.); (T.G.)
| | - Anelia Bivolarska
- Department of Medical Biochemistry, Faculty of Pharmacy, Medical University of Plovdiv, Vasil Aprilov Str. 15A, 4002 Plovdiv, Bulgaria; (K.M.); (A.B.); (I.D.); (M.C.)
| | - Ivica Dimov
- Department of Medical Biochemistry, Faculty of Pharmacy, Medical University of Plovdiv, Vasil Aprilov Str. 15A, 4002 Plovdiv, Bulgaria; (K.M.); (A.B.); (I.D.); (M.C.)
| | - Mariya Choneva
- Department of Medical Biochemistry, Faculty of Pharmacy, Medical University of Plovdiv, Vasil Aprilov Str. 15A, 4002 Plovdiv, Bulgaria; (K.M.); (A.B.); (I.D.); (M.C.)
| | - Vesela Kokova
- Department of Pharmacology, Toxicology, and Pharmacotherapy, Faculty of Pharmacy, Medical University of Plovdiv, Vasil Aprilov Str. 15A, 4002 Plovdiv, Bulgaria; (K.S.); (V.K.)
| | - Saleh Alseekh
- Center of Plant Systems Biology and Biotechnology, 14, Sveti Knyaz Boris I Pokrastitel, Str., 4023 Plovdiv, Bulgaria; (M.B.); (S.A.); (V.I.); (E.V.); (T.G.)
- Max Planck Institute of Molecular Plant Physiology, 1 Am Muehlenberg, 14476 Potsdam, Germany
| | - Valentina Ivanova
- Center of Plant Systems Biology and Biotechnology, 14, Sveti Knyaz Boris I Pokrastitel, Str., 4023 Plovdiv, Bulgaria; (M.B.); (S.A.); (V.I.); (E.V.); (T.G.)
| | - Emil Vatov
- Center of Plant Systems Biology and Biotechnology, 14, Sveti Knyaz Boris I Pokrastitel, Str., 4023 Plovdiv, Bulgaria; (M.B.); (S.A.); (V.I.); (E.V.); (T.G.)
| | - Tsanko Gechev
- Center of Plant Systems Biology and Biotechnology, 14, Sveti Knyaz Boris I Pokrastitel, Str., 4023 Plovdiv, Bulgaria; (M.B.); (S.A.); (V.I.); (E.V.); (T.G.)
| | - Tsvetelina Mladenova
- Department of Botany and Biological Education, Faculty of Biology, University of Plovdiv “Paisii Hilendarski”, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria; (T.M.); (R.M.); (K.T.); (P.S.); (D.G.)
| | - Rumen Mladenov
- Department of Botany and Biological Education, Faculty of Biology, University of Plovdiv “Paisii Hilendarski”, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria; (T.M.); (R.M.); (K.T.); (P.S.); (D.G.)
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Medical University of Plovdiv, Vasil Aprilov Str. 15A, 4002 Plovdiv, Bulgaria
| | - Krasimir Todorov
- Department of Botany and Biological Education, Faculty of Biology, University of Plovdiv “Paisii Hilendarski”, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria; (T.M.); (R.M.); (K.T.); (P.S.); (D.G.)
| | - Plamen Stoyanov
- Department of Botany and Biological Education, Faculty of Biology, University of Plovdiv “Paisii Hilendarski”, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria; (T.M.); (R.M.); (K.T.); (P.S.); (D.G.)
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Medical University of Plovdiv, Vasil Aprilov Str. 15A, 4002 Plovdiv, Bulgaria
| | - Donika Gyuzeleva
- Department of Botany and Biological Education, Faculty of Biology, University of Plovdiv “Paisii Hilendarski”, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria; (T.M.); (R.M.); (K.T.); (P.S.); (D.G.)
| | - Mihaela Popova
- Faculty of Pharmacy, Medical University of Plovdiv, Vasil Aprilov Str. 15A, 4002 Plovdiv, Bulgaria;
| | - Elisaveta Apostolova
- Department of Pharmacology, Toxicology, and Pharmacotherapy, Faculty of Pharmacy, Medical University of Plovdiv, Vasil Aprilov Str. 15A, 4002 Plovdiv, Bulgaria; (K.S.); (V.K.)
- Research Institute, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria
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Lee SY, Jang SJ, Jeong HB, Lee JH, Kim GW, Venkatesh J, Back S, Kwon JK, Choi DM, Kim JI, Kim GJ, Kang BC. Leaky mutations in the zeaxanthin epoxidase in Capsicum annuum result in bright-red fruit containing a high amount of zeaxanthin. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:469-487. [PMID: 38180307 DOI: 10.1111/tpj.16619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/21/2023] [Indexed: 01/06/2024]
Abstract
Fruit color is one of the most important traits in peppers due to its esthetic value and nutritional benefits and is determined by carotenoid composition, resulting from diverse mutations of carotenoid biosynthetic genes. The EMS204 line, derived from an EMS mutant population, presents bright-red color, compared with the wild type Yuwolcho cultivar. HPLC analysis indicates that EMS204 fruit contains more zeaxanthin and less capsanthin and capsorubin than Yuwolcho. MutMap was used to reveal the color variation of EMS204 using an F3 population derived from a cross of EMS204 and Yuwolcho, and the locus was mapped to a 2.5-Mbp region on chromosome 2. Among the genes in the region, a missense mutation was found in ZEP (zeaxanthin epoxidase) that results in an amino acid sequence alteration (V291 → I). A color complementation experiment with Escherichia coli and ZEP in vitro assay using thylakoid membranes revealed decreased enzymatic activity of EMS204 ZEP. Analysis of endogenous plant hormones revealed a significant reduction in abscisic acid content in EMS204. Germination assays and salinity stress experiments corroborated the lower ABA levels in the seeds. Virus-induced gene silencing showed that ZEP silencing also results in bright-red fruit containing less capsanthin but more zeaxanthin than control. A germplasm survey of red color accessions revealed no similar carotenoid profiles to EMS204. However, a breeding line containing a ZEP mutation showed a very similar carotenoid profile to EMS204. Our results provide a novel breeding strategy to develop red pepper cultivars containing high zeaxanthin contents using ZEP mutations.
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Affiliation(s)
- Seo-Young Lee
- Department of Agriculture, Forestry, and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - So-Jeong Jang
- Department of Agriculture, Forestry, and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Hyo-Bong Jeong
- Department of Agriculture, Forestry, and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Joung-Ho Lee
- Department of Agriculture, Forestry, and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Geon Woo Kim
- Department of Agriculture, Forestry, and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jelli Venkatesh
- Department of Agriculture, Forestry, and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Seungki Back
- Department of Agriculture, Forestry, and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jin-Kyung Kwon
- Department of Agriculture, Forestry, and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Da-Min Choi
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Jeong-Il Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, 61186, Republic of Korea
- Kumho Life Science Laboratory, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Geun-Joong Kim
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Byoung-Cheorl Kang
- Department of Agriculture, Forestry, and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
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5
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Park M, Shin SY, Moon H, Choi W, Shin C. Analysis of the global transcriptome and miRNAome associated with seed dormancy during seed maturation in rice (Oryza sativa L. cv. Nipponbare). BMC PLANT BIOLOGY 2024; 24:215. [PMID: 38532331 DOI: 10.1186/s12870-024-04928-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 03/19/2024] [Indexed: 03/28/2024]
Abstract
BACKGROUND Seed dormancy is a biological mechanism that prevents germination until favorable conditions for the subsequent generation of plants are encountered. Therefore, this mechanism must be effectively established during seed maturation. Studies investigating the transcriptome and miRNAome of rice embryos and endosperms at various maturation stages to evaluate seed dormancy are limited. This study aimed to compare the transcriptome and miRNAome of rice seeds during seed maturation. RESULTS Oryza sativa L. cv. Nipponbare seeds were sampled for embryos and endosperms at three maturation stages: 30, 45, and 60 days after heading (DAH). The pre-harvest sprouting (PHS) assay was conducted to assess the level of dormancy in the seeds at each maturation stage. At 60 DAH, the PHS rate was significantly increased compared to those at 30 and 45 DAH, indicating that the dormancy is broken during the later maturation stage (45 DAH to 60 DAH). However, the largest number of differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRs) were identified between 30 and 60 DAH in the embryo and endosperm, implying that the gradual changes in genes and miRNAs from 30 to 60 DAH may play a significant role in breaking seed dormancy. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses confirmed that DEGs related to plant hormones were most abundant in the embryo during 45 DAH to 60 DAH and 30 DAH to 60 DAH transitions. Alternatively, most of the DEGs in the endosperm were related to energy and abiotic stress. MapMan analysis and quantitative real-time polymerase chain reaction identified four newly profiled auxin-related genes (OsSAUR6/12/23/25) and one ethylene-related gene (OsERF087), which may be involved in seed dormancy during maturation. Additionally, miRNA target prediction (psRNATarget) and degradome dataset (TarDB) indicated a potential association between osa-miR531b and ethylene biosynthesis gene (OsACO4), along with osa-miR390-5p and the abscisic acid (ABA) exporter-related gene (OsMATE19) as factors involved in seed dormancy. CONCLUSIONS Analysis of the transcriptome and miRNAome of rice embryos and endosperms during seed maturation provided new insights into seed dormancy, particularly its relationship with plant hormones such as ABA, auxin, and ethylene.
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Affiliation(s)
- Minsu Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sang-Yoon Shin
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hongman Moon
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Woochang Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Chanseok Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea.
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea.
- Research Center for Plant Plasticity, Seoul National University, Seoul, 08826, Republic of Korea.
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6
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Westhoff P, Weber APM. The role of metabolomics in informing strategies for improving photosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1696-1713. [PMID: 38158893 DOI: 10.1093/jxb/erad508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
Photosynthesis plays a vital role in acclimating to and mitigating climate change, providing food and energy security for a population that is constantly growing, and achieving an economy with zero carbon emissions. A thorough comprehension of the dynamics of photosynthesis, including its molecular regulatory network and limitations, is essential for utilizing it as a tool to boost plant growth, enhance crop yields, and support the production of plant biomass for carbon storage. Photorespiration constrains photosynthetic efficiency and contributes significantly to carbon loss. Therefore, modulating or circumventing photorespiration presents opportunities to enhance photosynthetic efficiency. Over the past eight decades, substantial progress has been made in elucidating the molecular basis of photosynthesis, photorespiration, and the key regulatory mechanisms involved, beginning with the discovery of the canonical Calvin-Benson-Bassham cycle. Advanced chromatographic and mass spectrometric technologies have allowed a comprehensive analysis of the metabolite patterns associated with photosynthesis, contributing to a deeper understanding of its regulation. In this review, we summarize the results of metabolomics studies that shed light on the molecular intricacies of photosynthetic metabolism. We also discuss the methodological requirements essential for effective analysis of photosynthetic metabolism, highlighting the value of this technology in supporting strategies aimed at enhancing photosynthesis.
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Affiliation(s)
- Philipp Westhoff
- CEPLAS Plant Metabolomics and Metabolism Laboratory, Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
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7
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Yoshida T, Fernie AR. Hormonal regulation of plant primary metabolism under drought. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1714-1725. [PMID: 37712613 DOI: 10.1093/jxb/erad358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/13/2023] [Indexed: 09/16/2023]
Abstract
Phytohormones are essential signalling molecules globally regulating many processes of plants, including their growth, development, and stress responses. The promotion of growth and the enhancement of stress resistance have to be balanced, especially under adverse conditions such as drought stress, because of limited resources. Plants cope with drought stress via various strategies, including the transcriptional regulation of stress-responsive genes and the adjustment of metabolism, and phytohormones play roles in these processes. Although abscisic acid (ABA) is an important signal under drought, less attention has been paid to other phytohormones. In this review, we summarize progress in the understanding of phytohormone-regulated primary metabolism under water-limited conditions, especially in Arabidopsis thaliana, and highlight recent findings concerning the amino acids associated with ABA metabolism and signalling. We also discuss how phytohormones function antagonistically and synergistically in order to balance growth and stress responses.
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Affiliation(s)
- Takuya Yoshida
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
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8
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Zhang Y, Wiese L, Fang H, Alseekh S, Perez de Souza L, Scossa F, Molloy J, Christmann M, Fernie AR. Synthetic biology identifies the minimal gene set required for paclitaxel biosynthesis in a plant chassis. MOLECULAR PLANT 2023; 16:1951-1961. [PMID: 37897038 DOI: 10.1016/j.molp.2023.10.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/04/2023] [Accepted: 10/25/2023] [Indexed: 10/29/2023]
Abstract
The diterpenoid paclitaxel (Taxol) is a chemotherapy medication widely used as a first-line treatment against several types of solid cancers. The supply of paclitaxel from natural sources is limited. However, missing knowledge about the genes involved in several specific metabolic steps of paclitaxel biosynthesis has rendered it difficult to engineer the full pathway. In this study, we used a combination of transcriptomics, cell biology, metabolomics, and pathway reconstitution to identify the complete gene set required for the heterologous production of paclitaxel. We identified the missing steps from the current model of paclitaxel biosynthesis and confirmed the activity of most of the missing enzymes via heterologous expression in Nicotiana benthamiana. Notably, we identified a new C4β-C20 epoxidase that could overcome the first bottleneck of metabolic engineering. We used both previously characterized and newly identified oxomutases/epoxidases, taxane 1β-hydroxylase, taxane 9α-hydroxylase, taxane 9α-dioxygenase, and phenylalanine-CoA ligase, to successfully biosynthesize the key intermediate baccatin III and to convert baccatin III into paclitaxel in N. benthamiana. In combination, these approaches establish a metabolic route to taxoid biosynthesis and provide insights into the unique chemistry that plants use to generate complex bioactive metabolites.
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Affiliation(s)
- Youjun Zhang
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria.
| | - Lorenz Wiese
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Hao Fang
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany; Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14476 Potsdam, Germany
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Leonardo Perez de Souza
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Research Center for Genomics and Bioinformatics (CREA-GB), Via Ardeatina 546, 00178 Rome, Italy
| | - John Molloy
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14476 Potsdam, Germany
| | - Mathias Christmann
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria.
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9
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Gyuzeleva D, Benina M, Ivanova V, Vatov E, Alseekh S, Mladenova T, Mladenov R, Todorov K, Bivolarska A, Stoyanov P. Metabolome Profiling of Marrubium peregrinum L. and Marrubium friwaldskyanum Boiss Reveals Their Potential as Sources of Plant-Based Pharmaceuticals. Int J Mol Sci 2023; 24:17035. [PMID: 38069358 PMCID: PMC10707198 DOI: 10.3390/ijms242317035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/22/2023] [Accepted: 11/25/2023] [Indexed: 12/18/2023] Open
Abstract
Marrubium species have been used since ancient times as food additives and curative treatments. Their phytochemical composition and various pharmacological activities were the focus of a number of scientific investigations but no comprehensive metabolome profiling to identify the numerous primary and secondary metabolites has been performed so far. This study aimed to generate a comprehensive picture of the total metabolite content of two Marrubium species-M. peregrinum and M. friwaldskyanum-to provide detailed information about the main primary and secondary metabolites. In addition, the elemental composition was also evaluated. For this purpose, non-targeted metabolomic analyses were conducted using GC-MS, UPLC-MS/MS and ICP-MS approaches. Nearly 500 compounds and 12 elements were detected and described. The results showed a strong presence of phenolic acids, flavonoids and their glucosides, which are generally of great interest due to their various pharmacological activities. Furthermore, tissue-specific analyses for M. friwaldskyanum stem, leaves and flowers were carried out in order to outline the sources of potentially important bioactive molecules. The results generated from this study depict the Marrubium metabolome and reveal its dual scientific importance-from one side, providing information about the metabolites that is fundamental and vital for the survival of these species, and from the other side, defining the large diversity of secondary substances that are a potential source of phytotherapeutic agents.
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Affiliation(s)
- Donika Gyuzeleva
- Department of Botany and Biological Education, Faculty of Biology, University of Plovdiv “Paisii Hilendarski”, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria; (D.G.); (T.M.)
| | - Maria Benina
- Center of Plant Systems Biology and Biotechnology, 14 Sveti Kniaz Boris I Pokrastitel Str., 4023 Plovdiv, Bulgaria
| | - Valentina Ivanova
- Center of Plant Systems Biology and Biotechnology, 14 Sveti Kniaz Boris I Pokrastitel Str., 4023 Plovdiv, Bulgaria
| | - Emil Vatov
- Center of Plant Systems Biology and Biotechnology, 14 Sveti Kniaz Boris I Pokrastitel Str., 4023 Plovdiv, Bulgaria
| | - Saleh Alseekh
- Center of Plant Systems Biology and Biotechnology, 14 Sveti Kniaz Boris I Pokrastitel Str., 4023 Plovdiv, Bulgaria
- Max Planck Institute for Molecular Plant Physiology, 1, Am Mühlenberg, 14476 Potsdam, Germany
| | - Tsvetelina Mladenova
- Department of Botany and Biological Education, Faculty of Biology, University of Plovdiv “Paisii Hilendarski”, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria; (D.G.); (T.M.)
| | - Rumen Mladenov
- Department of Botany and Biological Education, Faculty of Biology, University of Plovdiv “Paisii Hilendarski”, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria; (D.G.); (T.M.)
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Medical University of Plovdiv, 15A Vasil Aprilov Blvd., 4002 Plovdiv, Bulgaria
| | - Krasimir Todorov
- Department of Botany and Biological Education, Faculty of Biology, University of Plovdiv “Paisii Hilendarski”, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria; (D.G.); (T.M.)
| | - Anelia Bivolarska
- Department of Medical Biochemistry, Faculty of Pharmacy, Medical University of Plovdiv, 15A Vasil Aprilov Blvd., 4002 Plovdiv, Bulgaria
| | - Plamen Stoyanov
- Department of Botany and Biological Education, Faculty of Biology, University of Plovdiv “Paisii Hilendarski”, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria; (D.G.); (T.M.)
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Medical University of Plovdiv, 15A Vasil Aprilov Blvd., 4002 Plovdiv, Bulgaria
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10
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Duque-Jaramillo A, Ulmer N, Alseekh S, Bezrukov I, Fernie AR, Skirycz A, Karasov TL, Weigel D. The genetic and physiological basis of Arabidopsis thaliana tolerance to Pseudomonas viridiflava. THE NEW PHYTOLOGIST 2023; 240:1961-1975. [PMID: 37667565 DOI: 10.1111/nph.19241] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 08/15/2023] [Indexed: 09/06/2023]
Abstract
The opportunistic pathogen Pseudomonas viridiflava colonizes > 50 agricultural crop species and is the most common Pseudomonas in the phyllosphere of European Arabidopsis thaliana populations. Belonging to the P. syringae complex, it is genetically and phenotypically distinct from well-characterized P. syringae sensu stricto. Despite its prevalence, we lack knowledge of how A. thaliana responds to its native isolates at the molecular level. Here, we characterize the host response in an A. thaliana - P. viridiflava pathosystem. We measured host and pathogen growth in axenic infections and used immune mutants, transcriptomics, and metabolomics to determine defense pathways influencing susceptibility to P. viridiflava infection. Infection with P. viridiflava increased jasmonic acid (JA) levels and the expression of ethylene defense pathway marker genes. The immune response in a susceptible host accession was delayed compared with a tolerant one. Mechanical injury rescued susceptibility, consistent with an involvement of JA. The JA/ethylene pathway is important for suppression of P. viridiflava, yet suppression capacity varies between accessions. Our results shed light on how A. thaliana can suppress the ever-present P. viridiflava, but further studies are needed to understand how P. viridiflava evades this suppression to spread broadly across A. thaliana populations.
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Affiliation(s)
| | - Nina Ulmer
- Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Ilja Bezrukov
- Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Aleksandra Skirycz
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
- Boyce Thompson Institute, Cornell University, Ithaca, 14850, USA
| | - Talia L Karasov
- Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
- School of Biological Sciences, University of Utah, Salt Lake City, 84112, USA
| | - Detlef Weigel
- Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, 72074, Germany
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11
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Bulut M, Wendenburg R, Bitocchi E, Bellucci E, Kroc M, Gioia T, Susek K, Papa R, Fernie AR, Alseekh S. A comprehensive metabolomics and lipidomics atlas for the legumes common bean, chickpea, lentil and lupin. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1152-1171. [PMID: 37285370 DOI: 10.1111/tpj.16329] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/09/2023] [Accepted: 05/24/2023] [Indexed: 06/09/2023]
Abstract
Legumes represent an important component of human and livestock diets; they are rich in macro- and micronutrients such as proteins, dietary fibers and polyunsaturated fatty acids. Whilst several health-promoting and anti-nutritional properties have been associated with grain content, in-depth metabolomics characterization of major legume species remains elusive. In this article, we used both gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) to assess the metabolic diversity in the five legume species commonly grown in Europe, including common bean (Phaseolus vulgaris), chickpea (Cicer arietinum), lentil (Lens culinaris), white lupin (Lupinus albus) and pearl lupin (Lupinus mutabilis), at the tissue level. We were able to detect and quantify over 3400 metabolites covering major nutritional and anti-nutritional compounds. Specifically, the metabolomics atlas includes 224 derivatized metabolites, 2283 specialized metabolites and 923 lipids. The data generated here will serve the community as a basis for future integration to metabolomics-assisted crop breeding and facilitate metabolite-based genome-wide association studies to dissect the genetic and biochemical bases of metabolism in legume species.
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Affiliation(s)
- Mustafa Bulut
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Regina Wendenburg
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, Ancona, 60131, Italy
| | - Elisa Bellucci
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, Ancona, 60131, Italy
| | - Magdalena Kroc
- Legume Genomics Team, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, Poznan, 60-479, Poland
| | - Tania Gioia
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, 85100, Italy
| | - Karolina Susek
- Legume Genomics Team, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, Poznan, 60-479, Poland
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, Ancona, 60131, Italy
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center for Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center for Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
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12
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Vrobel O, Tarkowski P. Can plant hormonomics be built on simple analysis? A review. PLANT METHODS 2023; 19:107. [PMID: 37833752 PMCID: PMC10576392 DOI: 10.1186/s13007-023-01090-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/08/2023] [Indexed: 10/15/2023]
Abstract
The field of plant hormonomics focuses on the qualitative and quantitative analysis of the hormone complement in plant samples, akin to other omics sciences. Plant hormones, alongside primary and secondary metabolites, govern vital processes throughout a plant's lifecycle. While active hormones have received significant attention, studying all related compounds provides valuable insights into internal processes. Conventional single-class plant hormone analysis employs thorough sample purification, short analysis and triple quadrupole tandem mass spectrometry. Conversely, comprehensive hormonomics analysis necessitates minimal purification, robust and efficient separation and better-performing mass spectrometry instruments. This review summarizes the current status of plant hormone analysis methods, focusing on sample preparation, advances in chromatographic separation and mass spectrometric detection, including a discussion on internal standard selection and the potential of derivatization. Moreover, current approaches for assessing the spatiotemporal distribution are evaluated. The review touches on the legitimacy of the term plant hormonomics by exploring the current status of methods and outlining possible future trends.
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Affiliation(s)
- Ondřej Vrobel
- Department of Biochemistry, Faculty of Science, Palacky University, Olomouc, Czech Republic
- Czech Advanced Technology and Research Institute, Palacky University, Olomouc, Czech Republic
- Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Crop Research Institute, Olomouc, Czech Republic
| | - Petr Tarkowski
- Czech Advanced Technology and Research Institute, Palacky University, Olomouc, Czech Republic.
- Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Crop Research Institute, Olomouc, Czech Republic.
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13
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Segarra-Medina C, Alseekh S, Fernie AR, Rambla JL, Pérez-Clemente RM, Gómez-Cádenas A, Zandalinas SI. Abscisic acid promotes plant acclimation to the combination of salinity and high light stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108008. [PMID: 37690143 DOI: 10.1016/j.plaphy.2023.108008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/24/2023] [Accepted: 09/05/2023] [Indexed: 09/12/2023]
Abstract
Plants encounter combinations of different abiotic stresses such as salinity (S) and high light (HL). These environmental conditions have a detrimental effect on plant growth and development, posing a threat to agricultural production. Metabolic changes play a crucial role in enabling plants to adapt to fluctuations in their environment. Furthermore, hormones such as abscisic acid (ABA), jasmonic acid (JA) and salicylic acid (SA) have been previously identified as regulators of plant responses to different abiotic stresses. Here we studied the response of Arabidopsis wild type (Col and Ler) plants and mutants impaired in hormone biosynthesis (aba2-11 and aba1-1 in ABA, aos in JA and sid2 in SA) to the combination of S and HL (S + HL). Our findings showed that aba2-11 plants displayed reduced growth, impaired photosystem II (PSII) function, increased leaf damage, and decreased survival compared to Col when subjected to stress combination. However, aos and sid2 mutants did not display significant changes in response to S + HL compared to Col, indicating a key role for ABA in promoting plant tolerance to S + HL and suggesting a marginal role for JA and SA in this process. In addition, we revealed differences in the metabolic response of plants to S + HL compared to S or HL. The analysis of altered metabolic pathways under S + HL suggested that the accumulation of flavonoids is ABA-dependent, whereas the accumulation of branched-chain amino acids (BCAAs) and proline is ABA-independent. Therefore, our study uncovered a key function for ABA in regulating the accumulation of different flavonoids in plants during S + HL.
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Affiliation(s)
- Clara Segarra-Medina
- Department of Biology, Biochemistry and Natural Sciences, Universitat Jaume I, 12071, Castellón, Spain
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany; Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany; Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - José L Rambla
- Department of Biology, Biochemistry and Natural Sciences, Universitat Jaume I, 12071, Castellón, Spain
| | - Rosa M Pérez-Clemente
- Department of Biology, Biochemistry and Natural Sciences, Universitat Jaume I, 12071, Castellón, Spain
| | - Aurelio Gómez-Cádenas
- Department of Biology, Biochemistry and Natural Sciences, Universitat Jaume I, 12071, Castellón, Spain.
| | - Sara I Zandalinas
- Department of Biology, Biochemistry and Natural Sciences, Universitat Jaume I, 12071, Castellón, Spain.
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14
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Oh SW, Imran M, Kim EH, Park SY, Lee SG, Park HM, Jung JW, Ryu TH. Approach strategies and application of metabolomics to biotechnology in plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1192235. [PMID: 37636096 PMCID: PMC10451086 DOI: 10.3389/fpls.2023.1192235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023]
Abstract
Metabolomics refers to the technology for the comprehensive analysis of metabolites and low-molecular-weight compounds in a biological system, such as cells or tissues. Metabolites play an important role in biological phenomena through their direct involvement in the regulation of physiological mechanisms, such as maintaining cell homeostasis or signal transmission through protein-protein interactions. The current review aims provide a framework for how the integrated analysis of metabolites, their functional actions and inherent biological information can be used to understand biological phenomena related to the regulation of metabolites and how this information can be applied to safety assessments of crops created using biotechnology. Advancement in technology and analytical instrumentation have led new ways to examine the convergence between biology and chemistry, which has yielded a deeper understanding of complex biological phenomena. Metabolomics can be utilized and applied to safety assessments of biotechnology products through a systematic approach using metabolite-level data processing algorithms, statistical techniques, and database development. The integration of metabolomics data with sequencing data is a key step towards improving additional phenotypical evidence to elucidate the degree of environmental affects for variants found in genome associated with metabolic processes. Moreover, information analysis technology such as big data, machine learning, and IT investment must be introduced to establish a system for data extraction, selection, and metabolomic data analysis for the interpretation of biological implications of biotechnology innovations. This review outlines the integrity of metabolomics assessments in determining the consequences of genetic engineering and biotechnology in plants.
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15
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Fiorillo A, Parmagnani AS, Visconti S, Mannino G, Camoni L, Maffei ME. 14-3-3 Proteins and the Plasma Membrane H +-ATPase Are Involved in Maize ( Zea mays) Magnetic Induction. PLANTS (BASEL, SWITZERLAND) 2023; 12:2887. [PMID: 37571041 PMCID: PMC10421175 DOI: 10.3390/plants12152887] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023]
Abstract
The geomagnetic field (GMF) is a natural component of the biosphere, and, during evolution, all organisms experienced its presence while some evolved the ability to perceive magnetic fields (MF). We studied the response of 14-3-3 proteins and the plasma membrane (PM) proton pump H+-ATPase to reduced GMF values by lowering the GMF intensity to a near-null magnetic field (NNMF). Seedling morphology, H+-ATPase activity and content, 14-3-3 protein content, binding to PM and phosphorylation, gene expression, and ROS quantification were assessed in maize (Zea mays) dark-grown seedlings. Phytohormone and melatonin quantification were also assessed by LG-MS/MS. Our results suggest that the GMF regulates the PM H+-ATPase, and that NNMF conditions alter the proton pump activity by reducing the binding of 14-3-3 proteins. This effect was associated with both a reduction in H2O2 and downregulation of genes coding for enzymes involved in ROS production and scavenging, as well as calcium homeostasis. These early events were followed by the downregulation of IAA synthesis and gene expression and the increase in both cytokinin and ABA, which were associated with a reduction in root growth. The expression of the homolog of the MagR gene, ZmISCA2, paralleled that of CRY1, suggesting a possible role of ISCA in maize magnetic induction. Interestingly, melatonin, a widespread molecule present in many kingdoms, was increased by the GMF reduction, suggesting a still unknown role of this molecule in magnetoreception.
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Affiliation(s)
- Anna Fiorillo
- Department of Biology, Tor Vergata University of Rome, Via della Ricerca Scientifica, 00133 Rome, Italy; (A.F.); (S.V.)
| | - Ambra S. Parmagnani
- Department of Life Sciences and Systems Biology, University of Turin, Via Quarello 15/a, 10135 Turin, Italy; (A.S.P.); (G.M.)
| | - Sabina Visconti
- Department of Biology, Tor Vergata University of Rome, Via della Ricerca Scientifica, 00133 Rome, Italy; (A.F.); (S.V.)
| | - Giuseppe Mannino
- Department of Life Sciences and Systems Biology, University of Turin, Via Quarello 15/a, 10135 Turin, Italy; (A.S.P.); (G.M.)
| | - Lorenzo Camoni
- Department of Biology, Tor Vergata University of Rome, Via della Ricerca Scientifica, 00133 Rome, Italy; (A.F.); (S.V.)
| | - Massimo E. Maffei
- Department of Life Sciences and Systems Biology, University of Turin, Via Quarello 15/a, 10135 Turin, Italy; (A.S.P.); (G.M.)
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16
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Zeng Q, Johnson KB, Mukhtar S, Nason S, Huntley R, Millet F, Yang CH, Hassani MA, Zuverza-Mena N, Sundin GW. Aureobasidium pullulans from the Fire Blight Biocontrol Product, Blossom Protect, Induces Host Resistance in Apple Flowers. PHYTOPATHOLOGY 2023; 113:1192-1201. [PMID: 36794987 DOI: 10.1094/phyto-12-22-0452-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Fire blight, caused by Erwinia amylovora, is a devastating disease of apple. Blossom Protect, a product that contains Aureobasidium pullulans as the active ingredient, is one of the most effective biological controls of fire blight. It has been postulated that the mode of action of A. pullulans is to compete against and antagonize epiphytic growth of E. amylovora on flowers, but recent studies have found that flowers treated with Blossom Protect harbored similar to or only slightly reduced E. amylovora populations compared with nontreated flowers. In this study, we tested the hypothesis that A. pullulans-mediated biocontrol of fire blight is the result of induced host resistance. We found that PR genes in the systemic acquired resistance pathway, but not genes in the induced systemic resistance pathway, were induced in hypanthial tissue of apple flowers after the Blossom Protect treatment. Additionally, the induction of PR gene expression was coupled with an increase of plant-derived salicylic acid in this tissue. After inoculation with E. amylovora, PR gene expression was suppressed in nontreated flowers, but in flowers pretreated with Blossom Protect, the heightened PR expression offset the immune repression caused by E. amylovora, and prevented infection. Temporal and spatial analysis of PR gene induction showed that induction of PR genes occurred 2 days after the Blossom Protect treatment, and required direct flower-yeast contact. Finally, we observed deterioration of the epidermal layer of the hypanthium in some of the Blossom Protect-treated flowers, suggesting that PR gene induction in flowers may be a result of pathogenesis by A. pullulans.
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Affiliation(s)
- Quan Zeng
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511
| | - Kenneth B Johnson
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Salma Mukhtar
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511
| | - Sara Nason
- Department of Environmental Science and Forestry, The Connecticut Agricultural Experiment Station, New Haven, CT 06511
- Department of Analytical Chemistry, Connecticut Agricultural Experiment Station, New Haven, CT 06511
| | - Regan Huntley
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511
| | - Felicia Millet
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT 06269
| | - Ching-Hong Yang
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211
| | - M Amine Hassani
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511
| | - Nubia Zuverza-Mena
- Department of Analytical Chemistry, Connecticut Agricultural Experiment Station, New Haven, CT 06511
| | - George W Sundin
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824
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17
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López CM, Alseekh S, Torralbo F, Martínez Rivas FJ, Fernie AR, Amil-Ruiz F, Alamillo JM. Transcriptomic and metabolomic analysis reveals that symbiotic nitrogen fixation enhances drought resistance in common bean. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:3203-3219. [PMID: 36883579 DOI: 10.1093/jxb/erad083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/28/2023] [Indexed: 05/21/2023]
Abstract
Common bean (Phaseolus vulgaris L.), one of the most important legume crops, uses atmospheric nitrogen through symbiosis with soil rhizobia, reducing the need for nitrogen fertilization. However, this legume is particularly sensitive to drought conditions, prevalent in arid regions where this crop is cultured. Therefore, studying the response to drought is important to sustain crop productivity. We have used integrated transcriptomic and metabolomic analysis to understand the molecular responses to water deficit in a marker-class common bean accession cultivated under N2 fixation or fertilized with nitrate (NO3-). RNA-seq revealed more transcriptional changes in the plants fertilized with NO3- than in the N2-fixing plants. However, changes in N2-fixing plants were more associated with drought tolerance than in those fertilized with NO3-. N2-fixing plants accumulated more ureides in response to drought, and GC/MS and LC/MS analysis of primary and secondary metabolite profiles revealed that N2-fixing plants also had higher levels of abscisic acid, proline, raffinose, amino acids, sphingolipids, and triacylglycerols than those fertilized with NO3-. Moreover, plants grown under nitrogen fixation recovered from drought better than plants fertilized with NO3-. Altogether we show that common bean plants grown under symbiotic nitrogen fixation were more protected against drought than the plants fertilized with nitrate.
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Affiliation(s)
- Cristina Mª López
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas, Campus de Excelencia Internacional Agroalimentario, CEIA3, Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Fernando Torralbo
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas, Campus de Excelencia Internacional Agroalimentario, CEIA3, Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, 14071 Córdoba, Spain
| | | | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Francisco Amil-Ruiz
- Servicio Central de Apoyo a la Investigación (SCAI), Unidad de Bioinformática, Campus de Rabanales, Córdoba, Spain
| | - Josefa M Alamillo
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas, Campus de Excelencia Internacional Agroalimentario, CEIA3, Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, 14071 Córdoba, Spain
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18
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Wu J, Sun W, Sun C, Xu C, Li S, Li P, Xu H, Zhu D, Li M, Yang L, Wei J, Hanzawa A, Tapati SJ, Uenoyama R, Miyazaki M, Rahman A, Wu S. Cold stress induces malformed tomato fruits by breaking the feedback loops of stem cell regulation in floral meristem. THE NEW PHYTOLOGIST 2023; 237:2268-2283. [PMID: 36564973 DOI: 10.1111/nph.18699] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Fruit malformation is a major constrain in fruit production worldwide resulting in substantial economic losses. The farmers for decades noticed that the chilling temperature before blooming often caused malformed fruits. However, the molecular mechanism underlying this phenomenon is unclear. Here we examined the fruit development in response to cold stress in tomato, and demonstrated that short-term cold stress increased the callose accumulation in both shoot apical and floral meristems, resulting in the symplastic isolation and altered intercellular movement of WUS. In contrast to the rapidly restored SlWUS transcription during the recovery from cold stress, the callose removal was delayed due to obstructed plasmodesmata. The delayed reinstatement of cell-to-cell transport of SlWUS prevented the activation of SlCLV3 and TAG1, causing the interrupted feedback inhibition of SlWUS expression, leading to the expanded stem cell population and malformed fruits. We further showed that the callose dynamics in response to short-term cold stress presumably exploits the mechanism of bud dormancy during the seasonal growth, involving two antagonistic hormones, abscisic acid and gibberellin. Our results provide a novel insight into the cold stress regulated malformation of fruit.
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Affiliation(s)
- Junqing Wu
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenru Sun
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chao Sun
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chunmiao Xu
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shuang Li
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Pengxue Li
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huimin Xu
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Danyang Zhu
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Meng Li
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liling Yang
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jinbo Wei
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Aya Hanzawa
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate, 020-8550, Japan
| | - Sumaiya Jannat Tapati
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate, 020-8550, Japan
| | - Reiko Uenoyama
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate, 020-8550, Japan
| | - Masao Miyazaki
- Department of Biological Chemistry and Food Science, Faculty of Agriculture, Iwate University, Morioka, Iwate, 020-8550, Japan
| | - Abidur Rahman
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate, 020-8550, Japan
- Department of Plant Bio Sciences, Faculty of Agriculture, Iwate University, Morioka, Iwate, 020-8550, Japan
| | - Shuang Wu
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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19
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Julca I, Mutwil-Anderwald D, Manoj V, Khan Z, Lai SK, Yang LK, Beh IT, Dziekan J, Lim YP, Lim SK, Low YW, Lam YI, Tjia S, Mu Y, Tan QW, Nuc P, Choo LM, Khew G, Shining L, Kam A, Tam JP, Bozdech Z, Schmidt M, Usadel B, Kanagasundaram Y, Alseekh S, Fernie A, Li HY, Mutwil M. Genomic, transcriptomic, and metabolomic analysis of Oldenlandia corymbosa reveals the biosynthesis and mode of action of anti-cancer metabolites. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36807520 DOI: 10.1111/jipb.13469] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 02/18/2023] [Indexed: 06/18/2023]
Abstract
Plants accumulate a vast array of secondary metabolites, which constitute a natural resource for pharmaceuticals. Oldenlandia corymbosa belongs to the Rubiaceae family, and has been used in traditional medicine to treat different diseases, including cancer. However, the active metabolites of the plant, their biosynthetic pathway and mode of action in cancer are unknown. To fill these gaps, we exposed this plant to eight different stress conditions and combined different omics data capturing gene expression, metabolic profiles, and anti-cancer activity. Our results show that O. corymbosa extracts are active against breast cancer cell lines and that ursolic acid is responsible for this activity. Moreover, we assembled a high-quality genome and uncovered two genes involved in the biosynthesis of ursolic acid. Finally, we also revealed that ursolic acid causes mitotic catastrophe in cancer cells and identified three high-confidence protein binding targets by Cellular Thermal Shift Assay (CETSA) and reverse docking. Altogether, these results constitute a valuable resource to further characterize the biosynthesis of active metabolites in the Oldenlandia group, while the mode of action of ursolic acid will allow us to further develop this valuable compound.
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Affiliation(s)
- Irene Julca
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | | | - Vaishnervi Manoj
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - Zahra Khan
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - Soak Kuan Lai
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - Lay K Yang
- Shared Analytics, Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, 138671, Singapore
| | - Ing T Beh
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - Jerzy Dziekan
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - Yoon P Lim
- Department of Biochemistry, National University of Singapore, Singapore, 117596, Singapore
| | - Shen K Lim
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, 117596, Singapore
| | - Yee W Low
- Singapore Botanic Gardens, Singapore, 259569, Singapore
| | - Yuen I Lam
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - Seth Tjia
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - Qiao W Tan
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - Przemyslaw Nuc
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, 61-614, Poland
| | - Le M Choo
- Singapore Botanic Gardens, Singapore, 259569, Singapore
| | - Gillian Khew
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
- Singapore Botanic Gardens, Singapore, 259569, Singapore
| | - Loo Shining
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - Antony Kam
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | | | - Bjoern Usadel
- IBG-4 Bioinformatics, Forschungszentrum Jülich, Jülich, 52428, Germany
| | - Yoganathan Kanagasundaram
- Shared Analytics, Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, 138671, Singapore
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, 14476, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Alisdair Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, 14476, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Hoi Y Li
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
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20
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Jeblick T, Leisen T, Steidele CE, Albert I, Müller J, Kaiser S, Mahler F, Sommer F, Keller S, Hückelhoven R, Hahn M, Scheuring D. Botrytis hypersensitive response inducing protein 1 triggers noncanonical PTI to induce plant cell death. PLANT PHYSIOLOGY 2023; 191:125-141. [PMID: 36222581 PMCID: PMC9806589 DOI: 10.1093/plphys/kiac476] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/20/2022] [Indexed: 05/28/2023]
Abstract
According to their lifestyle, plant pathogens are divided into biotrophic and necrotrophic organisms. Biotrophic pathogens exclusively nourish living host cells, whereas necrotrophic pathogens rapidly kill host cells and nourish cell walls and cell contents. To this end, the necrotrophic fungus Botrytis cinerea secretes large amounts of phytotoxic proteins and cell wall-degrading enzymes. However, the precise role of these proteins during infection is unknown. Here, we report on the identification and characterization of the previously unknown toxic protein hypersensitive response-inducing protein 1 (Hip1), which induces plant cell death. We found the adoption of a structurally conserved folded Alternaria alternata Alt a 1 protein structure to be a prerequisite for Hip1 to exert its necrosis-inducing activity in a host-specific manner. Localization and the induction of typical plant defense responses by Hip1 indicate recognition as a pathogen-associated molecular pattern at the plant plasma membrane. In contrast to other secreted toxic Botrytis proteins, the activity of Hip1 does not depend on the presence of the receptor-associated kinases BRI1-associated kinase 1 and suppressor of BIR1-1. Our results demonstrate that recognition of Hip1, even in the absence of obvious enzymatic or pore-forming activity, induces strong plant defense reactions eventually leading to plant cell death. Botrytis hip1 overexpression strains generated by CRISPR/Cas9 displayed enhanced infection, indicating the virulence-promoting potential of Hip1. Taken together, Hip1 induces a noncanonical defense response which might be a common feature of structurally conserved fungal proteins from the Alt a 1 family.
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Affiliation(s)
- Tanja Jeblick
- Plant Pathology, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Thomas Leisen
- Plant Pathology, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Christina E Steidele
- Phytopathology, TUM School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Isabell Albert
- Molecular Plant Physiology, FAU Erlangen, Erlangen 91058, Germany
| | - Jonas Müller
- Plant Pathology, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Sabrina Kaiser
- Plant Pathology, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Florian Mahler
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Frederik Sommer
- Molecular Biotechnology & Systems Biology, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern 67663, Germany
- Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Graz 8010, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Ralph Hückelhoven
- Phytopathology, TUM School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Matthias Hahn
- Plant Pathology, University of Kaiserslautern, Kaiserslautern 67663, Germany
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21
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Identification and Quantification of Key Phytochemicals, Phytohormones, and Antioxidant Properties in Coccinia grandis during Fruit Ripening. Antioxidants (Basel) 2022; 11:antiox11112218. [DOI: 10.3390/antiox11112218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/12/2022] Open
Abstract
Coccinia grandis contains secondary metabolites, such as flavonoids, phenolic acids, terpenoids, alkaloids, sterols, and glycosides, which are known to have in vitro antioxidant, antidiabetic, anti-inflammatory, and antidyslipidemic activities. C. grandis fruits change dramatically during ripening, and the differences in the phytochemicals contribute to various uses. This study reports the phytochemical compounds and antioxidant activities during ripening of C. grandis for the first time. Characterizations were conducted on the physiologically active substances in C. grandis fruits at three ripening stages, and a total of 25 peaks were identified. Key phytochemicals in the ripening stages of C. grandis were identified, and the major substances that contributed to antioxidant properties were selected and quantitatively analyzed. Although the concentration of tiliroside increased during aging, hydroxycinnamic acid (chlorogenic and p-coumaric acids), flavonols (rutin), and triterpenes (cucurbitacins B and D) with antioxidant effects decreased. Therefore, phenolic compounds and cucurbitacins dominate immature C. grandis quantitatively. Regarding phytohormones, the gibberellin A4 content decreased as the fruits matured, but indoleacetic acid and salicylic acid increased with fruit maturity. The antioxidant capacities determined by DPPH and ABTS consistently decreased with increasing maturity. Accordingly, the extracts of immature C. grandis fruits have high levels of bioactive compounds and can be used to develop food additives and health supplements.
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22
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Siemiatkowska B, Chiara M, Badiger BG, Riboni M, D'Avila F, Braga D, Salem MAA, Martignago D, Colanero S, Galbiati M, Giavalisco P, Tonelli C, Juenger TE, Conti L. GIGANTEA Is a Negative Regulator of Abscisic Acid Transcriptional Responses and Sensitivity in Arabidopsis. PLANT & CELL PHYSIOLOGY 2022; 63:1285-1297. [PMID: 35859344 DOI: 10.1093/pcp/pcac102] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 07/11/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Transcriptional reprogramming plays a key role in drought stress responses, preceding the onset of morphological and physiological acclimation. The best-characterized signal regulating gene expression in response to drought is the phytohormone abscisic acid (ABA). ABA-regulated gene expression, biosynthesis and signaling are highly organized in a diurnal cycle, so that ABA-regulated physiological traits occur at the appropriate time of day. The mechanisms that underpin such diel oscillations in ABA signals are poorly characterized. Here we uncover GIGANTEA (GI) as a key gatekeeper of ABA-regulated transcriptional and physiological responses. Time-resolved gene expression profiling by RNA sequencing under different irrigation scenarios indicates that gi mutants produce an exaggerated ABA response, despite accumulating wild-type levels of ABA. Comparisons with ABA-deficient mutants confirm the role of GI in controlling ABA-regulated genes, and the analysis of leaf temperature, a read-out for transpiration, supports a role for GI in the control of ABA-regulated physiological processes. Promoter regions of GI/ABA-regulated transcripts are directly targeted by different classes of transcription factors (TFs), especially PHYTOCHROME-INTERACTING FACTOR and -BINDING FACTOR, together with GI itself. We propose a model whereby diel changes in GI control oscillations in ABA responses. Peak GI accumulation at midday contributes to establishing a phase of reduced ABA sensitivity and related physiological responses, by gating DNA binding or function of different classes of TFs that cooperate or compete with GI at target regions.
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Affiliation(s)
- Beata Siemiatkowska
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria, 26, Milano 20133, Italy
| | - Matteo Chiara
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria, 26, Milano 20133, Italy
| | - Bhaskara G Badiger
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Matteo Riboni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria, 26, Milano 20133, Italy
| | - Francesca D'Avila
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, Via Antonio di Rudinì, 8, Milano 20142, Italy
| | - Daniele Braga
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, Via Antonio di Rudinì, 8, Milano 20142, Italy
| | - Mohamed Abd Allah Salem
- Department of Pharmacognosy, Faculty of Pharmacy, Menoufia University, Gamal Abd El Nasr st., Shibin Elkom, Menoufia 32511, Egypt
| | - Damiano Martignago
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria, 26, Milano 20133, Italy
| | - Sara Colanero
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria, 26, Milano 20133, Italy
| | - Massimo Galbiati
- Istituto di Biologia e Biotecnologia Agraria-IBBA, CNR, Via Edoardo Bassini, 15, Milano 20133, Italy
| | - Patrick Giavalisco
- Max Planck Institute for Biology of Ageing, Joseph Stelzmann Str. 9b, Cologne 50931, Germany
| | - Chiara Tonelli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria, 26, Milano 20133, Italy
| | - Thomas E Juenger
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Lucio Conti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria, 26, Milano 20133, Italy
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23
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Sageman-Furnas K, Nurmi M, Contag M, Plötner B, Alseekh S, Wiszniewski A, Fernie AR, Smith LM, Laitinen RAE. A. thaliana Hybrids Develop Growth Abnormalities through Integration of Stress, Hormone and Growth Signaling. PLANT & CELL PHYSIOLOGY 2022; 63:944-954. [PMID: 35460255 PMCID: PMC9282726 DOI: 10.1093/pcp/pcac056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
Hybrids between Arabidopsis thaliana accessions are important in revealing the consequences of epistatic interactions in plants. F1 hybrids between the A. thaliana accessions displaying either defense or developmental phenotypes have been revealing the roles of the underlying epistatic genes. The interaction of two naturally occurring alleles of the OUTGROWTH-ASSOCIATED KINASE (OAK) gene in Sha and Lag2-2, previously shown to cause a similar phenotype in a different allelic combination in A. thaliana, was required for the hybrid phenotype. Outgrowth formation in the hybrids was associated with reduced levels of salicylic acid, jasmonic acid and abscisic acid in petioles and the application of these hormones mitigated the formation of the outgrowths. Moreover, different abiotic stresses were found to mitigate the outgrowth phenotype. The involvement of stress and hormone signaling in outgrowth formation was supported by a global transcriptome analysis, which additionally revealed that TCP1, a transcription factor known to regulate leaf growth and symmetry, was downregulated in the outgrowth tissue. These results demonstrate that a combination of natural alleles of OAK regulates growth and development through the integration of hormone and stress signals and highlight the importance of natural variation as a resource to discover the function of gene variants that are not present in the most studied accessions of A. thaliana.
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Affiliation(s)
- Katelyn Sageman-Furnas
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Markus Nurmi
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Meike Contag
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Björn Plötner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Andrew Wiszniewski
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Lisa M Smith
- School of Biosciences and Institute for Sustainable Food, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
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24
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Advances in Plant Metabolomics and Its Applications in Stress and Single-Cell Biology. Int J Mol Sci 2022; 23:ijms23136985. [PMID: 35805979 PMCID: PMC9266571 DOI: 10.3390/ijms23136985] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/19/2022] [Accepted: 06/19/2022] [Indexed: 02/04/2023] Open
Abstract
In the past two decades, the post-genomic era envisaged high-throughput technologies, resulting in more species with available genome sequences. In-depth multi-omics approaches have evolved to integrate cellular processes at various levels into a systems biology knowledge base. Metabolomics plays a crucial role in molecular networking to bridge the gaps between genotypes and phenotypes. However, the greater complexity of metabolites with diverse chemical and physical properties has limited the advances in plant metabolomics. For several years, applications of liquid/gas chromatography (LC/GC)-mass spectrometry (MS) and nuclear magnetic resonance (NMR) have been constantly developed. Recently, ion mobility spectrometry (IMS)-MS has shown utility in resolving isomeric and isobaric metabolites. Both MS and NMR combined metabolomics significantly increased the identification and quantification of metabolites in an untargeted and targeted manner. Thus, hyphenated metabolomics tools will narrow the gap between the number of metabolite features and the identified metabolites. Metabolites change in response to environmental conditions, including biotic and abiotic stress factors. The spatial distribution of metabolites across different organs, tissues, cells and cellular compartments is a trending research area in metabolomics. Herein, we review recent technological advancements in metabolomics and their applications in understanding plant stress biology and different levels of spatial organization. In addition, we discuss the opportunities and challenges in multiple stress interactions, multi-omics, and single-cell metabolomics.
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25
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Metabolomics-based profiling for quality assessment and revealing the impact of drying of Turmeric (Curcuma longa L.). Sci Rep 2022; 12:10288. [PMID: 35717541 PMCID: PMC9206664 DOI: 10.1038/s41598-022-13882-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/05/2022] [Indexed: 01/09/2023] Open
Abstract
Turmeric, the rhizomes of Curcuma longa L., is one of the top selling spices, food preservatives, and food colorants. In addition, it exhibits health promoting benefits owing to its unique phytochemical composition. Nevertheless, it is commonly subjected to heat drying, hence, the dried powder is the most used form and can easily be adulterated with allied species. Therefore, our research aimed to profile the phytochemical composition and investigate the impact of drying of turmeric. Extraction and fractionation followed by LC- and GC–MS analysis resulted in the identification of a total of 161 metabolites belonged to various phytochemical classes. Moreover, multivariate data analysis identified curcuminoids, terpecurcumins, and organic acids as potential markers for drying. Based on the applied analytical techniques in combination with chemometrics, these investigations have succeeded to provide good coverage of the metabolome of turmeric in both fresh and dried forms.
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26
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Saiz-Fernández I, Đorđević B, Kerchev P, Černý M, Jung T, Berka M, Fu CH, Horta Jung M, Brzobohatý B. Differences in the Proteomic and Metabolomic Response of Quercus suber and Quercus variabilis During the Early Stages of Phytophthora cinnamomi Infection. Front Microbiol 2022; 13:894533. [PMID: 35770156 PMCID: PMC9234522 DOI: 10.3389/fmicb.2022.894533] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/11/2022] [Indexed: 12/23/2022] Open
Abstract
Phytophthora cinnamomi Rands is a cosmopolite pathogen of woody plants which during the last couple of centuries has spread all over the world from its center of origin in Southeast Asia. In contrast to Chinese cork oak (Quercus variabilis Blume) forests native to Asia, which are generally healthy despite the presence of the pathogen, the populations of Cork oaks (Quercus suber L.) in Europe have been severely decimated by P. cinnamomi. The present study aims at identifying the differences in the early proteomic and metabolomic response of these two tree species that lead to their differences in susceptibility to P. cinnamomi. By using micropropagated clonal plants, we tried to minimize the plant-to-plant differences in the defense response that is maximized by the high intraspecific genetic variability inherent to the Quercus genus. The evolution on the content of Phytophthora proteins in the roots during the first 36 h after inoculation suggests a slower infection process in Q. variabilis plants. These plants displayed a significant decrease in sugars in the roots, together with a downregulation of proteins related to carbon metabolism. In the leaves, the biggest changes in proteomic profiling were observed 16 h after inoculation, and included increased abundance of peroxidases, superoxide dismutases and glutathione S-transferases in Q. variabilis plants, which probably contributed to decrease its susceptibility to P. cinnamomi.
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Affiliation(s)
- Iñigo Saiz-Fernández
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Phytophthora Research Centre, Mendel University in Brno, Brno, Czechia
| | - Biljana Đorđević
- Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Phytophthora Research Centre, Mendel University in Brno, Brno, Czechia
| | - Pavel Kerchev
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Phytophthora Research Centre, Mendel University in Brno, Brno, Czechia
| | - Martin Černý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Phytophthora Research Centre, Mendel University in Brno, Brno, Czechia
| | - Thomas Jung
- Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Phytophthora Research Centre, Mendel University in Brno, Brno, Czechia
| | - Miroslav Berka
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Phytophthora Research Centre, Mendel University in Brno, Brno, Czechia
| | - Chuen-Hsu Fu
- Forest Protection Division, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Marília Horta Jung
- Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Phytophthora Research Centre, Mendel University in Brno, Brno, Czechia
| | - Břetislav Brzobohatý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Phytophthora Research Centre, Mendel University in Brno, Brno, Czechia
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Martínez-Rivas FJ, Blanco-Portales R, Molina-Hidalgo FJ, Caballero JL, Perez de Souza L, Alseekh S, Fernie AR, Muñoz-Blanco J, Rodríguez-Franco A. Azacytidine arrests ripening in cultivated strawberry (Fragaria × ananassa) by repressing key genes and altering hormone contents. BMC PLANT BIOLOGY 2022; 22:278. [PMID: 35672704 PMCID: PMC9172142 DOI: 10.1186/s12870-022-03670-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Strawberry ripening involves a number of irreversible biochemical reactions that cause sensory changes through accumulation of sugars, acids and other compounds responsible for fruit color and flavor. The process, which is strongly dependent on methylation marks in other fruits such as tomatoes and oranges, is highly controlled and coordinated in strawberry. RESULTS Repeated injections of the hypomethylating compound 5-azacytidine (AZA) into green and unripe Fragaria × ananassa receptacles fully arrested the ripening of the fruit. The process, however, was reversible since treated fruit parts reached full maturity within a few days after AZA treatment was stopped. Transcriptomic analyses showed that key genes responsible for the biosynthesis of anthocyanins, phenylpropanoids, and hormones such as abscisic acid (ABA) were affected by the AZA treatment. In fact, AZA downregulated genes associated with ABA biosynthetic genes but upregulated genes associated with its degradation. AZA treatment additionally downregulated a number of essential transcription factors associated with the regulation and control of ripening. Metabolic analyses revealed a marked imbalance in hormone levels, with treated parts accumulating auxins, gibberellins and ABA degradation products, as well as metabolites associated with unripe fruits. CONCLUSIONS AZA completely halted strawberry ripening by altering the hormone balance, and the expression of genes involves in hormone biosynthesis and degradation processes. These results contradict those previously obtained in other climacteric and fleshly fruits, where AZA led to premature ripening. In any case, our results suggests that the strawberry ripening process is governed by methylation marks.
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Affiliation(s)
- Félix Juan Martínez-Rivas
- Department of Biochemistry and Molecular Biology, University of Cordoba, Edificio Severo Ochoa, Campus de Rabanales, E-14014, Córdoba, Spain.
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
| | - Rosario Blanco-Portales
- Department of Biochemistry and Molecular Biology, University of Cordoba, Edificio Severo Ochoa, Campus de Rabanales, E-14014, Córdoba, Spain
| | - Francisco Javier Molina-Hidalgo
- Department of Biochemistry and Molecular Biology, University of Cordoba, Edificio Severo Ochoa, Campus de Rabanales, E-14014, Córdoba, Spain
| | - José Luis Caballero
- Department of Biochemistry and Molecular Biology, University of Cordoba, Edificio Severo Ochoa, Campus de Rabanales, E-14014, Córdoba, Spain
| | - Leonardo Perez de Souza
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Ruski Blvd. 139, 4000, Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Ruski Blvd. 139, 4000, Plovdiv, Bulgaria
| | - Juan Muñoz-Blanco
- Department of Biochemistry and Molecular Biology, University of Cordoba, Edificio Severo Ochoa, Campus de Rabanales, E-14014, Córdoba, Spain.
| | - Antonio Rodríguez-Franco
- Department of Biochemistry and Molecular Biology, University of Cordoba, Edificio Severo Ochoa, Campus de Rabanales, E-14014, Córdoba, Spain.
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Salem MA, Aborehab NM, Al-Karmalawy AA, Fernie AR, Alseekh S, Ezzat SM. Potential Valorization of Edible Nuts By-Products: Exploring the Immune-Modulatory and Antioxidants Effects of Selected Nut Shells Extracts in Relation to Their Metabolic Profiles. Antioxidants (Basel) 2022; 11:462. [PMID: 35326112 PMCID: PMC8944461 DOI: 10.3390/antiox11030462] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 02/05/2023] Open
Abstract
The immune system is a potent army that defends our body against various infections and diseases through innate and adaptive immunity. Herbal medicine is one of the essential sources for enhancing immunity because of affordability, availability, minor side effects, and consumers' preferences. Hazelnuts, walnuts, almonds, and peanuts are among the most widespread edible nuts that are rich in phenolics, fats, fibers, vitamins, proteins, and minerals. The potential of nut shells in phytoremediation has attracted increasing attention as a sustainable solution for waste recycling. Here, we determined the in vitro immune-modulatory activity as well as the metabolite profile of the four nut shell extracts. The addition of the extracts to LPS-stimulated macrophages, especially peanut and walnut shells, has downregulated the gene expression of AP-1, TNF-α, IL-8, iNOS, and COX-2 expression levels. Significant antioxidant capabilities and immune-modulatory effects have been traced for peanut shells. UPLC-MS metabolic profiling of the four nut shell extracts allowed the detection of a relatively high level of phenolic compounds in peanut shells. Intriguingly, a significant correlation between the antioxidant capacity and the total phenolic content was found, indicating the contribution of the phenolic compounds to the antioxidant properties and hence the immune-modulatory activity. Furthermore, molecular docking and structure-activity relationship (SAR) studies revealed kaempferol rutinoside and proanthocyanidin A5' as potential iNOS inhibitors.
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Affiliation(s)
- Mohamed A. Salem
- Department of Pharmacognosy and Natural Products, Faculty of Pharmacy, Menoufia University, Gamal Abd El Nasr St., Shibin Elkom 32511, Egypt
| | - Nora M. Aborehab
- Department of Biochemistry, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza 12451, Egypt;
| | - Ahmed A. Al-Karmalawy
- Department of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta 34518, Egypt;
| | - Alisdair R. Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany;
- Center for Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany;
- Center for Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Shahira M. Ezzat
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Kasr El-Ainy Street, Cairo 11562, Egypt;
- Department of Pharmacognosy, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza 12451, Egypt
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Simeoni F, Skirycz A, Simoni L, Castorina G, de Souza LP, Fernie AR, Alseekh S, Giavalisco P, Conti L, Tonelli C, Galbiati M. The AtMYB60 transcription factor regulates stomatal opening by modulating oxylipin synthesis in guard cells. Sci Rep 2022; 12:533. [PMID: 35017563 PMCID: PMC8752683 DOI: 10.1038/s41598-021-04433-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/06/2021] [Indexed: 12/04/2022] Open
Abstract
Stomata are epidermal pores formed by pairs of specialized guard cells, which regulate gas exchanges between the plant and the atmosphere. Modulation of transcription has emerged as an important level of regulation of stomatal activity. The AtMYB60 transcription factor was previously identified as a positive regulator of stomatal opening, although the details of its function remain unknown. Here, we propose a role for AtMYB60 as a negative modulator of oxylipins synthesis in stomata. The atmyb60-1 mutant shows reduced stomatal opening and accumulates increased levels of 12-oxo-phytodienoic acid (12-OPDA), jasmonic acid (JA) and jasmonoyl-L-isoleucine (JA-Ile) in guard cells. We provide evidence that 12-OPDA triggers stomatal closure independently of JA and cooperatively with abscisic acid (ABA) in atmyb60-1. Our study highlights the relevance of oxylipins metabolism in stomatal regulation and indicates AtMYB60 as transcriptional integrator of ABA and oxylipins responses in guard cells.
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Affiliation(s)
- Fabio Simeoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | | | - Laura Simoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Giulia Castorina
- Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy
| | | | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Center for Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Patrick Giavalisco
- Metabolomics Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Lucio Conti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Chiara Tonelli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Massimo Galbiati
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale Delle Ricerche, Milan, Italy.
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Fàbregas N, Fernie AR. The reliance of phytohormone biosynthesis on primary metabolite precursors. JOURNAL OF PLANT PHYSIOLOGY 2022; 268:153589. [PMID: 34896926 DOI: 10.1016/j.jplph.2021.153589] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/06/2021] [Accepted: 12/06/2021] [Indexed: 05/07/2023]
Abstract
There is some debate as to whether phytohormone metabolites should be classified as primary or secondary metabolites. Phytohormones have profound effects on growth - a typical trait of primary metabolites - yet several of them are formed from secondary metabolite precursors. This is further exacerbated by the blurred distinction between primary and secondary metabolism. What is clearer, however, is that phytohormones display distinctive regulatory mechanisms from other metabolites. Moreover, by contrast to microbial and mammalian systems, the majority of plant metabolite receptors characterized to date are hormone receptors. Here, we provide an overview of the metabolic links between primary metabolism and phytohormone biosynthesis in an attempt to complement recent reviews covering the signaling crosstalk between elements of core metabolism and the phytohormones. In doing so, we cover the biosynthesis of both the classical metabolic phytohormones namely auxins, salicylic acid, jasmonate, ethylene, cytokinins, brassinosteroids, gibberellins and abscisic acid as well as recently described plant growth regulators which have been proposed as novel phytohormones namely strigolactones blumenols, zaxinone and β-cyclocitral as well as melatonin. For each hormone, we describe the primary metabolite precursors which fuel its synthesis, act as conjugates or in the case of 2-oxoglutarate act more directly as a co-substrate in the biosynthesis of gibberellin, auxin and salicylic acid. Furthermore, several amino acids operate as hormone conjugates, such as jasmonate-conjugates. In reviewing the biosynthesis of all the phytohormones simultaneously, the exceptional intricacy of the biochemical interplay that underpins their interaction emerges.
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Affiliation(s)
- Norma Fàbregas
- Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany.
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany.
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31
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Salem MA, Zayed A. Liquid Chromatography-Tandem Mass Spectrometry-Based Profiling of Plant Hormones. Methods Mol Biol 2022; 2462:125-133. [PMID: 35152385 DOI: 10.1007/978-1-0716-2156-1_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Phytohormones plays crucial physiological functions in plants, where they are involved in plant development, reproduction, defense, and many other functions. Phytohormones production has been found to be regulated in response to abiotic and biotic factors affecting the plant metabolism, and therefore, biosynthesis of primary and secondary metabolites. Thus, the detection and quantification of phytohormones in different plant tissues are essential to be determined unraveling the various plant metabolic pathways and behavior. Yet phytohormones analysis is always problematic, since they are found in extremely low concentrations and have a wide range of chemical and physicochemical properties. As a result, the ideal method should start with an appropriate extraction procedure followed by quantification by highly sensitive instrumental techniques providing precise and robust results. The current chapter presents an improved extraction method based on liquid-liquid extraction from a 50-mg aliquot of plant tissue for analysis of the major classes of phytohormones. Then, mass spectrometry (MS) analysis is conducted using quadrupole/linear ion trap (QLIT) mass analyzer equipped with electrospray ionization (ESI) source after a liquid chromatographic separation step. The developed method demonstrates an appropriate feasibility addressing biological questions related to phytohormones production and regulation.
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Affiliation(s)
- Mohamed A Salem
- Department of Pharmacognosy, Faculty of Pharmacy, Menoufia University, Menoufia, Egypt.
| | - Ahmed Zayed
- Department of Pharmacognosy, College of Pharmacy, Tanta University, Tanta, Egypt
- Institute of Bioprocess Engineering, Technical University of Kaiserslautern, Kaiserslautern, Germany
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32
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Serrano-Pérez E, Romero-Losada AB, Morales-Pineda M, García-Gómez ME, Couso I, García-González M, Romero-Campero FJ. Transcriptomic and Metabolomic Response to High Light in the Charophyte Alga Klebsormidium nitens. FRONTIERS IN PLANT SCIENCE 2022; 13:855243. [PMID: 35599877 PMCID: PMC9121098 DOI: 10.3389/fpls.2022.855243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/28/2022] [Indexed: 05/04/2023]
Abstract
The characterization of the molecular mechanisms, such as high light irradiance resistance, that allowed plant terrestralization is a cornerstone in evolutionary studies since the conquest of land by plants played a pivotal role in life evolution on Earth. Viridiplantae or the green lineage is divided into two clades, Chlorophyta and Streptophyta, that in turn splits into Embryophyta or land plants and Charophyta. Charophyta are used in evolutionary studies on plant terrestralization since they are generally accepted as the extant algal species most closely related to current land plants. In this study, we have chosen the facultative terrestrial early charophyte alga Klebsormidium nitens to perform an integrative transcriptomic and metabolomic analysis under high light in order to unveil key mechanisms involved in the early steps of plants terrestralization. We found a fast chloroplast retrograde signaling possibly mediated by reactive oxygen species and the inositol polyphosphate 1-phosphatase (SAL1) and 3'-phosphoadenosine-5'-phosphate (PAP) pathways inducing gene expression and accumulation of specific metabolites. Systems used by both Chlorophyta and Embryophyta were activated such as the xanthophyll cycle with an accumulation of zeaxanthin and protein folding and repair mechanisms constituted by NADPH-dependent thioredoxin reductases, thioredoxin-disulfide reductases, and peroxiredoxins. Similarly, cyclic electron flow, specifically the pathway dependent on proton gradient regulation 5, was strongly activated under high light. We detected a simultaneous co-activation of the non-photochemical quenching mechanisms based on LHC-like stress related (LHCSR) protein and the photosystem II subunit S that are specific to Chlorophyta and Embryophyta, respectively. Exclusive Embryophyta systems for the synthesis, sensing, and response to the phytohormone auxin were also activated under high light in K. nitens leading to an increase in auxin content with the concomitant accumulation of amino acids such as tryptophan, histidine, and phenylalanine.
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Affiliation(s)
- Emma Serrano-Pérez
- Microalgae Systems Biology and Biotechnology Research Group, Institute for Plant Biochemistry and Photosynthesis, Universidad de Sevilla – Consejo Superior de Investigaciones Científicas, Seville, Spain
- Department of Computer Science and Artificial Intelligence, Universidad de Sevilla, Seville, Spain
| | - Ana B. Romero-Losada
- Microalgae Systems Biology and Biotechnology Research Group, Institute for Plant Biochemistry and Photosynthesis, Universidad de Sevilla – Consejo Superior de Investigaciones Científicas, Seville, Spain
- Department of Computer Science and Artificial Intelligence, Universidad de Sevilla, Seville, Spain
| | - María Morales-Pineda
- Microalgae Systems Biology and Biotechnology Research Group, Institute for Plant Biochemistry and Photosynthesis, Universidad de Sevilla – Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - M. Elena García-Gómez
- Microalgae Systems Biology and Biotechnology Research Group, Institute for Plant Biochemistry and Photosynthesis, Universidad de Sevilla – Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Inmaculada Couso
- Microalgae Systems Biology and Biotechnology Research Group, Institute for Plant Biochemistry and Photosynthesis, Universidad de Sevilla – Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Mercedes García-González
- Microalgae Systems Biology and Biotechnology Research Group, Institute for Plant Biochemistry and Photosynthesis, Universidad de Sevilla – Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Francisco J. Romero-Campero
- Microalgae Systems Biology and Biotechnology Research Group, Institute for Plant Biochemistry and Photosynthesis, Universidad de Sevilla – Consejo Superior de Investigaciones Científicas, Seville, Spain
- Department of Computer Science and Artificial Intelligence, Universidad de Sevilla, Seville, Spain
- *Correspondence: Francisco J. Romero-Campero,
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Fadoul HE, Martínez Rivas FJ, Neumann K, Balazadeh S, Fernie AR, Alseekh S. Comparative Molecular and Metabolic Profiling of Two Contrasting Wheat Cultivars under Drought Stress. Int J Mol Sci 2021; 22:13287. [PMID: 34948086 PMCID: PMC8707805 DOI: 10.3390/ijms222413287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 11/16/2022] Open
Abstract
Drought is one of the most important threats to plants and agriculture; therefore, understanding of the mechanisms of drought tolerance is crucial for breeding of new tolerant varieties. Here, we assessed the effects of a long-term water deficit stress simulated on a precision phenotyping system on some morphological criteria and metabolite traits, as well as the expression of drought associated transcriptional factors of two contrasting drought-responsive African wheat cultivars, Condor and Wadielniel. The current study showed that under drought stress Wadielniel exhibits significant higher tillering and height compared to Condor. Further, we used gas chromatography and ultra-high performance liquid chromatography mass-spectrometry to identify compounds that change between the two cultivars upon drought. Partial least square discriminant analysis (PLS-DA) revealed that 50 metabolites with a possible role in drought stress regulation were significantly changed in both cultivars under water deficit stress. These metabolites included several amino acids, most notably proline, some organic acids, and lipid classes PC 36:3 and TAG 56:9, which were significantly altered under drought stress. Here, the results discussed in the context of understanding the mechanisms involved in the drought response of wheat cultivars, as the phenotype parameters, metabolite content and expression of drought associated transcriptional factors could also be used for potential crop improvement under drought stress.
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Affiliation(s)
- Hind Emad Fadoul
- Department of Botany, Faculty of Science, University of Khartoum, Khartoum 11115, Sudan
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Félix Juan Martínez Rivas
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; (F.J.M.R.); (S.B.); (A.R.F.)
| | - Kerstin Neumann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Seeland, Germany;
| | - Salma Balazadeh
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; (F.J.M.R.); (S.B.); (A.R.F.)
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Alisdair R. Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; (F.J.M.R.); (S.B.); (A.R.F.)
- Center of Plant Systems Biology and Biotechnology, Ruski Blvd. 139, 4000 Plovdiv, Bulgaria
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; (F.J.M.R.); (S.B.); (A.R.F.)
- Center of Plant Systems Biology and Biotechnology, Ruski Blvd. 139, 4000 Plovdiv, Bulgaria
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Fàbregas N, Fernie AR. The interface of central metabolism with hormone signaling in plants. Curr Biol 2021; 31:R1535-R1548. [PMID: 34875246 DOI: 10.1016/j.cub.2021.09.070] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Amongst the myriad of metabolites produced by plants, primary metabolites and hormones play crucial housekeeping roles in the cell and are essential for proper plant growth and development. While the biosynthetic pathways of primary metabolism are well characterized, those of hormones are yet to be completely defined. Central metabolism provides precursors for hormone biosynthesis and the regulation and function of primary metabolites and hormones are tightly entwined. The combination of reverse genetics and technological advances in our ability to evaluate the levels of the molecular entities of the cell (transcripts, proteins and metabolites) has led to considerable improvements in our understanding of both the regulatory interaction between primary metabolites and hormones and its coordination in response to different conditions. Here, we provide an overview of the interaction of primary and hormone metabolism at the metabolic and signaling levels, as well as a perspective regarding the tools that can be used to tackle our current knowledge gaps at the signaling level.
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Affiliation(s)
- Norma Fàbregas
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany.
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany.
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Mironenka J, Różalska S, Bernat P. Potential of Trichoderma harzianum and Its Metabolites to Protect Wheat Seedlings against Fusarium culmorum and 2,4-D. Int J Mol Sci 2021; 22:ijms222313058. [PMID: 34884860 PMCID: PMC8657962 DOI: 10.3390/ijms222313058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/26/2021] [Accepted: 11/26/2021] [Indexed: 11/16/2022] Open
Abstract
Wheat is a critically important crop. The application of fungi, such as Trichoderma harzianum, to protect and improve crop yields could become an alternative solution to synthetic chemicals. However, the interaction between the fungus and wheat in the presence of stress factors at the molecular level has not been fully elucidated. In the present work, we exposed germinating seeds of wheat (Triticum aestivum) to the plant pathogen Fusarium culmorum and the popular herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) in the presence of T. harzianum or its extracellular metabolites. Then, the harvested roots and shoots were analyzed using spectrometry, 2D-PAGE, and MALDI-TOF/MS techniques. Although F. culmorum and 2,4-D were found to disturb seed germination and the chlorophyll content, T. harzianum partly alleviated these negative effects and reduced the synthesis of zearalenone by F. culmorum. Moreover, T. harzianum decreased the activity of oxidoreduction enzymes (CAT and SOD) and the contents of the oxylipins 9-Hode, 13-Hode, and 13-Hotre induced by stress factors. Under the influence of various growth conditions, changes were observed in over 40 proteins from the wheat roots. Higher volumes of proteins and enzymes performing oxidoreductive functions, such as catalase, ascorbate peroxidase, cytochrome C peroxidase, and Cu/Zn superoxide dismutase, were found in the Fusarium-inoculated and 2,4-D-treated wheat roots. Additionally, observation of the level of 12-oxo-phytodienoic acid reductase involved in the oxylipin signaling pathway in wheat showed an increase. Trichoderma and its metabolites present in the system leveled out the mentioned proteins to the control volumes. Among the 30 proteins examined in the shoots, the expression of the proteins involved in photosynthesis and oxidative stress response was found to be induced in the presence of the herbicide and the pathogen. In summary, these proteomic and metabolomic studies confirmed that the presence of T. harzianum results in the alleviation of oxidative stress in wheat induced by 2,4-D or F. culmorum.
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Ezzat SM, Abdallah HMI, Yassen NN, Radwan RA, Mostafa ES, Salama MM, Salem MA. Phenolics from Physalis peruviana fruits ameliorate streptozotocin-induced diabetes and diabetic nephropathy in rats via induction of autophagy and apoptosis regression. Biomed Pharmacother 2021; 142:111948. [PMID: 34385108 DOI: 10.1016/j.biopha.2021.111948] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 07/10/2021] [Accepted: 07/14/2021] [Indexed: 11/28/2022] Open
Abstract
The objective of our study was to evaluate the effect of Physalis peruviana L. fruits in the management of diabetes and diabetic nephropathy in relation to its metabolic profile. In-vitro α-amylase, β-glucosidase, and lipase inhibition activities were assessed for the ethanolic extract (EtOH) and its subfractions. Ethyl acetate (EtOAc) fraction showed the highest α-amylase, β-glucosidase, and lipase inhibition effect. In vivo antihyperglycemic testing of EtOAc in streptozotocin (STZ)-induced diabetic rats showed that it decreased the blood glucose level, prevented the reduction in body weight, improved serum indicators of kidney injury (urea, uric acid, creatinine), and function (albumin and total protein). EtOAc increased autophagic parameters (LC3B, AMPK) and depressed mTOR contents. Histopathology revealed that EtOAc ameliorated the pathological features and decreased the glycogen content induced by STZ. The immunohistochemical analysis showed that EtOAc reduced P53 expression as compared to the STZ-diabetic group. UPLC-ESI-MS/MS metabolite profiling of EtOAc allowed the identification of several phenolic compounds. Among the isolated compounds, gallic acid, its methylated dimer and the glycosides of quercetin had promising α-amylase and β-glucosidase inhibition activity. The results suggest that the phenolic-rich fraction has a protective effects against diabetic nephropathy presumably via enhancing autophagy (AMPK/mTOR pathway) and prevention of apoptosis (P53 suppression).
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Affiliation(s)
- Shahira M Ezzat
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo 11562, Egypt; Department of Pharmacognosy, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza 12451, Egypt.
| | - Heba M I Abdallah
- Department of Pharmacology, Medical Research Division, National Research Centre (ID: 60014618), P.O. 12622, Dokki, Cairo, Egypt.
| | - Noha N Yassen
- Department of Pathology, Medical Research Division, National Research Centre (ID: 60014618), P.O. 12622, Dokki, Cairo, Egypt.
| | - Rasha A Radwan
- Department of Biochemistry, Faculty of Pharmacy, Sinai University, East Kantara Branch, New City El Ismailia 41611, Egypt.
| | - Eman S Mostafa
- Department of Pharmacognosy, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza 12451, Egypt.
| | - Maha M Salama
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo 11562, Egypt; Department of Pharmacognosy, Faculty of Pharmacy, The British University in Egypt, El Sherouk City, Suez Desert Road, Cairo 11837, Egypt.
| | - Mohamed A Salem
- Department of Pharmacognosy, Faculty of Pharmacy, Menoufia University, Gamal Abd El Nasr st., Shibin Elkom 32511, Menoufia, Egypt.
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Salem MA, Zayed A, Alseekh S, Fernie AR, Giavalisco P. The integration of MS-based metabolomics and multivariate data analysis allows for improved quality assessment of Zingiber officinale Roscoe. PHYTOCHEMISTRY 2021; 190:112843. [PMID: 34311278 DOI: 10.1016/j.phytochem.2021.112843] [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: 02/03/2021] [Revised: 06/09/2021] [Accepted: 06/12/2021] [Indexed: 06/13/2023]
Abstract
Ginger (Zingiber officinale Roscoe) is consumed for health-promoting effects and as a food condiment. Comprehensive phytochemical analysis, other than gingerols and shogaols, has not yet been deeply investigated. Hence, the current research aimed to establish a non-targeted metabolomics approach for the discrimination between fresh ginger rhizome samples collected from four different producing countries, i.e., China, India, Pakistan, and Peru. In addition, lab-dried samples were analyzed to trace drying-induced metabolites. A comprehensive extraction procedure was carried out resulting in production of polar and non-polar fractions. The polar fraction was analyzed by ultra-performance liquid chromatography coupled with Fourier transform tandem mass spectrometry (UPLC-C18-FT-MS/MS) and gas chromatography coupled with time-of-flight mass spectrometry (GC-TOF-MS) post derivatization. UPLC-C8-FT-MS/MS was used for analysis of non-polar fraction. Results revealed for identification of a total of 253 metabolites. In addition, multivariate data analysis (MVDA), including principal component analysis (PCA) demonstrated clustering of Asian specimens. Several metabolites with a characteristic pattern for the origin revealing the highest contents of bioactive metabolites in the Peruvian product. Moreover, chemical markers identified, including [6]-gingerol and [6]-shogaol discriminating between fresh and dried samples. Furthermore, abundances of some primary metabolites, including amino acids and cinnamic acid, have confirmed the biosynthetic pathway of gingerols and their transformation upon drying to shogaols. The proposed approach can be applied as a potential candidate for quality assessment of ginger and other medicinal plants.
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Affiliation(s)
- Mohamed A Salem
- Department of Pharmacognosy, Faculty of Pharmacy, Menoufia University, Gamal Abd El Nasr St., Shibin Elkom, 32511, Menoufia, Egypt.
| | - Ahmed Zayed
- Department of Pharmacognosy, College of Pharmacy, Tanta University, Elguish Street, Medical Campus, 31527, Tanta, Egypt; Institute of Bioprocess Engineering, Technical University of Kaiserslautern, Gottlieb-Daimler-Str. 49, 67663, Kaiserslautern, Germany.
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany; Center for Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria.
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany; Center for Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria.
| | - Patrick Giavalisco
- Max Planck Institute for Biology of Ageing, Joseph Stelzmann Str. 9b, 50931, Cologne, Germany.
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Ultra-high-performance liquid chromatography high-resolution mass spectrometry variants for metabolomics research. Nat Methods 2021; 18:733-746. [PMID: 33972782 DOI: 10.1038/s41592-021-01116-4] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/12/2021] [Indexed: 02/03/2023]
Abstract
Ultra-high-performance liquid chromatography high-resolution mass spectrometry (UHPLC-HRMS) variants currently represent the best tools to tackle the challenges of complexity and lack of comprehensive coverage of the metabolome. UHPLC offers flexible and efficient separation coupled with high-sensitivity detection via HRMS, allowing for the detection and identification of a broad range of metabolites. Here we discuss current common strategies for UHPLC-HRMS-based metabolomics, with a focus on expanding metabolome coverage.
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Straube H, Niehaus M, Zwittian S, Witte CP, Herde M. Enhanced nucleotide analysis enables the quantification of deoxynucleotides in plants and algae revealing connections between nucleoside and deoxynucleoside metabolism. THE PLANT CELL 2021; 33:270-289. [PMID: 33793855 PMCID: PMC8136904 DOI: 10.1093/plcell/koaa028] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/12/2020] [Indexed: 05/02/2023]
Abstract
Detecting and quantifying low-abundance (deoxy)ribonucleotides and (deoxy)ribonucleosides in plants remains difficult; this is a major roadblock for the investigation of plant nucleotide (NT) metabolism. Here, we present a method that overcomes this limitation, allowing the detection of all deoxy- and ribonucleotides as well as the corresponding nucleosides from the same plant sample. The method is characterized by high sensitivity and robustness enabling the reproducible detection and absolute quantification of these metabolites even if they are of low abundance. Employing the new method, we analyzed Arabidopsis thaliana null mutants of CYTIDINE DEAMINASE, GUANOSINE DEAMINASE, and NUCLEOSIDE HYDROLASE 1, demonstrating that the deoxyribonucleotide (dNT) metabolism is intricately interwoven with the catabolism of ribonucleosides (rNs). In addition, we discovered a function of rN catabolic enzymes in the degradation of deoxyribonucleosides in vivo. We also determined the concentrations of dNTs in several mono- and dicotyledonous plants, a bryophyte, and three algae, revealing a correlation of GC to AT dNT ratios with genomic GC contents. This suggests a link between the genome and the metabolome previously discussed but not experimentally addressed. Together, these findings demonstrate the potential of this new method to provide insight into plant NT metabolism.
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Affiliation(s)
- Henryk Straube
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Markus Niehaus
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Sarah Zwittian
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Claus-Peter Witte
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Marco Herde
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
- Author for correspondence:
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Straube H, Witte CP, Herde M. Analysis of Nucleosides and Nucleotides in Plants: An Update on Sample Preparation and LC-MS Techniques. Cells 2021; 10:689. [PMID: 33804650 PMCID: PMC8003640 DOI: 10.3390/cells10030689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023] Open
Abstract
Nucleotides fulfill many essential functions in plants. Compared to non-plant systems, these hydrophilic metabolites have not been adequately investigated in plants, especially the less abundant nucleotide species such as deoxyribonucleotides and modified or damaged nucleotides. Until recently, this was mainly due to a lack of adequate methods for in-depth analysis of nucleotides and nucleosides in plants. In this review, we focus on the current state-of-the-art of nucleotide analysis in plants with liquid chromatography coupled to mass spectrometry and describe recent major advances. Tissue disruption, quenching, liquid-liquid and solid-phase extraction, chromatographic strategies, and peculiarities of nucleotides and nucleosides in mass spectrometry are covered. We describe how the different steps of the analytical workflow influence each other, highlight the specific challenges of nucleotide analysis, and outline promising future developments. The metabolite matrix of plants is particularly complex. Therefore, it is likely that nucleotide analysis methods that work for plants can be applied to other organisms as well. Although this review focuses on plants, we also discuss advances in nucleotide analysis from non-plant systems to provide an overview of the analytical techniques available for this challenging class of metabolites.
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Affiliation(s)
| | - Claus-Peter Witte
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, 30419 Hannover, Germany;
| | - Marco Herde
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, 30419 Hannover, Germany;
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Enfissi EMA, Drapal M, Perez-Fons L, Nogueira M, Berry HM, Almeida J, Fraser PD. New plant breeding techniques and their regulatory implications: An opportunity to advance metabolomics approaches. JOURNAL OF PLANT PHYSIOLOGY 2021; 258-259:153378. [PMID: 33631493 DOI: 10.1016/j.jplph.2021.153378] [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: 11/14/2020] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 05/21/2023]
Abstract
Over the previous decades, biotechnological innovations have led to improved agricultural productivity, more nutritious foods and lower chemical usage. Both in western societies and Low Medium Income Countries (LMICs). However, the projected increases in the global population, means the production of nutritious food stuffs must increase dramatically. Building on existing genetic modification technologies a series of New Plant Breeding Technologies (NPBT) has recently emerged. These approaches include, Agro-infiltration, grafting, cis and intragenesis and gene editing technologies. How these new techniques should be regulated has fostered considerable debate. Concerns have also been raised, to ensure over-regulation does not arise, creating administrative and economic burden. In this article the existing landscape of genetically modified crops is reviewed and the potential of several New Plant Breeding Techniques (NPBT) described. Metabolomics is an omic technology that has developed in a concurrent manner with biotechnological advances in plant breeding. There is potentially further opportunities to advance our metabolomic technologies to characterise the outputs of New Plant Breeding Technologies, in a manner that is beneficial both from an academic, biosafety and industrial perspective.
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Affiliation(s)
- Eugenia M A Enfissi
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, TW20 0EX, United Kingdom
| | - Margit Drapal
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, TW20 0EX, United Kingdom
| | - Laura Perez-Fons
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, TW20 0EX, United Kingdom
| | - Marilise Nogueira
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, TW20 0EX, United Kingdom
| | - Harriet M Berry
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, TW20 0EX, United Kingdom
| | - Juliana Almeida
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, TW20 0EX, United Kingdom
| | - Paul D Fraser
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, TW20 0EX, United Kingdom.
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Yoshida T, Yamaguchi-Shinozaki K. Metabolic engineering: Towards water deficiency adapted crop plants. JOURNAL OF PLANT PHYSIOLOGY 2021; 258-259:153375. [PMID: 33609854 DOI: 10.1016/j.jplph.2021.153375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
Water deficiency caused by drought is one of the severe environmental conditions limiting plant growth, development, and yield. In this review article, we will summarize the changes in transcription, metabolism, and phytohormones under drought stress conditions and show the key transcription factors in these processes. We will also highlight the recent attempts to enhance stress tolerance without growth retardation and discuss the perspective on the development of stress adapted crops by engineering transcription factors.
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Affiliation(s)
- Takuya Yoshida
- Max-Planck-Institut Für Molekulare Pflanzenphysiologie, 14476, Potsdam-Golm, Germany; Centre of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria.
| | - Kazuko Yamaguchi-Shinozaki
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 113-8657, Tokyo, Japan; Research Institute for Agricultural and Life Sciences, Tokyo University of Agriculture, 156-8502, Tokyo, Japan
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Saiz-Fernández I, Černý M, Skalák J, Brzobohatý B. Split-root systems: detailed methodology, alternative applications, and implications at leaf proteome level. PLANT METHODS 2021; 17:7. [PMID: 33422104 PMCID: PMC7797125 DOI: 10.1186/s13007-020-00706-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/31/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Split-root systems (SRS) have many applications in plant sciences, but their implementation, depending on the experimental design, can be difficult and time-consuming. Additionally, the system is not exempt from limitations, since the time required for the establishment of the SRS imposes a limit to how early in plant development experiments can be performed. Here, we optimized and explained in detail a method for establishing a SRS in young Arabidopsis thaliana seedlings, both in vitro and in soil. RESULTS We found that the partial de-rooting minimized the recovery time compared to total de-rooting, thus allowing the establishment of the split-root system in younger plants. Analysis of changes in the Arabidopsis leaf proteome following the de-rooting procedure highlighted the distinct metabolic alterations that totally and partially de-rooted plants undergo during the healing process. This system was also validated for its use in drought experiments, as it offers a way to apply water-soluble compounds to plants subjected to drought stress. By growing plants in a split-root system with both halves being water-deprived, it is possible to apply the required compound to one half of the root system, which can be cut from the main plant once the compound has been absorbed, thus minimizing rehydration and maintaining drought conditions. CONCLUSIONS Partial de-rooting is the suggested method for obtaining split-root systems in small plants like Arabidopsis thaliana, as growth parameters, survival rate, and proteomic analysis suggest that is a less stressful procedure than total de-rooting, leading to a final rosette area much closer to that of uncut plants. Additionally, we provide evidence that split root-systems can be used in drought experiments where water-soluble compounds are applied with minimal effects of rehydration.
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Affiliation(s)
- Iñigo Saiz-Fernández
- Phytophthora Research Centre, Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Zemědělská 3, 613 00, Brno, Czech Republic.
| | - Martin Černý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Zemědělská 3, 613 00, Brno, Czech Republic
| | - Jan Skalák
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Zemědělská 3, 613 00, Brno, Czech Republic
- Functional Genomics & Proteomics of Plants, CEITEC MU, Central European Institute of Technology, Kamenice 5, 625 00, Brno, Czech Republic
| | - Břetislav Brzobohatý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Zemědělská 3, 613 00, Brno, Czech Republic
- CEITEC-Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-61300, Brno, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265, Brno, Czech Republic
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Integrated Proteomic and Metabolomic Profiling of Phytophthora cinnamomi Attack on Sweet Chestnut ( Castanea sativa) Reveals Distinct Molecular Reprogramming Proximal to the Infection Site and Away from It. Int J Mol Sci 2020; 21:ijms21228525. [PMID: 33198329 PMCID: PMC7697766 DOI: 10.3390/ijms21228525] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 01/15/2023] Open
Abstract
Phytophthora cinnamomi is one of the most invasive tree pathogens that devastates wild and cultivated forests. Due to its wide host range, knowledge of the infection process at the molecular level is lacking for most of its tree hosts. To expand the repertoire of studied Phytophthora-woody plant interactions and identify molecular mechanisms that can facilitate discovery of novel ways to control its spread and damaging effects, we focused on the interaction between P. cinnamomi and sweet chestnut (Castanea sativa), an economically important tree for the wood processing industry. By using a combination of proteomics, metabolomics, and targeted hormonal analysis, we mapped the effects of P. cinnamomi attack on stem tissues immediately bordering the infection site and away from it. P. cinnamomi led to a massive reprogramming of the chestnut proteome and accumulation of the stress-related hormones salicylic acid (SA) and jasmonic acid (JA), indicating that stem inoculation can be used as an easily accessible model system to identify novel molecular players in P. cinnamomi pathogenicity.
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