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Vignesh A, Amal TC, Sivalingam R, Selvakumar S, Vasanth K. Unraveling the impact of nanopollution on plant metabolism and ecosystem dynamics. Plant Physiol Biochem 2024; 210:108598. [PMID: 38608503 DOI: 10.1016/j.plaphy.2024.108598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/09/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024]
Abstract
Nanopollution (NPOs), a burgeoning consequence of the widespread use of nanoparticles (NPs) across diverse industrial and consumer domains, has emerged as a critical environmental issue. While extensive research has scrutinized the repercussions of NPs pollution on ecosystems and human health, scant attention has been directed towards unraveling its implications for plant life. This comprehensive review aims to bridge this gap by delving into the nuanced interplay between NPOs and plant metabolism, encompassing both primary and secondary processes. Our exploration encompasses an in-depth analysis of the intricate mechanisms governing the interaction between plants and NPs. This involves a thorough examination of how physicochemical properties such as size, shape, and surface characteristics influence the uptake and translocation of NPs within plant tissues. The impact of NPOs on primary metabolic processes, including photosynthesis, respiration, nutrient uptake, and water transport. Additionally, this study explored the multifaceted alterations in secondary metabolism, shedding light on the synthesis and modulation of secondary metabolites in response to NPs exposure. In assessing the consequences of NPOs for plant life, we scrutinize the potential implications for plant growth, development, and environmental interactions. The intricate relationships revealed in this review underscore the need for a holistic understanding of the plant-NPs dynamics. As NPs become increasingly prevalent in ecosystems, this investigation establishes a fundamental guide that underscores the importance of additional research to shape sustainable environmental management strategies and address the extensive effects of NPs on the development of plant life and environmental interactions.
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Affiliation(s)
- Arumugam Vignesh
- Department of Botany, Nallamuthu Gounder Mahalingam College (Autonomous), Bharathiar University (Affiliated), Pollachi, 642 001, Tamil Nadu, India
| | - Thomas Cheeran Amal
- ICAR - Central Institute for Cotton Research, RS, Coimbatore, 641 003, Tamil Nadu, India
| | | | - Subramaniam Selvakumar
- Department of Biochemistry, Bharathiar University, Coimbatore, 641 046, Tamil Nadu, India
| | - Krishnan Vasanth
- Department of Botany, Bharathiar University, Coimbatore, 641 046, Tamil Nadu, India.
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2
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Cai Y, Xu H, Xu C, Zuo Z. Adjusting function of camphor on primary metabolism in Cinnamomum camphora stressed by high temperature. Plant Sci 2024; 339:111956. [PMID: 38101618 DOI: 10.1016/j.plantsci.2023.111956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 12/04/2023] [Accepted: 12/09/2023] [Indexed: 12/17/2023]
Abstract
Cinnamomum camphora has great economic value for its wide utilization in traditional medicine and furniture material, and releases lots of monoterpenes to tolerate high temperature. To uncover the adjusting function of monoterpenes on primary metabolism and promoting their utilization as anti-high temperature agents, the photosynthetic capacities, primary metabolite levels, cell ultrastructure and associated gene expression were surveyed in C. camphora when it was blocked monoterpene biosynthesis with fosmidomycin (Fos) and fumigated with camphor (a typical monoterpene in the plant) under high temperature (Fos+38 °C+camphor). Compared with the control (28 °C), high temperature at 38 °C decreased the starch content and starch grain size, and increased the fructose, glucose, sucrose and soluble sugar content. Meanwhile, high temperature also raised the lipid content, with the increase of lipid droplet size and numbers. These variations were further intensified in Fos+ 38 °C treatment. Compared with Fos+ 38 °C treatment, Fos+ 38 °C+camphor treatment improved the starch accumulation by promoting 4 gene expression in starch biosynthesis, and lowered the sugar content by suppressing 3 gene expression in pentose phosphate pathway and promoting 15 gene expression in glycolysis and tricarboxylic acid cycle. Meanwhile, Fos+ 38 °C+camphor treatment also lowered the lipid content, which may be caused by the down-regulation of 2 genes in fatty acid formation and up-regulation of 4 genes in fatty acid decomposition. Although Fos+ 38 °C+camphor treatment improved the photosynthetic capacities in contrast to Fos+ 38 °C treatment, it cannot explain the variations of these primary metabolite levels. Therefore, camphor should adjust related gene expression to maintain the primary metabolism in C. camphora tolerating high temperature.
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Affiliation(s)
- Yuyan Cai
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; Zhejiang Provincial Key Laboratory of Forest Aromatic Plants-based Healthcare Functions, Zhejiang A&F University, Hangzhou 311300, China; Shanghai Baoshan District Forestry Station, Shanghai 200940, China
| | - Haozhe Xu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; Zhejiang Provincial Key Laboratory of Forest Aromatic Plants-based Healthcare Functions, Zhejiang A&F University, Hangzhou 311300, China
| | - Chenyi Xu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; Zhejiang Provincial Key Laboratory of Forest Aromatic Plants-based Healthcare Functions, Zhejiang A&F University, Hangzhou 311300, China
| | - Zhaojiang Zuo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; Zhejiang Provincial Key Laboratory of Forest Aromatic Plants-based Healthcare Functions, Zhejiang A&F University, Hangzhou 311300, China.
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Vergara-Diaz O, Velasco-Serrano E, Invernón-Garrido A, Katamadze A, Yoldi-Achalandabaso A, Serret MD, Vicente R. Quinoa panicles contribute to carbon assimilation and are more tolerant to salt stress than leaves. J Plant Physiol 2024; 292:154161. [PMID: 38142485 DOI: 10.1016/j.jplph.2023.154161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/20/2023] [Accepted: 12/08/2023] [Indexed: 12/26/2023]
Abstract
Contribution of inflorescences to seed filling have attracted great attention given the resilience of this photosynthetic organ to stressful conditions. However, studies have been almost exclusively focused to small grain cereals. In this study, we aimed to explore these responses in quinoa, as a climate resilient seed crop of elevated economic and nutritious potential. We compared the physiological and metabolic performance of panicles and leaves of two quinoa cultivars growing under contrasting salinity levels. Plant growth, photosynthetic and transpiratory gas exchange and chlorophyll fluorescence were monitored in inflorescences and leaves throughout the experiment. At flowering stage, young and mature leaves and panicles were sampled for key metabolic markers related to carbon, nitrogen and secondary metabolisms. When subjected to salt stress, panicles showed attenuated declines on photosynthesis, water use, pigments, amino acids, and protein levels as compared to leaves. In fact, the assimilation rates, together with a high hexose content evidenced an active photosynthetic role of the panicle under optimal and salt stress conditions. Moreover, we also found significant genotypic variability for physiological and metabolic traits of panicles and leaves, which emphasizes the study of genotype-dependent stress responses at the whole plant level. We conclude that quinoa panicles are less affected by salt stress than leaves, which encourages further research and exploitation of this organ for crop improvement and stress resilience considering the high natural diversity.
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Affiliation(s)
- Omar Vergara-Diaz
- Plant Ecophysiology and Metabolism Group, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157, Oeiras, Portugal.
| | - Elena Velasco-Serrano
- Integrative Crop Ecophysiology Group, Section of Plant Physiology, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain; AGROTECNIO-CERCA Center, 25198, Lleida, Spain.
| | - Alicia Invernón-Garrido
- Integrative Crop Ecophysiology Group, Section of Plant Physiology, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain; AGROTECNIO-CERCA Center, 25198, Lleida, Spain.
| | - Artūrs Katamadze
- Plant Ecophysiology and Metabolism Group, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157, Oeiras, Portugal.
| | - Ander Yoldi-Achalandabaso
- Plant Ecophysiology and Metabolism Group, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157, Oeiras, Portugal; FisioClimaCO(2) Group, Department of Plant Biology and Ecology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48080, Bilbao, Spain.
| | - Maria Dolores Serret
- Integrative Crop Ecophysiology Group, Section of Plant Physiology, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain; AGROTECNIO-CERCA Center, 25198, Lleida, Spain.
| | - Rubén Vicente
- Plant Ecophysiology and Metabolism Group, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157, Oeiras, Portugal.
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Xin J, Che T, Huang X, Yan H, Jiang S. A comprehensive view of metabolic responses to CYP98 perturbation in ancestral plants. Plant Physiol Biochem 2023; 201:107793. [PMID: 37276808 DOI: 10.1016/j.plaphy.2023.107793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/20/2023] [Accepted: 05/22/2023] [Indexed: 06/07/2023]
Abstract
Cytochrome P450 monooxygenase 98 (CYP98) is a critical rate-limiting enzyme of the phenylpropanoid pathway. One of the end-product of the phenylpropanoid pathway is a lignin monomer, although the occurrence of lignin in bryophytes is controversial. Here we investigated the functions of PpCYP98 in Physcomitrium patens by transcriptome and metabolome analyses. We identified 5266 differentially expressed genes (DEGs) and 68 differentially abundant secondary metabolites between wild-type and ΔPpCYP98 gametophores. Of the identified metabolites, 23 phenolic acids were identified, with only one showing upregulation. Among the phenolic acids, 4-coumaroyl tartaric acid and chlorogenic acid showed significant decreases. Declines were also observed in coniferylaldehyde and coniferin, precursor substances and downstream products of the lignin monomer coniferyl alcohol, respectively. Thus, the pre-lignin synthesis pathway already exists in bryophytes, and PpCYP98 plays vital roles in this pathway. Besides, most flavonoids show significant reductions, including eriodyctiol, dihydroquecetin, and dihydromyricetin, whereas naringenin chalone and dihydrokaempferol were increased after PpCYP98 knockout. Therefore, the synthesis of flavonoids shares the core pathway with phenylpropanoids and mainly starts from caffeoyl-CoA, that is the compound of divergence between the two pathways in moss. PpCYP98 showed systemic effects on metabolisms, including carbohydrate, fatty acid, and hormonal signaling transductions, suggesting that PpCYP98 might indirectly regulate carbon influx allocation. Our results demonstrated roles of PpCYP98 were essential for the development of the early landing plant.
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Affiliation(s)
- Jiankang Xin
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China.
| | - Tianmin Che
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China.
| | - Xiaolong Huang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China; Key Laboratory of Plant Physiology and Development Regulation, Guizhou Normal University, Guiyang, 550001, China; Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, 550001, China.
| | - Huiqing Yan
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China.
| | - Shan Jiang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China; College of International Education, Guizhou Normal University, Guiyang, 550001, China.
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5
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Zhang T, Peng JT, Klair A, Dickinson AJ. Non-canonical and developmental roles of the TCA cycle in plants. Curr Opin Plant Biol 2023; 74:102382. [PMID: 37210789 PMCID: PMC10524895 DOI: 10.1016/j.pbi.2023.102382] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/11/2023] [Accepted: 04/18/2023] [Indexed: 05/23/2023]
Abstract
Over recent years, our understanding of the tricarboxylic acid cycle (TCAC) in living organisms has expanded beyond its canonical role in cellular energy production. In plants, TCAC metabolites and related enzymes have important roles in physiology, including vacuolar function, chelation of metals and nutrients, photorespiration, and redox regulation. Research in other organisms, including animals, has demonstrated unexpected functions of the TCAC metabolites in a number of biological processes, including signaling, epigenetic regulation, and cell differentiation. Here, we review the recent progress in discovery of non-canonical roles of the TCAC. We then discuss research on these metabolites in the context of plant development, with a focus on research related to tissue-specific functions of the TCAC. Additionally, we review research describing connections between TCAC metabolites and phytohormone signaling pathways. Overall, we discuss the opportunities and challenges in discovering new functions of TCAC metabolites in plants.
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Affiliation(s)
- Tao Zhang
- Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Jesus T Peng
- Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Amman Klair
- Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Alexandra J Dickinson
- Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA.
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Zhang M, Yu B, Zhang X, Deng B. Inhibition of nitrogen assimilation promotes carbon-based secondary metabolism in callus of Cyclocarya paliurus. J Plant Physiol 2023; 286:153998. [PMID: 37216742 DOI: 10.1016/j.jplph.2023.153998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/24/2023]
Abstract
The biosynthesis and accumulation of secondary metabolites are critical important to quality formation of medicinal plants, which are usually give way to primary processes and growth. Here, methionine sulfoximine (MSO) was used to inhibit the nitrogen assimilation in callus of Cyclocarya paliurus. The newly assimilated nitrogen characterized by 15N atom percentage excess, and the levels of amino acid and protein were reduced. The other primary processes such as carbohydrate metabolism and lipid metabolism were also repressed. In addition, the expression of the growth-related target of rapamycin (TOR) signaling was repressed, indicating nitrogen assimilation inhibition led to a systematic down-regulated primary metabolisms and resulted in a disruption of growth. In contrast, the biosynthesis of flavonoids and triterpenoids, antioxidase system, and the SnRK2-mediated abscisic acid (ABA) and jasmonic acid (JA) signaling were induced, which can improve plant stress resistance and defense. Nitrogen assimilation inhibition led to the carbon metabolic flux redirection from primary processes to secondary pathways, and facilitated the biosynthesis of flavonoids and triterpenoids in calluses of C. paliurus. Our results provide a comprehensive understanding of metabolic flux redirection between primary and secondary metabolic pathways and a potential means to improve the quality of medicinal plants.
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Affiliation(s)
- Mengjia Zhang
- School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Bangyou Yu
- School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Xiaoyan Zhang
- School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Bo Deng
- School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
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de Sousa A, AbdElgawad H, Fidalgo F, Teixeira J, Matos M, Tamagnini P, Fernandes R, Figueiredo F, Azenha M, Teles LO, Korany SM, Alsherif EA, Selim S, Beemster GTS, Asard H. Subcellular compartmentalization of aluminum reduced its hazardous impact on rye photosynthesis. Environ Pollut 2022; 315:120313. [PMID: 36228849 DOI: 10.1016/j.envpol.2022.120313] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Aluminum (Al) toxicity limits crops growth and production in acidic soils. Compared to roots, less is known about the toxic effects of Al in leaves. Al subcellular compartmentalization is also largely unknown. Using rye (Secale cereale L.) Beira (more tolerant) and RioDeva (more sensitive to Al) genotypes, we evaluated the patterns of Al accumulation in leaf cell organelles and the photosynthetic and metabolic changes to cope with Al toxicity. The tolerant genotype accumulated less Al in all organelles, except the vacuoles. This suggests that Al compartmentalization plays a role in Al tolerance of Beira genotype. PSII efficiency, stomatal conductance, pigment biosynthesis, and photosynthesis metabolism were less affected in the tolerant genotype. In the Calvin cycle, carboxylation was compromised by Al exposure in the tolerant genotype. Other Calvin cycle-related enzymes, phoshoglycerate kinase (PGK), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), triose-phosphate isomerase (TPI), and fructose 1,6-bisphosphatase (FBPase) activities decreased in the sensitive line after 48 h of Al exposure. Consequentially, carbohydrate and organic acid metabolism were affected in a genotype-specific manner, where sugar levels increased only in the tolerant genotype. In conclusion, Al transport to the leaf and compartmentalization in the vacuoles tolerant genotype's leaf cells provide complementary mechanisms of Al tolerance, protecting the photosynthetic apparatus and thereby sustaining growth.
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Affiliation(s)
- Alexandra de Sousa
- Plant Stress Lab - GreenUPorto Sustainable Agrifood Production Research Center, Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal; Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, B-2020, Antwerp, Belgium
| | - Hamada AbdElgawad
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, B-2020, Antwerp, Belgium; Botany and Microbiology Department, Faculty of Science, Beni-Suef University, 62511, Beni-Suef, Egypt.
| | - Fernanda Fidalgo
- Plant Stress Lab - GreenUPorto Sustainable Agrifood Production Research Center, Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Jorge Teixeira
- Plant Stress Lab - GreenUPorto Sustainable Agrifood Production Research Center, Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Manuela Matos
- Biosystems & Integrative Sciences Institute (BioISI), Department of Genetics and Biotechnology, UTAD- University of Trás-os-Montes e Alto-Douro, Quinta dos Prados, 5000-801, Vila Real, Portugal
| | - Paula Tamagnini
- HEMS-Histology and Electron Microscopy Service, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Rui Fernandes
- HEMS-Histology and Electron Microscopy Service, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Francisco Figueiredo
- HEMS-Histology and Electron Microscopy Service, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Manuel Azenha
- IQ-UP, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Luís Oliva Teles
- CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Rua dos Bragas n° 289, Porto, 4050-123, Portugal
| | - Shereen Magdy Korany
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Emad A Alsherif
- Botany and Microbiology Department, Faculty of Science, Beni-Suef University, 62511, Beni-Suef, Egypt; Biology Department, College of Science and Arts at Khulis, University of Jeddah, Jeddah, 21959, Saudi Arabia
| | - Samy Selim
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, 72341, Saudi Arabia
| | - Gerrit T S Beemster
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, B-2020, Antwerp, Belgium
| | - Han Asard
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, B-2020, Antwerp, Belgium
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Nguyen TH, Goossens A, Lacchini E. Jasmonate: A hormone of primary importance for plant metabolism. Curr Opin Plant Biol 2022; 67:102197. [PMID: 35248983 DOI: 10.1016/j.pbi.2022.102197] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/26/2022] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Over the years, jasmonates (JAs) have become recognized as one of the main plant hormones that regulate stress responses by activating defense programs and the production of specialized metabolites. High JA levels have been associated with reduced plant growth, supposedly as a result of the reallocation of carbon sources from primary growth to the biosynthesis of defense compounds. Recent advances suggest however that tight regulatory networks integrate several sensing pathways to steer plant metabolism, and thereby drive the trade-off between growth and defense. In this review, we discuss how JA influences primary metabolism and how it is connected to light-regulated processes, nutrient sensing and energy metabolism. Finally, we speculate that JA, in a conceptual parallelism with adrenaline for humans, overall boosts cellular processes to keep up with an increased metabolic demand during harsh times.
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Affiliation(s)
- Trang Hieu Nguyen
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium.
| | - Elia Lacchini
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium
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Yokoyama R, Kleven B, Gupta A, Wang Y, Maeda HA. 3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase as the gatekeeper of plant aromatic natural product biosynthesis. Curr Opin Plant Biol 2022; 67:102219. [PMID: 35550985 DOI: 10.1016/j.pbi.2022.102219] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/23/2022] [Accepted: 03/21/2022] [Indexed: 06/15/2023]
Abstract
The shikimate pathway connects the central carbon metabolism with the biosynthesis of aromatic amino acids-l-tyrosine, l-phenylalanine, and l-tryptophan-which play indispensable roles as precursors of numerous aromatic phytochemicals. Despite the importance of the shikimate pathway-derived products for both plant physiology and human society, the regulatory mechanism of the shikimate pathway remains elusive. This review summarizes the recent progress and current understanding on the plant 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAHP synthase or DHS) enzymes that catalyze the committed reaction of the shikimate pathway. We particularly focus on how the DHS activity is regulated in plants in comparison to those of microbes and discuss potential roles of DHS as the critical gatekeeper for the production of plant aromatic compounds.
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Affiliation(s)
- Ryo Yokoyama
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53705, USA.
| | - Bailey Kleven
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Anika Gupta
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Yuer Wang
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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10
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Angelovici R, Kliebenstein D. A plant balancing act: Meshing new and existing metabolic pathways towards an optimized system. Curr Opin Plant Biol 2022; 66:102173. [PMID: 35144143 DOI: 10.1016/j.pbi.2022.102173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/17/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Specialized metabolic pathways evolve from existing pathways, creating new functionality potentially boosting fitness. However, how these pathways are integrated into a pre-existing working and well-balanced metabolic system is unclear. They could be integrated to the system as a functional appendage, or they could be fully embedded into primary metabolism by establishing new biochemical and regulatory connections. A full integration into the primary metabolic system requires substantial system re-wiring and because of this complexity, the latter is often not experimentally pursued. New studies provide evidence that some specialized metabolic pathways are fully embedded in primary metabolism with extensive new regulatory and biochemical connections. This suggests, that we should consider whether other specialized metabolic pathways could be fully integrated rather than being simple appendages. In this mini review, we survey compelling evidence supporting that some specialized metabolic pathways are fully integrated and ask if these metabolites now act as de-facto primary metabolites?
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Affiliation(s)
- Ruthie Angelovici
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
| | - Dan Kliebenstein
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA; DynaMo Center of Excellence, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark.
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11
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Lou YR, Pichersky E, Last RL. Deep roots and many branches: Origins of plant-specialized metabolic enzymes in general metabolism. Curr Opin Plant Biol 2022; 66:102192. [PMID: 35217473 DOI: 10.1016/j.pbi.2022.102192] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Collectively, plants produce hundreds of thousands of specialized metabolites from simple building blocks such as amino acids, fatty acids, and isoprenoids. As additional specialized metabolic enzymes are described, there is increasing recognition of the importance of cooption of general metabolic enzymes to specialized metabolism by gene duplication, narrowing of expression, and alteration of enzymatic activities. Here, we examine how several classes of enzymes were each coopted multiple times. We demonstrate the simplicity of achieving the synthesis of analogous chemicals by coopting existing enzymes and summarize emerging insights that could inform rational metabolic engineering of both general and specialized metabolic enzymes.
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Affiliation(s)
- Yann-Ru Lou
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Eran Pichersky
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Robert L Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA.
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12
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Colinas M, Fitzpatrick TB. Coenzymes and the primary and specialized metabolism interface. Curr Opin Plant Biol 2022; 66:102170. [PMID: 35063913 DOI: 10.1016/j.pbi.2021.102170] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 12/06/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
In plants, primary and specialized metabolism have classically been distinguished as either essential for growth or required for survival in a particular environment. Coenzymes (organic cofactors) are essential for growth but their importance to specialized metabolism is often not considered. In line with the recent proposal of viewing primary and specialized metabolism as an integrated whole rather than segregated lots with a defined interface, we highlight here the importance of collating information on the regulation of coenzyme supply with metabolic demands using examples of vitamin B derived coenzymes. We emphasize that coenzymes can have enormous influence on the outcome of metabolic as well as engineered pathways and should be taken into account in the era of synthetic biology.
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Affiliation(s)
- Maite Colinas
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 80, D-07745 Jena, Germany.
| | - Teresa B Fitzpatrick
- Department of Botany and Plant Biology, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland.
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13
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Watkins JL, Facchini PJ. Compartmentalization at the interface of primary and alkaloid metabolism. Curr Opin Plant Biol 2022; 66:102186. [PMID: 35219143 DOI: 10.1016/j.pbi.2022.102186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/17/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Plants produce many compounds used by humans as medicines, including alkaloids of the benzylisoquinoline (BIA), monoterpene indole (MIA) and tropane classes. The biosynthetic pathways of these pharmaceutical alkaloids are complex and spatially segregated across several tissues, cell-types and organelles. This review discusses the origin of primary metabolic inputs required by these specialized biosynthetic pathways and considers aspects relevant to their spatial organization. These factors are important for alkaloid production both in the native plants and for synthetic biology pathway reconstruction in microorganisms.
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Affiliation(s)
- Jacinta L Watkins
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Peter J Facchini
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada.
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14
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Wang D, Chen F, Wang CY, Han X, Dai CC. Early stem growth mutation alters metabolic flux changes enhance sesquiterpenoids biosynthesis in Atractylodes lancea (Thunb.) DC. Plant Cell Tissue Organ Cult 2022; 149:467-483. [PMID: 35125570 PMCID: PMC8806136 DOI: 10.1007/s11240-022-02240-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
UNLABELLED Atractylodes lancea (Thunb.) DC. is a well-known medicinal herb in China, containing abundant active components, including a variety of sesquiterpenoids. Owing to a shortage of wild resources, artificial cultivation has become the main breeding mode, leading to the germplasm degradation. In preliminary research, our research group found that a mutant tissue culture seedling of A. lancea is an excellent germplasm resource, characterized by early stem growth and higher sesquiterpenoid content than that of the wild type. In this study, the physiological and biochemical mechanisms underlying efficient sesquiterpenoids synthesis by this mutant A. lancea were systematically evaluated. The results showed that the photosynthetic efficiency, central carbon metabolism efficiency, and energy metabolism efficiency were significantly improved in mutant A. lancea compared with the wild type, and the content of endogenous hormones, such as gibberellin and jasmonic acid, changed significantly. In addition, levels of key metabolites and the expression level of key genes in the mevalonate and 2-C-methyl-d-erythritol-4-phosphate pathways were significantly higher in mutant type than in wild type, resulting in elevated sesquiterpenoid synthesis in the mutant. These physiological and biochemical properties explain the rapid growth and high sesquiterpenoid content of mutant A. lancea. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11240-022-02240-5.
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Affiliation(s)
- Di Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, School of Life Sciences, Nanjing Normal University, Nanjing, 210023 China
- Nanjing Engineering Research Center for Functional Components Development of Featured Biological Resources, School of Life Sciences, Nanjing Normal University, Nanjing, 210023 China
| | - Fei Chen
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, School of Life Sciences, Nanjing Normal University, Nanjing, 210023 China
- Nanjing Engineering Research Center for Functional Components Development of Featured Biological Resources, School of Life Sciences, Nanjing Normal University, Nanjing, 210023 China
| | - Chun-Yan Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, School of Life Sciences, Nanjing Normal University, Nanjing, 210023 China
- Nanjing Engineering Research Center for Functional Components Development of Featured Biological Resources, School of Life Sciences, Nanjing Normal University, Nanjing, 210023 China
| | - Xu Han
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, School of Life Sciences, Nanjing Normal University, Nanjing, 210023 China
- Nanjing Engineering Research Center for Functional Components Development of Featured Biological Resources, School of Life Sciences, Nanjing Normal University, Nanjing, 210023 China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, School of Life Sciences, Nanjing Normal University, Nanjing, 210023 China
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15
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Abstract
Ageing in plants is a highly coordinated and complex process that starts with the birth of the plant or plant organ and ends with its death. A vivid manifestation of the final stage of leaf ageing is exemplified by the autumn colours of deciduous trees. Over the past decades, technological advances have allowed plant ageing to be studied on a systems biology level, by means of multi-omics approaches. Here, we review some of these studies and argue that these provide strong support for basic metabolic processes as drivers for ageing. In particular, core cellular processes that control the metabolism of chlorophyll, amino acids, sugars, DNA and reactive oxygen species correlate with leaf ageing. However, while multi-omics studies excel at identifying correlative processes and pathways, molecular genetic approaches can provide proof that such processes and pathways control ageing, by means of knock-out and ectopic expression of predicted regulatory genes. Therefore, we also review historic and current molecular evidence to directly test the hypotheses unveiled by the systems biology approaches. We found that the molecular genetic approaches, by and large, confirm the multi-omics-derived hypotheses with notable exceptions, where there is scant evidence that chlorophyll and DNA metabolism are important drivers of leaf ageing. We present a model that summarises the core cellular processes that drive leaf ageing and propose that developmental processes are tightly linked to primary metabolism to inevitably lead to ageing and death.
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Affiliation(s)
- Aakansha Kanojia
- Center of Plant Systems Biology and Biotechnology, Ruski 139 Blvd., Plovdiv, 4000, Bulgaria
| | - Deny K Shrestha
- School of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North, New Zealand
| | - Paul P Dijkwel
- School of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North, New Zealand.
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16
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Condori-Apfata JA, Batista-Silva W, Medeiros DB, Vargas JR, Valente LML, Pérez-Díaz JL, Fernie AR, Araújo WL, Nunes-Nesi A. Downregulation of the E2 Subunit of 2-Oxoglutarate Dehydrogenase Modulates Plant Growth by Impacting Carbon-Nitrogen Metabolism in Arabidopsis thaliana. Plant Cell Physiol 2021; 62:798-814. [PMID: 33693904 PMCID: PMC8484937 DOI: 10.1093/pcp/pcab036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 02/28/2021] [Accepted: 04/16/2021] [Indexed: 05/04/2023]
Abstract
In Arabidopsis thaliana, two genes encode the E2 subunit of the 2-oxoglutarate dehydrogenase (2-OGDH), a multimeric complex composed of three subunits. To functionally characterize the isoforms of E2 subunit, we isolated Arabidopsis mutant lines for each gene encoding the E2 subunit and performed a detailed molecular and physiological characterization of the plants under controlled growth conditions. The functional lack of expression of E2 subunit isoforms of 2-OGDH increased plant growth, reduced dark respiration and altered carbohydrate metabolism without changes in the photosynthetic rate. Interestingly, plants from e2-ogdh lines also exhibited reduced seed weight without alterations in total seed number. We additionally observed that downregulation of 2-OGDH activity led to minor changes in the levels of tricarboxylic acid cycle intermediates without clear correlation with the reduced expression of specific E2-OGDH isoforms. Furthermore, the e2-ogdh mutant lines exhibited a reduction by up to 25% in the leaf total amino acids without consistent changes in the amino acid profile. Taken together, our results indicate that the two isoforms of E2 subunit play a similar role in carbon-nitrogen metabolism, in plant growth and in seed weight.
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Affiliation(s)
- Jorge A Condori-Apfata
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
| | - Willian Batista-Silva
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
| | - David Barbosa Medeiros
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam Golm 14476, Germany
| | - Jonas Rafael Vargas
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
| | - Luiz M Lopes Valente
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
| | - Jorge Luis Pérez-Díaz
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
| | - Alisdair R Fernie
- * Corresponding authors: Alisdair R. Fernie, E-mail, ; Adriano Nunes-Nesi, E-mail,
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
| | - Adriano Nunes-Nesi
- * Corresponding authors: Alisdair R. Fernie, E-mail, ; Adriano Nunes-Nesi, E-mail,
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17
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Karagiannis E, Michailidis M, Skodra C, Molassiotis A, Tanou G. Silicon influenced ripening metabolism and improved fruit quality traits in apples. Plant Physiol Biochem 2021; 166:270-277. [PMID: 34130037 DOI: 10.1016/j.plaphy.2021.05.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/25/2021] [Indexed: 06/12/2023]
Abstract
The benefits of silicon against abiotic stress in different annual plant species have been described in many studies, however the regulation of ripening of fruit tree crops by silicon remains largely uncharacterized. Therefore, the present study aimed to explore the impact of foliar silicon application in the apple (cv. 'Fuji') fruit ripening traits along with the effect of silicon in the nutrient and metabolic changes in the fully expanded leaves, annual shoots, fruit outer pericarp (peel) and fruit mesocarp (skin) tissues. Data indicated that fruit firmness and apple peel color attributes, such as redness (a*) and percentage of red-blushed surface were induced by silicon application. Moreover, several fruit ripening traits, such as titratable acidity, soluble solid content and respiration rate were unaffected by silicon. Endogenous silicon level in leaves shoots and peel tissues were increased by exogenously applied silicon while several elements (i.e., P, Mg, Mn, Fe and Cu) were altered in the tested tissues that exposed to silicon. In addition, silicon increased the accumulation of total phenolic and total anthocyanin compounds in the various apple tissues. The level of various primary metabolites including sorbitol, fructose, maltose cellobiose, malic acid, phosphoric acid and gluconic acid was also notably affected by silicon in a tissue-specific manner. Overall, this study provides a valuable resource for future research, aiming in the elucidation of the role of silicon in fruit tree physiology.
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Affiliation(s)
- Evangelos Karagiannis
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, 57001, Thessaloniki, Greece.
| | - Michail Michailidis
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, 57001, Thessaloniki, Greece.
| | - Christina Skodra
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, 57001, Thessaloniki, Greece.
| | - Athanassios Molassiotis
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, 57001, Thessaloniki, Greece.
| | - Georgia Tanou
- Institute of Soil and Water Resources, ELGO-DEMETER, Thessaloniki, 57001, Greece.
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18
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Abstract
Potassium is a macroelement essential to many aspects of plant life, such as photosynthesis, phloem transport or cellular electrochemistry. Many enzymes in animals or microbes are known to be stimulated or activated by potassium (K+ ions). Several plant enzymes are also strictly K+-dependent, and this can be critical when plants are under K deficiency and thus intracellular K+ concentration is low. Although metabolic effects of low K conditions have been documented, there is presently no review focusing on roles of K+ for enzyme catalysis or activation in plants. In this mini-review, we compile the current knowledge on K+-requirement of plant enzymes and take advantage of structural data to present biochemical roles of K+. This information is instrumental to explain direct effects of low K+ content on metabolism and this is illustrated with recent metabolomics data.
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Affiliation(s)
- Jing Cui
- Research School of Biology, ANU Joint College of Sciences, Australian National University, 2601, Canberra, Australia
| | - Guillaume Tcherkez
- Research School of Biology, ANU Joint College of Sciences, Australian National University, 2601, Canberra, Australia; Institut de Recherche en Horticulture et Semences, INRAe Angers, Université d'Angers, 42 rue Georges Morel, 49070, Beaucouzé, France.
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19
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Kutty NN, Ghissing U, Mitra A. Revealing floral metabolite network in tuberose that underpins scent volatiles synthesis, storage and emission. Plant Mol Biol 2021; 106:533-554. [PMID: 34263437 DOI: 10.1007/s11103-021-01171-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 07/01/2021] [Indexed: 06/13/2023]
Abstract
The role of central carbon metabolism in the synthesis and emission of scent volatiles in tuberose flowers was revealed through measurement of changes in transcripts and metabolites levels. Tuberose or Agave amica (Medikus) Thiede & Govaerts is a widely cultivated ornamental plant in several subtropical countries. Little is known about metabolite networking involved in biosynthesis of specialized metabolites utilizing primary metabolites. In this study, metabolite profiling and gene expression analyses were carried out from six stages of maturation throughout floral lifespan. Multivariate analysis indicated distinction between early and late maturation stages. Further, the roles of sugars viz. sucrose, glucose and fructose in synthesis, glycosylation and emission of floral scent volatiles were studied. Transcript levels of an ABC G family transporter (picked up from the floral transcriptome) was in synchronization with terpene volatiles emission during the anthesis stage. A diversion from phenylpropanoid/benzenoid to flavonoid metabolism was observed as flowers mature. Further, it was suggested that this metabolic shift could be mediated by isoforms of 4-Coumarate-CoA ligase along with Myb308 transcription factor. Maximum glycosylation of floral scent volatiles was shown to occur at the late mature stage when emission declined, facilitating both storage and export from the floral tissues. Thus, this study provides an insight into floral scent volatiles synthesis, storage and emission by measuring changes at transcripts and metabolites levels in tuberose throughout floral lifespan.
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Affiliation(s)
- Nithya N Kutty
- Natural Product Biotechnology Group, Agricultural and Food Engineering Department, Indian Institute of Technology Kharagpur, Kharagpur, 721 302, India
| | - Upashana Ghissing
- Natural Product Biotechnology Group, Agricultural and Food Engineering Department, Indian Institute of Technology Kharagpur, Kharagpur, 721 302, India
| | - Adinpunya Mitra
- Natural Product Biotechnology Group, Agricultural and Food Engineering Department, Indian Institute of Technology Kharagpur, Kharagpur, 721 302, India.
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20
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Guan Y, Hu W, Xu Y, Sarengaowa, Ji Y, Yang X, Feng K. Proteomic analysis validates previous findings on wounding-responsive plant hormone signaling and primary metabolism contributing to the biosynthesis of secondary metabolites based on metabolomic analysis in harvested broccoli (Brassica oleracea L. var. italica). Food Res Int 2021; 145:110388. [PMID: 34112391 DOI: 10.1016/j.foodres.2021.110388] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 04/08/2021] [Accepted: 05/02/2021] [Indexed: 10/21/2022]
Abstract
The plant wound-response is a complex process that generates physiological modifications for protecting the wounded tissue. In this study, tandem mass tag (TMT)-based quantitative proteomic analysis was performed to clarify the comprehensive molecular mechanism for the wound-response of broccoli subjected to two wounding intensities (0.04 and 1.85 m2 kg-1 for florets and shreds, respectively). Furthermore, integrated proteomic and metabolomic analysis was performed to reveal the interaction among the critical metabolic pathway responses to wounding. The results show that a total of 399 proteins and 266 proteins were identified as differentially expressed proteins (DEPs) in florets and shreds broccoli compared to control, respectively. Furthermore, 167 DEPs were detected in shreds broccoli compared to the florets broccoli. Salicylic acid (SA) and ethylene (ET) biosynthesis were more susceptible to being induced by wounding with lower intensities, whereas, phenylpropanoid biosynthesis, aliphatic glucosinolate synthesis and jasmonic acid (JA) biosynthesis were more susceptible to being activated by wounding with higher intensities. The activation of starch and sucrose metabolism, TCA cycle, glycolysis, pentose phosphate could provide carbon sources and ATP for the production of amino acids including phenylalanine, valine, threonine, isoleucine, L-methionine, methionine and histidine. The motivation of carbohydrate metabolic pathways and amino acid biosynthesis-related pathways promotes the precursor levels for phenolic substances and glucosinolate synthesis. Furthermore, the accumulation of SA, ET and JA may activated secondary metabolite biosynthesis through the regulation of critical proteins involved in the corresponding metabolic pathways.
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Affiliation(s)
- Yuge Guan
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Wenzhong Hu
- College of Life Science, Dalian Minzu University, Dalian 116600, China; Key Laboratory of Biotechnology and Bioesources Utilization, Ministry of Education, Dalian 116600, China.
| | - Yongping Xu
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Sarengaowa
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Yaru Ji
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Xiaozhe Yang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Ke Feng
- College of Life Science, Dalian Minzu University, Dalian 116600, China; Key Laboratory of Biotechnology and Bioesources Utilization, Ministry of Education, Dalian 116600, China
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21
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Karagiannis E, Michailidis M, Skodra C, Stamatakis G, Dasenaki M, Ganopoulos I, Samiotaki M, Thomaidis NS, Molassiotis A, Tanou G. Proteo-metabolomic journey across olive drupe development and maturation. Food Chem 2021; 363:130339. [PMID: 34147896 DOI: 10.1016/j.foodchem.2021.130339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/31/2021] [Accepted: 06/05/2021] [Indexed: 12/20/2022]
Abstract
Maturity is one of the most important factors associated with the quality of olive products, however the molecular events underlying olive drupe development remain poorly characterized. Using proteomic and metabolomic approaches, this study investigated the changes in the olive drupes (cv. Chondrolia Chalkidikis) across six developmental stages (S1-S6) that characterize the dynamics of fruit growth and color. Primary metabolites, including carbohydrates and organic acids (i.e., xylose, malic acid), showed significant accumulation in the black maturation stage. Temporal changes in various secondary metabolites (e.g., oleuropein, oleacin and tyrosol) were also observed. Proteins involved in oxidation-reduction (i.e., LOX1/5), carbohydrate metabolism (i.e., GLUA, PG) and photosynthesis (i.e., chlorophyll a-b binding proteins) significantly altered in the turning black compared to the green mature stage. By providing the first proteometabolomic study of olive drupe development, this investigation offers a novel framework for further studies on this economically relevant crop.
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Affiliation(s)
- Evangelos Karagiannis
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, 57001, Thessaloniki-Thermi, Greece.
| | - Michail Michailidis
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, 57001, Thessaloniki-Thermi, Greece.
| | - Christina Skodra
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, 57001, Thessaloniki-Thermi, Greece.
| | - George Stamatakis
- Biomedical Sciences Research Center "Alexander Fleming", Vari 16672, Greece.
| | - Marilena Dasenaki
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece.
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, ELGO-DEMETER, Thessaloniki-Thermi 57001, Greece.
| | - Martina Samiotaki
- Biomedical Sciences Research Center "Alexander Fleming", Vari 16672, Greece.
| | - Nikolaos S Thomaidis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece.
| | - Athanassios Molassiotis
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, 57001, Thessaloniki-Thermi, Greece.
| | - Georgia Tanou
- Institute of Soil and Water Resources, ELGO-DEMETER, Thessaloniki-Thermi 57001, Greece.
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22
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Liao P, Lung SC, Chan WL, Hu M, Kong GKW, Bach TJ, Hao Q, Lo C, Chye ML. Overexpression and Inhibition of 3-Hydroxy-3-Methylglutaryl-CoA Synthase Affect Central Metabolic Pathways in Tobacco. Plant Cell Physiol 2021; 62:205-218. [PMID: 33340324 DOI: 10.1093/pcp/pcaa154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 11/28/2020] [Indexed: 06/12/2023]
Abstract
Little has been established on the relationship between the mevalonate (MVA) pathway and other metabolic pathways except for the sterol and glucosinolate biosynthesis pathways. In the MVA pathway, 3-hydroxy-3-methylglutaryl-CoA synthase (HMGS) catalyzes the condensation of acetoacetyl-CoA and acetyl-CoA to form 3-hydroxy-3-methylglutaryl-coenzyme A. Our previous studies had shown that, while the recombinant Brassica juncea HMGS1 (BjHMGS1) mutant S359A displayed 10-fold higher enzyme activity than wild-type (wt) BjHMGS1, transgenic tobacco overexpressing S359A (OE-S359A) exhibited higher sterol content, growth rate and seed yield than OE-wtBjHMGS1. Herein, untargeted proteomics and targeted metabolomics were employed to understand the phenotypic effects of HMGS overexpression in tobacco by examining which other metabolic pathways were affected. Sequential window acquisition of all theoretical mass spectra quantitative proteomics analysis on OE-wtBjHMGS1 and OE-S359A identified the misregulation of proteins in primary metabolism and cell wall modification, while some proteins related to photosynthesis and the tricarboxylic acid cycle were upregulated in OE-S359A. Metabolomic analysis indicated corresponding changes in carbohydrate, amino acid and fatty acid contents in HMGS-OEs, and F-244, a specific inhibitor of HMGS, was applied successfully on tobacco to confirm these observations. Finally, the crystal structure of acetyl-CoA-liganded S359A revealed that improved activity of S359A likely resulted from a loss in hydrogen bonding between Ser359 and acyl-CoA, which is evident in wtBjHMGS1. This work suggests that regulation of plant growth by HMGS can influence the central metabolic pathways. Furthermore, this study demonstrates that the application of the HMGS-specific inhibitor (F-244) in tobacco represents an effective approach for studying the HMGS/MVA pathway.
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Affiliation(s)
- Pan Liao
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Shiu-Cheung Lung
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Wai Lung Chan
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Menglong Hu
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | | | - Thomas J Bach
- Centre National de la Recherche Scientifique, UPR 2357, Institut de Biologie Mol�culaire des Plantes, Universit� de Strasbourg, Strasbourg 67084, France
| | - Quan Hao
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Clive Lo
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Mee-Len Chye
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
- State Key Laboratory of Agrobiotechnology, CUHK, Shatin, New Territories, Hong Kong, China
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23
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Xu W, Jin X, Yang M, Xue S, Luo L, Cao X, Zhang C, Qiao S, Zhang C, Li J, Wu J, Lv L, Zhao F, Wang N, Tan S, Lyu-Bu AG, Wang C, Wang X. Primary and secondary metabolites produced in Salvia miltiorrhiza hairy roots by an endophytic fungal elicitor from Mucor fragilis. Plant Physiol Biochem 2021; 160:404-412. [PMID: 33571807 DOI: 10.1016/j.plaphy.2021.01.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/16/2021] [Indexed: 06/12/2023]
Abstract
Salvia miltiorrhiza is one of the most commonly used medicinal materials in China. In recent years, the quality of S. miltiorrhiza has attracted much attention. Biotic and abiotic elicitors are widely used in cultivation to improve the quality of medicinal plants. We isolated an endophytic fungus, Mucor fragilis, from S. miltiorrhiza. We compared the effects of endophytic fungal elicitors with those of yeast extract together with silver ion, widely used together as effective elicitors, on S. miltiorrhiza hairy roots. Seventeen primary metabolites (amino acids and fatty acids) and five secondary metabolites (diterpenoids and phenolic acids) were analyzed after elicitor treatment. The mycelium extract promoted the accumulation of salvianolic acid B, rosmarinic acid, stearic acid, and oleic acid in S. miltiorrhiza hairy roots. Additionally, qPCR revealed that elicitors affect the accumulation of primary and secondary metabolites by regulating the expression of key genes (SmAACT, SmGGPPS, and SmPAL). This is the first detection of both the primary and secondary metabolites of S. miltiorrhiza hairy roots, and the results of this work should help guide the quality control of S. miltiorrhiza. In addition, the findings confirm that Mucor fragilis functions as an effective endophytic fungal elicitor with excellent application prospect for cultivation of medicinal plants.
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Affiliation(s)
- Wenjuan Xu
- School of Chinese Materia, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Xiaoyan Jin
- School of Chinese Materia, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Miao Yang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Song Xue
- School of bioengineering, Dalian University of Technology, Dalian, 116023, China
| | - Linglong Luo
- School of Chinese Materia, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Xupeng Cao
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Caijuan Zhang
- School of Life Science, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Sanyang Qiao
- School of Chinese Materia, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Chi Zhang
- School of Chinese Materia, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Junling Li
- School of Chinese Materia, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Jiahui Wu
- School of Chinese Materia, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Liqiao Lv
- School of Chinese Materia, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Fangyuan Zhao
- School of Chinese Materia, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Nan Wang
- School of Chinese Materia, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Shuting Tan
- School of Chinese Materia, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - A Ga Lyu-Bu
- School of Chinese Materia, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Chunguo Wang
- School of Chinese Materia, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Xueyong Wang
- School of Chinese Materia, Beijing University of Chinese Medicine, Beijing, 100029, China.
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Boersma AS, Kallscheuer N, Wiegand S, Rast P, Peeters SH, Mesman RJ, Heuer A, Boedeker C, Jetten MSM, Rohde M, Jogler M, Jogler C. Alienimonas californiensis gen. nov. sp. nov., a novel Planctomycete isolated from the kelp forest in Monterey Bay. Antonie Van Leeuwenhoek 2020; 113:1751-1766. [PMID: 31802338 DOI: 10.1007/s10482-019-01367-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 11/26/2019] [Indexed: 11/26/2022]
Abstract
Planctomycetes are environmentally and biotechnologically important bacteria and are often found in association with nutrient-rich (marine) surfaces. To allow a more comprehensive understanding of planctomycetal lifestyle and physiology we aimed at expanding the collection of axenic cultures with new isolates. Here, we describe the isolation and genomic and physiological characterisation of strain CA12T obtained from giant bladder kelp (Macrocystis pyrifera) in Monterey Bay, California, USA. 16S rRNA gene sequence and whole genome-based phylogenetic analysis showed that strain CA12T clusters within the family Planctomycetaceae and that it has a high 16S rRNA sequence similarity (82.3%) to Planctomicrobium piriforme DSM 26348T. The genome of strain CA12T has a length of 5,475,215 bp and a G+C content of 70.1%. The highest growth rates were observed at 27 °C and pH 7.5. Using different microscopic methods, we could show that CA12T is able to divide by consecutive polar budding, without completing a characteristic planctomycetal lifestyle switch. Based on our data, we suggest that the isolated strain represents a novel species within a novel genus. We thus propose the name Alienimonas gen. nov. with Alienimonas californiensis sp. nov. as type species of the novel genus and CA12T as type strain of the novel species.
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Affiliation(s)
- Alje S Boersma
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Nicolai Kallscheuer
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Sandra Wiegand
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Patrick Rast
- Leibniz Institute DSMZ Braunschweig, Brunswick, Germany
| | - Stijn H Peeters
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Rob J Mesman
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Anja Heuer
- Leibniz Institute DSMZ Braunschweig, Brunswick, Germany
| | | | - Mike S M Jetten
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Brunswick, Germany
| | - Mareike Jogler
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
- Leibniz Institute DSMZ Braunschweig, Brunswick, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands.
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Karagiannis E, Sarrou E, Michailidis M, Tanou G, Ganopoulos I, Bazakos C, Kazantzis K, Martens S, Xanthopoulou A, Molassiotis A. Fruit quality trait discovery and metabolic profiling in sweet cherry genebank collection in Greece. Food Chem 2021; 342:128315. [PMID: 33071194 DOI: 10.1016/j.foodchem.2020.128315] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/24/2020] [Accepted: 10/03/2020] [Indexed: 11/23/2022]
Abstract
The current study characterizes the physicochemical, sensory and bioactive compound traits of twenty-two sweet cherry accessions, namely breeding lines, landraces and modern cultivars, embodying the majority of Greek germplasm. The evaluated accessions differ in several quality traits including colour parameters and textural properties as well as sensory attributes, such as taste intensity and overall acceptance. Significant differences in primary metabolites, including fructose, glucose, sorbitol, malic acid were recorded among tested accessions. All genotypes were rich in polyphenols, primarily in quercetin-3,4-O-diglucoside, esculetin, rutin and neochlorogenic acid. An anthocyanins-related discrimination among accessions was also obtained based on cyanidin-3-O-rutinoside and peonidin glycosides content. Overall, the cultivars 'Tsolakeika' and 'Bakirtzeika' exhibited the higher consumer acceptance while the cultivars 'Vasiliadi' and 'Tragana Edessis-Naousis' and especially the breeding line 'TxAg33' contained high polyphenol levels. These results represent a valuable resource for future breeding efforts for sweet cherry cultivars with improved nutritional quality traits.
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26
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Cabral Gouveia GC, Galindo FS, Dantas Bereta Lanza MG, Caroline da Rocha Silva A, Pereira de Brito Mateus M, Souza da Silva M, Rimoldi Tavanti RF, Tavanti TR, Lavres J, Reis ARD. Selenium toxicity stress-induced phenotypical, biochemical and physiological responses in rice plants: Characterization of symptoms and plant metabolic adjustment. Ecotoxicol Environ Saf 2020; 202:110916. [PMID: 32800251 DOI: 10.1016/j.ecoenv.2020.110916] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/13/2020] [Accepted: 06/16/2020] [Indexed: 05/28/2023]
Abstract
Selenium (Se) at low concentration is considered benefit element to plants. The range between optimal and toxic concentration of Se is narrow and varies among plant species. This study aimed to evaluate the phenotypic, physiological and biochemical responses of four rice genotypes (BRS Esmeralda, BRSMG Relâmpago, BRS Bonança and Bico Ganga) grown hydroponically treated with sodium selenate (1.5 mM L-1). Selenium treated plants showed a dramatically decrease of soluble proteins, chlorophylls, and carotenoids concentration, resulting in the visual symptoms of toxicity characterized as leaf chlorosis and necrosis. Selenium toxicity caused a decrease on shoot and root dry weight of rice plants. Excess Se increased the oxidative stress monitored by the levels of hydrogen peroxide and lipid peroxidation. The enzymatic antioxidant system (catalase, superoxide dismutase, and ascorbate peroxidase) increased in response to Se supply. Interestingly, primary metabolism compounds such as sucrose, total sugars, nitrate, ammonia and amino acids increased in Se-treated plants. The increase in these metabolites may indicate a defense mechanism for the osmotic readjustment of rice plants to mitigate the toxicity caused by Se. However, these metabolites were not effective to minimize the damages on phenotypic traits such as leaf chlorosis and reduced shoot and root dry weight in response to excess Se. Increased sugars profile combined with antioxidant enzymes activities can be an effective biomarkers to indicate stress induced by Se in rice plants. This study shows the physiological attributes that must be taken into account for success in the sustainable cultivation of rice in environments containing excess Se.
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Affiliation(s)
| | | | | | | | | | | | | | | | - José Lavres
- University of Sao Paulo (USP), Center for Nuclear Energy in Agriculture (CENA), 13416-000, Piracicaba, SP, Brazil
| | - André Rodrigues Dos Reis
- São Paulo State University (UNESP), 15385-000, Ilha Solteira, SP, Brazil; São Paulo State University (UNESP), 17602-496, Tupã, SP, Brazil.
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27
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Wu L, Wang Z, Guan Y, Huang X, Shi H, Liu Y, Zhang X. The (p)ppGpp-mediated stringent response regulatory system globally inhibits primary metabolism and activates secondary metabolism in Pseudomonas protegens H78. Appl Microbiol Biotechnol 2020; 104:3061-3079. [PMID: 32009198 DOI: 10.1007/s00253-020-10421-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/18/2020] [Accepted: 01/26/2020] [Indexed: 01/08/2023]
Abstract
Pseudomonas protegens H78 produces multiple secondary metabolites, including antibiotics and iron carriers. The guanosine pentaphosphate or tetraphosphate ((p)ppGpp)-mediated stringent response is utilized by bacteria to survive during nutritional starvation and other stresses. RelA/SpoT homologues are responsible for the biosynthesis and degradation of the alarmone (p)ppGpp. Here, we investigated the global effect of relA/spoT dual deletion on the transcriptomic profiles, physiology, and metabolism of P. protegens H78 grown to mid- to late log phase. Transcriptomic profiling revealed that relA/spoT deletion globally upregulated the expression of genes involved in DNA replication, transcription, and translation; amino acid metabolism; carbohydrate and energy metabolism; ion transport and metabolism; and secretion systems. Bacterial growth was partially increased, while the cell survival rate was significantly reduced by relA/spoT deletion in H78. The utilization of some nutritional elements (C, P, S, and N) was downregulated due to relA/spoT deletion. In contrast, relA/spoT mutation globally inhibited the expression of secondary metabolic gene clusters (plt, phl, prn, ofa, fit, pch, pvd, and has). Correspondingly, antibiotic and iron carrier biosynthesis, iron utilization, and antibiotic resistance were significantly downregulated by the relA/spoT mutation. This work highlights that the (p)ppGpp-mediated stringent response regulatory system plays an important role in inhibiting primary metabolism and activating secondary metabolism in P. protegens.
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Affiliation(s)
- Lingyu Wu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zheng Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yejun Guan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xianqing Huang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Huimin Shi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yujie Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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Malheiros RSP, Gonçalves FCM, Brito FAL, Zsögön A, Ribeiro DM. Selenomethionine induces oxidative stress and modifies growth in rice (Oryza sativa L.) seedlings through effects on hormone biosynthesis and primary metabolism. Ecotoxicol Environ Saf 2020; 189:109942. [PMID: 31757514 DOI: 10.1016/j.ecoenv.2019.109942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/07/2019] [Accepted: 11/09/2019] [Indexed: 05/21/2023]
Abstract
Although the chemical characteristics of selenomethionine (SeMet) are similar to those of methionine (Met), the physiological activity of SeMet apparently differs in its ability to stimulate ethylene production in plant tissues. Since selenium alters root architecture of rice seedlings by modifying ethylene production, the investigation of the effect of SeMet and Met on rice growth would be a step forward towards unraveling factors that underlie selenium toxicity. Here, we report that SeMet increased concentrations of reactive oxygen species (ROS), inhibiting auxin and increasing ethylene production in rice seedlings. The effect of SeMet on seedlings was mediated by the inhibition of the abundance of transcripts encoding auxin transport and cell expansion proteins. Moreover, SeMet led to increased seedling respiration, which was positively correlated with organic acids consumption, but negatively with sugars consumption, thereby decreasing seedling growth. In contrast with SeMet treatment, Met did not affect ROS production, hormone biosynthesis and seedling growth, indicating an exclusive selenium effect. The singlet oxygen scavenger, 1,4-diazabicyclooctane, overrode the repressive effect of SeMet in seedling growth. Our results demonstrate a phytotoxic effect of SeMet for rice seedlings and reveal a relationship between reactive oxygen species, hormone homeostasis and carbon availability, which regulates growth responses.
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Affiliation(s)
- Rafael S P Malheiros
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Fabrício C M Gonçalves
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Fred A L Brito
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Agustín Zsögön
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Dimas M Ribeiro
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.
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29
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Sun J, Qiu C, Qian W, Wang Y, Sun L, Li Y, Ding Z. Ammonium triggered the response mechanism of lysine crotonylome in tea plants. BMC Genomics 2019; 20:340. [PMID: 31060518 PMCID: PMC6501322 DOI: 10.1186/s12864-019-5716-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 04/18/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Lysine crotonylation, as a novel evolutionarily conserved type of post-translational modifications, is ubiquitous and essential in cell biology. However, its functions in tea plants are largely unknown, and the full functions of lysine crotonylated proteins of tea plants in nitrogen absorption and assimilation remains unclear. Our study attempts to describe the global profiling of nonhistone lysine crotonylation in tea leaves and to explore how ammonium (NH4+) triggers the response mechanism of lysine crotonylome in tea plants. RESULTS Here, we performed the global analysis of crotonylome in tea leaves under NH4+ deficiency/resupply using high-resolution LC-MS/MS coupled with highly sensitive immune-antibody. A total of 2288 lysine crotonylation sites on 971 proteins were identified, of which contained in 15 types of crotonylated motifs. Most of crotonylated proteins were located in chloroplast (37%) and cytoplasm (33%). Compared with NH4+ deficiency, 120 and 151 crotonylated proteins were significantly changed at 3 h and 3 days of NH4+ resupply, respectively. Bioinformatics analysis showed that differentially expressed crotonylated proteins participated in diverse biological processes such as photosynthesis (PsbO, PsbP, PsbQ, Pbs27, PsaN, PsaF, FNR and ATPase), carbon fixation (rbcs, rbcl, TK, ALDO, PGK and PRK) and amino acid metabolism (SGAT, GGAT2, SHMT4 and GDC), suggesting that lysine crotonylation played important roles in these processes. Moreover, the protein-protein interaction analysis revealed that the interactions of identified crotonylated proteins diversely involved in photosynthesis, carbon fixation and amino acid metabolism. Interestingly, a large number of enzymes were crotonylated, such as Rubisco, TK, SGAT and GGAT, and their activities and crotonylation levels changed significantly by sensing ammonium, indicating a potential function of crotonylation in the regulation of enzyme activities. CONCLUSIONS The results indicated that the crotonylated proteins had a profound influence on metabolic process of tea leaves in response to NH4+ deficiency/resupply, which mainly involved in diverse aspects of primary metabolic processes by sensing NH4+, especially in photosynthesis, carbon fixation and amino acid metabolism. The data might serve as important resources for exploring the roles of lysine crotonylation in N metabolism of tea plants. Data were available via ProteomeXchange with identifier PXD011610.
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Affiliation(s)
- Jianhao Sun
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Chen Qiu
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Wenjun Qian
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Yu Wang
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Litao Sun
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Yusheng Li
- Fruit and Tea Technology Extension Station, Jinan, 250000, Shandong, China
| | - Zhaotang Ding
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, Shandong, China.
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30
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Brandl J, Aguilar-Pontes MV, Schäpe P, Noerregaard A, Arvas M, Ram AFJ, Meyer V, Tsang A, de Vries RP, Andersen MR. A community-driven reconstruction of the Aspergillus niger metabolic network. Fungal Biol Biotechnol 2018; 5:16. [PMID: 30275963 PMCID: PMC6158834 DOI: 10.1186/s40694-018-0060-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 09/17/2018] [Indexed: 11/17/2022] Open
Abstract
Background Aspergillus niger is an important fungus used in industrial applications for enzyme and acid production. To enable rational metabolic engineering of the species, available information can be collected and integrated in a genome-scale model to devise strategies for improving its performance as a host organism. Results In this paper, we update an existing model of A. niger metabolism to include the information collected from 876 publications, thereby expanding the coverage of the model by 940 reactions, 777 metabolites and 454 genes. In the presented consensus genome-scale model of A. niger iJB1325 , we integrated experimental data from publications and patents, as well as our own experiments, into a consistent network. This information has been included in a standardized way, allowing for automated testing and continuous improvements in the future. This repository of experimental data allowed the definition of 471 individual test cases, of which the model complies with 373 of them. We further re-analyzed existing transcriptomics and quantitative physiology data to gain new insights on metabolism. Additionally, the model contains 3482 checks on the model structure, thereby representing the best validated genome-scale model on A. niger developed until now. Strain-specific model versions for strains ATCC 1015 and CBS 513.88 have been created containing all data used for model building, thereby allowing users to adopt the models and check the updated version against the experimental data. The resulting model is compliant with the SBML standard and therefore enables users to easily simulate it using their preferred software solution. Conclusion Experimental data on most organisms are scattered across hundreds of publications and several repositories.To allow for a systems level understanding of metabolism, the data must be integrated in a consistent knowledge network. The A. niger iJB1325 model presented here integrates the available data into a highly curated genome-scale model to facilitate the simulation of flux distributions, as well as the interpretation of other genome-scale data by providing the metabolic context. Electronic supplementary material The online version of this article (10.1186/s40694-018-0060-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julian Brandl
- 1Technical University of Denmark, Soeltofts Plads, Building 223, 2800 Kongens Lyngby, Denmark
| | - Maria Victoria Aguilar-Pontes
- 2Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Paul Schäpe
- 6Berlin University of Technology, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Anders Noerregaard
- 1Technical University of Denmark, Soeltofts Plads, Building 223, 2800 Kongens Lyngby, Denmark
| | - Mikko Arvas
- 3VTT Technical Research Centre of Finland, Tietotie 2, 02044 Espoo, Finland.,7Present Address: Finnish Red Cross Blood Service, Helsinki, Finland
| | - Arthur F J Ram
- 5Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Vera Meyer
- 6Berlin University of Technology, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Adrian Tsang
- 4Concordia University, 7141 Sherbrooke Street West, H4B1R6 Montreal, Québec Canada
| | - Ronald P de Vries
- 2Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Mikael R Andersen
- 1Technical University of Denmark, Soeltofts Plads, Building 223, 2800 Kongens Lyngby, Denmark
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31
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Silva NCQ, de Souza GA, Pimenta TM, Brito FAL, Picoli EAT, Zsögön A, Ribeiro DM. Salt stress inhibits germination of Stylosanthes humilis seeds through abscisic acid accumulation and associated changes in ethylene production. Plant Physiol Biochem 2018; 130:399-407. [PMID: 30064096 DOI: 10.1016/j.plaphy.2018.07.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/09/2018] [Accepted: 07/21/2018] [Indexed: 05/13/2023]
Abstract
In Stylosanthes humilis, salt stress tolerance is associated with ethylene production by the seeds, however, how salt stress controls seed germination and ethylene production is poorly understood. Here, we studied the hormonal and metabolic changes triggered by salt stress on germination of S. humilis seeds. Salt stress led to decreased seed germination and ethylene production, concomitantly with higher abscisic acid (ABA) production by seeds. Treatment with NaCl and ABA promoted distinct changes in energy metabolism, allowing seeds to adapt to salt stress conditions. Treatment with the ABA biosynthesis inhibitor fluridone or ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) reversed the effects of salt stress on seed germination and ethylene production. Moreover, ethylene concentration was decreased by increasing the pH of the salt solution. High pH, however, did not influence concentration of ABA in seeds under salt stress. We conclude that biosynthesis of ABA and ethylene in response to salt stress constitutes a point of convergence that provides flexibility to regulate energy metabolism and embryo growth potential of S. humilis seeds within a given pH condition.
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Affiliation(s)
- Nilo C Q Silva
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | - Genaina A de Souza
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | - Thaline M Pimenta
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | - Fred A L Brito
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | - Edgard A T Picoli
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | - Agustín Zsögön
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | - Dimas M Ribeiro
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil.
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32
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Schenck CA, Maeda HA. Tyrosine biosynthesis, metabolism, and catabolism in plants. Phytochemistry 2018; 149:82-102. [PMID: 29477627 DOI: 10.1016/j.phytochem.2018.02.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 01/26/2018] [Accepted: 02/02/2018] [Indexed: 05/22/2023]
Abstract
L-Tyrosine (Tyr) is an aromatic amino acid (AAA) required for protein synthesis in all organisms, but synthesized de novo only in plants and microorganisms. In plants, Tyr also serves as a precursor of numerous specialized metabolites that have diverse physiological roles as electron carriers, antioxidants, attractants, and defense compounds. Some of these Tyr-derived plant natural products are also used in human medicine and nutrition (e.g. morphine and vitamin E). While the Tyr biosynthesis and catabolic pathways have been extensively studied in microbes and animals, respectively, those of plants have received much less attention until recently. Accumulating evidence suggest that the Tyr biosynthetic pathways differ between microbes and plants and even within the plant kingdom, likely to support the production of lineage-specific plant specialized metabolites derived from Tyr. The interspecies variations of plant Tyr pathway enzymes can now be used to enhance the production of Tyr and Tyr-derived compounds in plants and other synthetic biology platforms.
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Affiliation(s)
- Craig A Schenck
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Wang H, Ye X, Li J, Tan B, Chen P, Cheng J, Wang W, Zheng X, Feng J. Transcriptome profiling analysis revealed co-regulation of multiple pathways in jujube during infection by 'Candidatus Phytoplasma ziziphi'. Gene 2018; 665:82-95. [PMID: 29709641 DOI: 10.1016/j.gene.2018.04.070] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/09/2018] [Accepted: 04/24/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND Jujube witches' broom (JWB), caused by a phytoplasma, devastates jujube tree (Ziziphus jujuba) growth and production in Asia. Although host responses to phytoplasmas are studied at the phenotypic, physiological, biochemical and molecular levels, it remains unclear how a host plant responds at the molecular level during the primary stage of infection. METHODS To understand the response of the jujube tree to JWB infection, leaves were sampled at different times during the phytoplasma infection. Transcriptomic analyses at six stages were performed to reveal how phytoplasma infection affects Chinese jujube gene expression through the determination of the key differentially expressed genes (DEGs), and their related pathways. Quantitative real-time PCR was applied to validate 10 differentially expressed genes at different JWB phytoplasma infection stages. RESULTS A total of 25,067 unigenes were mapped to jujube genome reference sequences. In the first infection stage (0-2 weeks after grafting (WAG), a total of 582 jujube genes were differentially regulated but no visible symptoms appeared. Quite a few DEGs related to abscisic acid (ABA) and cytokinin (CTK) were down-regulated, while some related to jasmonic acid (JA) and salicylic acid (SA) were up-regulated, Genes related to plant-pathogen interaction were also differentially expressed. In the second infection stage (37-39WAG), witches' broom symptoms were visible, and a total of 4373 DEGs were identified. Genes involved in biosynthesis and signal transduction of ABA, brassinosteroid (BR), CTK, ethylene (ET), and auxin (IAA), GA, JA and SA, plant-pathogen interaction, flavonoid biosynthesis genes were significantly regulated, suggesting that jujube trees activated defense factors related to SA, JA, ABA and secondary metabolites to defend against phytoplasma infection. By the third infection stage (48-52WAG), serious symptoms occurred and 3386 DEGs were identified. Most DEGs involved in biosynthesis and signal transduction of JA, SA and GA were up-regulated, while those relating to ABA were down-regulated. Genes involved in plant-pathogen interaction were up- or down-regulated, while phenylpropanoid and flavonoid biosynthesis genes were significantly up-regulated. Meanwhile, DEGs involved in photosynthesis, chlorophyll and peroxisome biosynthesis, and carbohydrate metabolism were down-regulated. These results suggested that phytoplasma infection had completely destroyed jujube trees' defense system and had disturbed chlorophyll synthesis and photosynthetic activity in the infected leaves at the late stage, resulting in yellow leaves and other JWB symptoms. DISCUSSION The results in this report suggested that phytohormone biosynthesis and signal transduction, photosynthesis, and secondary metabolism all played important roles in the battle between colonization and defense in the interaction between Ca. Phytoplasma ziziphi and jujube.
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Affiliation(s)
- Huiyu Wang
- Colle of Forestry, Henan Agricultural University, 95 Wenhua Road, 450002 Zhengzhou, People's Republic of China
| | - Xia Ye
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, 450002 Zhengzhou, People's Republic of China
| | - Jidong Li
- Colle of Forestry, Henan Agricultural University, 95 Wenhua Road, 450002 Zhengzhou, People's Republic of China
| | - Bin Tan
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, 450002 Zhengzhou, People's Republic of China
| | - Peng Chen
- Colle of Forestry, Henan Agricultural University, 95 Wenhua Road, 450002 Zhengzhou, People's Republic of China
| | - Jun Cheng
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, 450002 Zhengzhou, People's Republic of China
| | - Wei Wang
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, 450002 Zhengzhou, People's Republic of China
| | - Xianbo Zheng
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, 450002 Zhengzhou, People's Republic of China
| | - Jiancan Feng
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, 450002 Zhengzhou, People's Republic of China; Colle of Forestry, Henan Agricultural University, 95 Wenhua Road, 450002 Zhengzhou, People's Republic of China.
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da Silva AC, de Oliveira Silva FM, Milagre JC, Omena-Garcia RP, Abreu MC, Mafia RG, Nunes-Nesi A, Alfenas AC. Eucalypt plants are physiologically and metabolically affected by infection with Ceratocystis fimbriata. Plant Physiol Biochem 2018; 123:170-179. [PMID: 29247937 DOI: 10.1016/j.plaphy.2017.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 12/01/2017] [Accepted: 12/02/2017] [Indexed: 05/25/2023]
Abstract
Ceratocystis wilt, caused by Ceratocystis fimbriata, is currently one of the most important disease in eucalypt plantations. Plants infected by C. fimbriata have lower volumetric growth, lower pulp yields and reduced timber values. The physiological bases of infection induced by this pathogen in eucalypt plant are not known. Therefore, this study aims to assess the physiological and metabolic changes in eucalypt clones that are resistant and susceptible to C. fimbriata. Once, we evaluated in detail their leaf gas exchange, chlorophyll a fluorescence, water potential, metabolite profiling and growth-related parameters. When inoculated, the susceptible clone displayed reduced water potential, CO2 assimilation rate, stomatal conductance, transpiration rate, photochemical quenching coefficient, electron transport rate, and root biomass. Inoculated resistant and susceptible clones both presented higher respiration rates than healthy plants. Many compounds of primary and secondary metabolism were significantly altered after fungal infection in both clones. These results suggest that, C. fimbriata interferes in the primary and secondary metabolism of plants that may be linked to the induction of defense mechanisms and that, due to water restrictions caused by the fungus in susceptible plants, there is a partial closure of the stomata to prevent water loss and a consequent reduction in photosynthesis and the transpiration rate, which in turn, leads to a decrease in the plant's growth-related. These results combined, allowed for a better understanding of the physiological and metabolic changes following the infectious process of C. fimbriata, which limit eucalypt plant growth.
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Affiliation(s)
- André Costa da Silva
- Departamento de Fitopatologia, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil.
| | | | | | | | - Mário Castro Abreu
- Departamento de Fitopatologia, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil.
| | | | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil.
| | - Acelino Couto Alfenas
- Departamento de Fitopatologia, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil.
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Krzyzaniak Y, Negrel J, Lemaitre-Guillier C, Clément G, Mouille G, Klinguer A, Trouvelot S, Héloir MC, Adrian M. Combined enzymatic and metabolic analysis of grapevine cell responses to elicitors. Plant Physiol Biochem 2018; 123:141-148. [PMID: 29241147 DOI: 10.1016/j.plaphy.2017.12.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/01/2017] [Accepted: 12/06/2017] [Indexed: 05/23/2023]
Abstract
Elicitors trigger plant defense responses, including phytoalexin production and cell-wall reinforcement. Primary metabolism plays an important role in these responses as it fuels the associated energetic costs and provides precursors for the synthesis of the numerous secondary metabolites involved in defenses against pathogens. In this context, we aimed to determine whether oligosaccharidic elicitors differing in their capacity to activate defense-associated secondary metabolism in grapevine would differently impact primary metabolism. To answer this question, cell suspensions were treated with two elicitors: an oligogalacturonide, and the β-glucan laminarin. Enzymatic activity assays together with targeted (HPLC) and global (GC-MS) analyses of metabolites were next performed to compare their impact on plant primary or secondary metabolism. The results showed that the oligogalacturonide, which induced the highest level of the phytoalexin resveratrol and the highest activity of stilbene synthase, also induced the highest activity of shikimate hydroxycinnamoyltransferase, a key enzyme involved in the synthesis of lignin. The oligogalacturonide-induced defenses had a significant impact on primary metabolism 24 h following elicitor treatment, with a reduced abundance of pyruvate and 2-oxoglutarate, together with an increase of a set of metabolites including carbohydrates and amino acids. Interestingly, an accumulation of galacturonate and gentiobiose was observed in the oligogalacturonide- and laminarin-treated cells, respectively, suggesting that both elicitors are rapidly hydrolyzed in grapevine cell suspension cultures.
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Affiliation(s)
- Yuko Krzyzaniak
- UMR Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comte, F-21000, Dijon, France.
| | - Jonathan Negrel
- UMR Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comte, F-21000, Dijon, France.
| | | | - Gilles Clément
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France.
| | - Grégory Mouille
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France.
| | - Agnès Klinguer
- UMR Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comte, F-21000, Dijon, France.
| | - Sophie Trouvelot
- UMR Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comte, F-21000, Dijon, France.
| | - Marie-Claire Héloir
- UMR Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comte, F-21000, Dijon, France.
| | - Marielle Adrian
- UMR Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comte, F-21000, Dijon, France.
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Abstract
Untargeted metabolomics refers to the high-throughput analysis of the metabolic state of a biological system (e.g., tissue, biological fluid, cell culture) based on the concentration profile of all measurable free low molecular weight metabolites. Gas chromatography-mass spectrometry (GC-MS), being a highly sensitive and high-throughput analytical platform, has been proven a useful tool for untargeted studies of primary metabolism in a variety of applications. As an omic analysis, GC-MS metabolomics is a multistep procedure; thus, standardization of an untargeted GC-MS metabolomics protocol requires the integrated optimization of pre-analytical, analytical, and computational steps. The main difference of GC-MS metabolomics compared to other metabolomics analytical platforms, including liquid chromatography-MS, is the need for the derivatization of the metabolite extracts into volatile and thermally stable derivatives, the latter being quantified in the metabolic profiles. This analytical step requires special care in the optimization of the untargeted GC-MS metabolomics experimental protocol. Moreover, both the derivatization of the original sample and the compound fragmentation that takes place in GC-MS impose specialized GC-MS metabolomic data identification, quantification, normalization and filtering methods. In this chapter, we describe the integrated protocol of untargeted GC-MS metabolomics with both the analytical and computational steps, focusing on the GC-MS specific parts, and provide details on any sample depending differences.
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Affiliation(s)
- Matthaios-Emmanouil P Papadimitropoulos
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology - Hellas (FORTH/ICE-HT), Patras, 26504, Greece
- Division of Genetics, Cell & Developmental Biology, Department of Biology, University of Patras, Patras, 26500, Greece
| | - Catherine G Vasilopoulou
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology - Hellas (FORTH/ICE-HT), Patras, 26504, Greece
- Human and Animal Physiology Laboratory, Department of Biology, University of Patras, Patras, 26500, Greece
| | - Christoniki Maga-Nteve
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology - Hellas (FORTH/ICE-HT), Patras, 26504, Greece
- School of Medicine, University of Patras, Patras, 26500, Greece
| | - Maria I Klapa
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology - Hellas (FORTH/ICE-HT), Patras, 26504, Greece.
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA.
- Department of Bioengineering, University of Maryland, College Park, MD 20742, USA.
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Patel J, Ariyaratne M, Ahmed S, Ge L, Phuntumart V, Kalinoski A, Morris PF. Dual functioning of plant arginases provides a third route for putrescine synthesis. Plant Sci 2017; 262:62-73. [PMID: 28716421 DOI: 10.1016/j.plantsci.2017.05.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 05/04/2017] [Accepted: 05/25/2017] [Indexed: 05/19/2023]
Abstract
Two biosynthetic routes are known for putrescine, an essential plant metabolite. Ornithine decarboxylase (ODC) converts ornithine directly to putrescine, while a second route for putrescine biosynthesis utilizes arginine decarboxylase (ADC) to convert arginine to agmatine, and two additional enzymes, agmatine iminohydrolase (AIH) and N-carbamoyl putrescine aminohydrolase (NLP1) to complete this pathway. Here we show that plants can use ADC and arginase/agmatinase (ARGAH) as a third route for putrescine synthesis. Transformation of Arabidopsis thaliana ADC2, and any of the arginases from A. thaliana (ARGAH1, or ARGHA2) or the soybean gene Glyma.03g028000 (GmARGAH) into a yeast strain deficient in ODC, fully complemented the mutant phenotype. In vitro assays using purified recombinant enzymes of AtADC1 and AtARGAH2 were used to show that these enzymes can function in concert to convert arginine to agmatine and putrescine. Transient expression analysis of the soybean genes (Glyma.06g007500, ADC; Glyma.03g028000 GmARGAH) and the A. thaliana ADC2 and ARGAH genes in leaves of Nicotiana benthamiana, showed that these proteins are localized to the chloroplast. Experimental support for this pathway also comes from the fact that expression of AtARGAH, but not AtAIH or AtNLP1, is co-regulated with AtADC2 in response to drought, oxidative stress, wounding, and methyl jasmonate treatments. Based on the high affinity of ARGAH2 for agmatine, its co-localization with ADC2, and typically low arginine levels in many plant tissues, we propose that these two enzymes can be major contributors to putrescine synthesis in many A. thaliana stress responses.
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Affiliation(s)
- Jigar Patel
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, United States
| | - Menaka Ariyaratne
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, United States
| | - Sheaza Ahmed
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, United States
| | - Lingxiao Ge
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, United States
| | - Vipaporn Phuntumart
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, United States
| | - Andrea Kalinoski
- Department of Surgery, University of Toledo, 3000 Arlington Ave, Toledo, OH 43614, United States
| | - Paul F Morris
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, United States.
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Copley TR, Aliferis KA, Kliebenstein DJ, Jabaji SH. An integrated RNAseq- 1H NMR metabolomics approach to understand soybean primary metabolism regulation in response to Rhizoctonia foliar blight disease. BMC Plant Biol 2017; 17:84. [PMID: 28449662 PMCID: PMC5408482 DOI: 10.1186/s12870-017-1020-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 03/27/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND Rhizoctonia solani AG1-IA is a devastating phytopathogen causing Rhizoctonia foliar blight (RFB) of soybean worldwide with yield losses reaching 60%. Plant defense mechanisms are complex and information from different metabolic pathways is required to thoroughly understand plant defense regulation and function. Combining information from different "omics" levels such as transcriptomics, metabolomics, and proteomics is required to gain insights into plant metabolism and its regulation. As such, we studied fluctuations in soybean metabolism in response to R. solani infection at early and late disease stages using an integrated transcriptomics-metabolomics approach, focusing on the regulation of soybean primary metabolism and oxidative stress tolerance. RESULTS Transcriptomics (RNAseq) and metabolomics (1H NMR) data were analyzed individually and by integration using bidirectional orthogonal projections to latent structures (O2PLS) to reveal possible links between the metabolome and transcriptome during early and late infection stages. O2PLS analysis detected 516 significant transcripts, double that reported in the univariate analysis, and more significant metabolites than detected in partial least squares discriminant analysis. Strong separation of treatments based on integration of the metabolomes and transcriptomes of the analyzed soybean leaves was revealed, similar trends as those seen in analyses done on individual datasets, validating the integration method being applied. Strong fluctuations of soybean primary metabolism occurred in glycolysis, the TCA cycle, photosynthesis and photosynthates in response to R. solani infection. Data were validated using quantitative real-time PCR on a set of specific markers as well as randomly selected genes. Significant increases in transcript and metabolite levels involved in redox reactions and ROS signaling, such as peroxidases, thiamine, tocopherol, proline, L-alanine and GABA were also recorded. Levels of ethanol increased 24 h post-infection in soybean leaves, and alcohol dehydrogenase (ADH) loss-of-function mutants of Arabidopsis thaliana had higher necrosis than wild type plants. CONCLUSIONS As a proof-of-concept, this study offers novel insights into the biological correlations and identification of candidate genes and metabolites that can be used in soybean breeding for resistance to R. solani AG1-IA infection. Additionally, these findings imply that alcohol and its associated gene product ADH may have important roles in plant resistance to R. solani AG1-IA causing foliar blight.
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Affiliation(s)
- Tanya R. Copley
- Plant Science Department, McGill University, Ste-Anne-de-Bellevue, Quebec, H9X 3V9 Canada
| | - Konstantinos A. Aliferis
- Department of Plant Science, Laboratory of Pesticide Science, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece
| | | | - Suha H. Jabaji
- Plant Science Department, McGill University, Ste-Anne-de-Bellevue, Quebec, H9X 3V9 Canada
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Li J, Yang X, Liu X, Yu H, Du C, Li M, He D. Proteomic analysis of the compatible interaction of wheat and powdery mildew (Blumeria graminis f. sp. tritici). Plant Physiol Biochem 2017; 111:234-243. [PMID: 27951493 DOI: 10.1016/j.plaphy.2016.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 11/30/2016] [Accepted: 12/02/2016] [Indexed: 05/20/2023]
Abstract
Proteome characteristics of wheat leaves with the powdery mildew pathogen Blumeria graminis f. sp. tritici (Bgt) infection were investigated by two-dimensional electrophoresis and tandem MALDI-TOF/TOF-MS. We identified 46 unique proteins which were differentially expressed at 24, 48, and 72 h post-inoculation. The functional classification of these proteins showed that most of them were involved in photosynthesis, carbohydrate and nitrogen metabolism, defense responses, and signal transduction. Upregulated proteins included primary metabolism pathways and defense responses, while proteins related to photosynthesis and signal transduction were mostly downregulated. As expected, more antioxidative proteins were activated at the later infection stage than the earlier stage, suggesting that the antioxidative system of host plays a role in maintaining the compatible interaction between wheat and powdery mildew. A high accumulation of 6-phosphogluconate dehydrogenase and isocitrate dehydrogenase in infected leaves indicated the regulation of the TCA cycle and pentose phosphate pathway in parallel to the activation of host defenses. The downregulation of MAPK5 could be facilitated for the compatible interaction of wheat plants and Bgt. qRT-PCR analysis supported the data of protein expression profiles. Our results reveal the relevance of primary plant metabolism and defense responses during compatible interaction, and provide new insights into the biology of susceptible wheat in response to Bgt infection.
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Affiliation(s)
- Jie Li
- Key Laboratory of Regulating and Controlling Crop Growth and Development (Henan Agriculture University) Ministry of Education; Collaborative Innovation Center of Henan Grain Crops; College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Xiwen Yang
- Key Laboratory of Regulating and Controlling Crop Growth and Development (Henan Agriculture University) Ministry of Education; Collaborative Innovation Center of Henan Grain Crops; College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Xinhao Liu
- Lab of Plant Protection, Kaifeng Agriculture and Forestry Science Institute, Kaifeng, Henan 475004, China
| | - Haibo Yu
- Key Laboratory of Regulating and Controlling Crop Growth and Development (Henan Agriculture University) Ministry of Education; Collaborative Innovation Center of Henan Grain Crops; College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Congyang Du
- Key Laboratory of Regulating and Controlling Crop Growth and Development (Henan Agriculture University) Ministry of Education; Collaborative Innovation Center of Henan Grain Crops; College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Mengda Li
- Key Laboratory of Regulating and Controlling Crop Growth and Development (Henan Agriculture University) Ministry of Education; Collaborative Innovation Center of Henan Grain Crops; College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Dexian He
- Key Laboratory of Regulating and Controlling Crop Growth and Development (Henan Agriculture University) Ministry of Education; Collaborative Innovation Center of Henan Grain Crops; College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China.
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Veprinskiy V, Heizinger L, Plach MG, Merkl R. Assessing in silico the recruitment and functional spectrum of bacterial enzymes from secondary metabolism. BMC Evol Biol 2017; 17:36. [PMID: 28125959 PMCID: PMC5270213 DOI: 10.1186/s12862-017-0886-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 01/16/2017] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Microbes, plants, and fungi synthesize an enormous number of metabolites exhibiting rich chemical diversity. For a high-level classification, metabolism is subdivided into primary (PM) and secondary (SM) metabolism. SM products are often not essential for survival of the organism and it is generally assumed that SM enzymes stem from PM homologs. RESULTS We wanted to assess evolutionary relationships and function of bona fide bacterial PM and SM enzymes. Thus, we analyzed the content of 1010 biosynthetic gene clusters (BGCs) from the MIBiG dataset; the encoded bacterial enzymes served as representatives of SM. The content of 15 bacterial genomes known not to harbor BGCs served as a representation of PM. Enzymes were categorized on their EC number and for these enzyme functions, frequencies were determined. The comparison of PM/SM frequencies indicates a certain preference for hydrolases (EC class 3) and ligases (EC class 6) in PM and of oxidoreductases (EC class 1) and lyases (EC class 4) in SM. Based on BLAST searches, we determined pairs of PM/SM homologs and their functional diversity. Oxidoreductases, transferases (EC class 2), lyases and isomerases (EC class 5) form a tightly interlinked network indicating that many protein folds can accommodate different functions in PM and SM. In contrast, the functional diversity of hydrolases and especially ligases is significantly limited in PM and SM. For the most direct comparison of PM/SM homologs, we restricted for each BGC the search to the content of the genome it comes from. For each homologous hit, the contribution of the genomic neighborhood to metabolic pathways was summarized in BGC-specific html-pages that are interlinked with KEGG; this dataset can be downloaded from https://www.bioinf.ur.de . CONCLUSIONS Only few reaction chemistries are overrepresented in bacterial SM and at least 55% of the enzymatic functions present in BGCs possess PM homologs. Many SM enzymes arose in PM and Nature utilized the evolvability of enzymes similarly to establish novel functions both in PM and SM. Future work aimed at the elucidation of evolutionary routes that have interconverted a PM enzyme into an SM homolog can profit from our BGC-specific annotations.
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Affiliation(s)
- Valery Veprinskiy
- Faculty of Mathematics and Computer Science, University of Hagen, D-58084, Hagen, Germany
| | - Leonhard Heizinger
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, D-93040, Regensburg, Germany
| | - Maximilian G Plach
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, D-93040, Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, D-93040, Regensburg, Germany.
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Abstract
Photorespiration is a central component of photosynthesis; however to better understand its role it should be viewed in the context of an integrated metabolic network rather than a series of individual reactions that operate independently. Isotopically nonstationary 13C metabolic flux analysis (INST-MFA), which is based on transient labeling studies at metabolic steady state, offers a comprehensive platform to quantify plant central metabolism. In this chapter, we describe the application of INST-MFA to investigate metabolism in leaves. Leaves are an autotrophic tissue, assimilating CO2 over a diurnal period implying that the metabolic steady state is limited to less than 12 h and thus requiring an INST-MFA approach. This strategy results in a comprehensive unified description of photorespiration, Calvin cycle, sucrose and starch synthesis, tricarboxylic acid (TCA) cycle, and amino acid biosynthetic fluxes. We present protocols of the experimental aspects for labeling studies: transient 13CO2 labeling of leaf tissue, sample quenching and extraction, mass spectrometry (MS) analysis of isotopic labeling data, measurement of sucrose and amino acids in vascular exudates, and provide details on the computational flux estimation using INST-MFA.
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Affiliation(s)
- Fangfang Ma
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Lara J Jazmin
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Doug K Allen
- Donald Danforth Plant Science Center, St. Louis, MO, USA.
- United States Department of Agriculture, Agricultural Research Service, St. Louis, MO, USA.
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Kojima R, Arai T, Matsufuji H, Kasumi T, Watanabe T, Ogihara J. The relationship between the violet pigment PP-V production and intracellular ammonium level in Penicillium purpurogenum. AMB Express 2016; 6:43. [PMID: 27368914 PMCID: PMC4930434 DOI: 10.1186/s13568-016-0215-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 06/24/2016] [Indexed: 01/01/2023] Open
Abstract
Penicillium purpurogenum is the fungus that produces an azaphilone pigment. However, details about the pigment biosynthesis pathway are unknown. The violet pigment PP-V is the one of the main pigments biosynthesized by this fungus. This pigment contains an amino group in a pyran ring as its core structure. We focused on this pigment and examined the relationship between intracellular ammonium concentration and pigment production using glutamine as a nitrogen source. The intracellular ammonium level decreased about 1.5-fold in conditions favoring PP-V production. Moreover, P. purpurogenum was transferred to medium in which it commonly produces the related pigment PP-O after cultivating it in the presence or absence of glutamine to investigate whether this fungus biosynthesizes PP-V using surplus ammonium in cells. Only mycelia cultured in medium containing 10 mM glutamine produced the violet pigment, and simultaneously intracellular ammonium levels decreased under this condition. From comparisons of the amount of PP-V that was secreted with quantity of surplus intracellular ammonium, it is suggested that P. purpurogenum maintains ammonium homeostasis by excreting waste ammonium as PP-V.
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Xu G, Singh S, Barnaby J, Buyer J, Reddy V, Sicher R. Effects of growth temperature and carbon dioxide enrichment on soybean seed components at different stages of development. Plant Physiol Biochem 2016; 108:313-322. [PMID: 27494565 DOI: 10.1016/j.plaphy.2016.07.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 07/21/2016] [Accepted: 07/26/2016] [Indexed: 05/28/2023]
Abstract
Soybean plants were grown to maturity in controlled environment chambers and at the onset of flowering three temperature treatments were imposed that provided optimum [28/24 °C], low [22/18 °C] or high [36/32 °C] chamber air temperatures. In addition, plants were treated continuously with either 400 or 800 μmol mol-1 CO2. Seeds were harvested at 42, 53, 69 and 95 days after planting (i.e., final maturity). This study quantified 51 metabolites in developing soybean seeds, plus total lipids and proteins were measured at maturity. About 80% of measured soluble carbohydrates, amines and organic acids decreased to low levels in mature seeds, although important exceptions were raffinose, ribose/arabinose, citrate and all eight fatty acids. This suggested that the metabolism of young seeds supported lipid and protein synthesis. A total of 35 and 9 metabolites differed among temperature and CO2 treatments, respectively, and treatment effects were predominately observed on the first and second samplings. However, shikimate, pinitol and oleate were increased by high temperature treatments in mature seeds. The above results indicated that CO2 enrichment primarily altered metabolite levels during the initial stages of seed development and this was likely due to enhanced photosynthate formation in leaves.
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Affiliation(s)
- Guangli Xu
- Crop Systems and Climate Change Laboratory, U.S.D.A.-Agricultural Research Service, Room 342, Building 001, BARC-west, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
| | - Shardendu Singh
- Crop Systems and Climate Change Laboratory, U.S.D.A.-Agricultural Research Service, Room 342, Building 001, BARC-west, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
| | - Jinyoung Barnaby
- Crop Systems and Climate Change Laboratory, U.S.D.A.-Agricultural Research Service, Room 342, Building 001, BARC-west, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
| | - Jeffrey Buyer
- Sustainable Agricultural Systems Laboratory, U.S.D.A.-Agricultural Research Service, Room 245, Building 001, BARC-west, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
| | - Vangimalla Reddy
- Crop Systems and Climate Change Laboratory, U.S.D.A.-Agricultural Research Service, Room 342, Building 001, BARC-west, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
| | - Richard Sicher
- Crop Systems and Climate Change Laboratory, U.S.D.A.-Agricultural Research Service, Room 342, Building 001, BARC-west, 10300 Baltimore Avenue, Beltsville, MD 20705, USA.
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Swain S, Myers ZA, Siriwardana CL, Holt BF. The multifaceted roles of NUCLEAR FACTOR-Y in Arabidopsis thaliana development and stress responses. Biochim Biophys Acta Gene Regul Mech 2016; 1860:636-644. [PMID: 27989935 DOI: 10.1016/j.bbagrm.2016.10.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/26/2016] [Accepted: 10/27/2016] [Indexed: 01/03/2023]
Abstract
NUCLEAR FACTOR-Y (NF-Y) is a heterotrimeric transcription factor (TF) consisting of evolutionarily distinct NF-YA, NF-YB and NF-YC subunits. The functional NF-Y heterotrimer binds to CCAAT elements in eukaryotic gene promoters and influences their expression. The genome of the model organism Arabidopsis thaliana encodes 10 distinct NF-YA, NF-YB, and NF-YC proteins, allowing for enormous combinatorial and functional diversity. Two decades of research have elucidated the importance of NF-Ys in plant growth, development and stress responses; however, the molecular mechanisms of action remain largely unexplored. Intriguingly, recent evidence suggests that NF-Ys are frequently associated with other groups of TFs, expanding the potential NF-Y combinatorial complexity. Further, information regarding the regulation of individual NF-Y subunits at the transcriptional and post-transcriptional level is beginning to emerge. In this review, we will identify developing trends within the NF-Y field and discuss recent progress towards a better understanding of NF-Y function, molecular action, and regulation in the context of Arabidopsis. This article is part of a Special Issue entitled: Nuclear Factor Y in Development and Disease, edited by Prof. Roberto Mantovani.
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Affiliation(s)
- Swadhin Swain
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, United States
| | - Zachary A Myers
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, United States
| | - Chamindika L Siriwardana
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, United States
| | - Ben F Holt
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, United States.
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Orf I, Schwarz D, Kaplan A, Kopka J, Hess WR, Hagemann M, Klähn S. CyAbrB2 Contributes to the Transcriptional Regulation of Low CO2 Acclimation in Synechocystis sp. PCC 6803. Plant Cell Physiol 2016; 57:2232-2243. [PMID: 27638927 DOI: 10.1093/pcp/pcw146] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 07/29/2016] [Indexed: 06/06/2023]
Abstract
Acclimation to low CO2 conditions in cyanobacteria involves the co-ordinated regulation of genes mainly encoding components of the carbon-concentrating mechanism (CCM). Making use of several independent microarray data sets, a core set of CO2-regulated genes was defined for the model strain Synechocystis sp. PCC 6803. On the transcriptional level, the CCM is mainly regulated by the well-characterized transcriptional regulators NdhR (= CcmR) and CmpR. However, the role of an additional regulatory protein, namely cyAbrB2 belonging to the widely distributed AbrB regulator family that was originally characterized in the genus Bacillus, is less defined. Here we present results of transcriptomic and metabolic profiling of the wild type and a ΔcyabrB2 mutant of Synechocystis sp. PCC 6803 after shifts from high CO2 (5% in air, HC) to low CO2 (0.04%, LC). Evaluation of the transcriptomic data revealed that cyAbrB2 is involved in the regulation of several CCM-related genes such as sbtA/B, ndhF3/ndhD3/cupA and cmpABCD under LC conditions, but apparently acts supplementary to NdhR and CmpR. Under HC conditions, cyAbrB2 deletion affects the transcript abundance of PSII subunits, light-harvesting components and Calvin-Benson-Bassham cycle enzymes. These changes are also reflected by down-regulation of primary metabolite pools. The data suggest a role for cyAbrB2 in adjusting primary carbon and nitrogen metabolism to photosynthetic activity under fluctuating environmental conditions. The findings were integrated into the current knowledge about the acquisition of inorganic carbon (Ci), the CCM and parts of its regulation on the transcriptional level.
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Affiliation(s)
- Isabel Orf
- Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, Potsdam-Golm, Germany
| | - Doreen Schwarz
- Plant Physiology Department, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Aaron Kaplan
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
| | - Joachim Kopka
- Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, Potsdam-Golm, Germany
| | - Wolfgang R Hess
- Genetics & Experimental Bioinformatics, Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - Martin Hagemann
- Plant Physiology Department, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Stephan Klähn
- Genetics & Experimental Bioinformatics, Institute of Biology III, University of Freiburg, Freiburg, Germany
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Batista Silva W, Daloso DM, Fernie AR, Nunes-Nesi A, Araújo WL. Can stable isotope mass spectrometry replace radiolabelled approaches in metabolic studies? Plant Sci 2016; 249:59-69. [PMID: 27297990 DOI: 10.1016/j.plantsci.2016.05.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 04/21/2016] [Accepted: 05/13/2016] [Indexed: 05/03/2023]
Abstract
Metabolic pathways and the key regulatory points thereof can be deduced using isotopically labelled substrates. One prerequisite is the accurate measurement of the labeling pattern of targeted metabolites. The subsequent estimation of metabolic fluxes following incubation in radiolabelled substrates has been extensively used. Radiolabelling is a sensitive approach and allows determination of total label uptake since the total radiolabel content is easy to detect. However, the incubation of cells, tissues or the whole plant in a stable isotope enriched environment and the use of either mass spectrometry or nuclear magnetic resonance techniques to determine label incorporation within specific metabolites offers the possibility to readily obtain metabolic information with higher resolution. It additionally also offers an important complement to other post-genomic strategies such as metabolite profiling providing insights into the regulation of the metabolic network and thus allowing a more thorough description of plant cellular function. Thus, although safety concerns mean that stable isotope feeding is generally preferred, the techniques are in truth highly complementary and application of both approaches in tandem currently probably provides the best route towards a comprehensive understanding of plant cellular metabolism.
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Affiliation(s)
- Willian Batista Silva
- Max Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa-MG, Brazil.
| | - Danilo M Daloso
- Max-Planck-Institute of Molecular Plant Physiology Am Mühlenberg 1, 14476,Golm Potsdam, Germany.
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology Am Mühlenberg 1, 14476,Golm Potsdam, Germany.
| | - Adriano Nunes-Nesi
- Max Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa-MG, Brazil.
| | - Wagner L Araújo
- Max Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa-MG, Brazil.
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Sharma N, Chauhan RS, Sood H. Discerning picroside-I biosynthesis via molecular dissection of in vitro shoot regeneration in Picrorhiza kurroa. Plant Cell Rep 2016; 35:1601-1615. [PMID: 27038441 DOI: 10.1007/s00299-016-1976-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/28/2016] [Indexed: 06/05/2023]
Abstract
Expression analysis of primary and secondary metabolic pathways genes vis-à-vis shoot regeneration revealed developmental regulation of picroside-I biosynthesis in Picrorhiza kurroa. Picroside-I (P-I) is an important iridoid glycoside used in several herbal formulations for treatment of various disorders. P-I is synthesized in shoots of Picrorhiza kurroa and Picrorhiza scrophulariiflora. Current study reports on understanding P-I biosynthesis in different morphogenetic stages, viz. plant segment (PS), callus initiation (CI), callus mass (CM), shoot primordia (SP), multiple shoots (MS) and fully developed (FD) stages of P. kurroa. Expression analysis of genes involved in primary and secondary metabolism revealed that genes encoding HMGR, PMK, DXPS, ISPE, GS, G10H, DAHPS and PAL enzymes of MVA, MEP, iridoid and shikimate/phenylpropanoid pathways showed significant modulation of expression in SP, MS and FD stages in congruence with P-I content compared to CM stage. While HK, PK, ICDH, MDH and G6PDH showed high expression in MS and FD stages of P. kurroa, RBA, HisK and CytO showed high expression with progress in regeneration of shoots. Quantitative expression analysis of secondary metabolism genes at two temperatures revealed that 7 genes HMGR, PMK, DXPS, GS, G10H, DAHPS and PAL showed high transcript abundance (32-87-folds) in FD stage derived from leaf and root segments at 15 °C compared to 25 °C in P. kurroa. Further screening of these genes at species level showed high expression pattern in P. kurroa (6-19-folds) vis-à-vis P. scrophulariiflora that was in corroboration with P-I content. Therefore, current study revealed developmental regulation of P-I biosynthesis in P. kurroa which would be useful in designing a suitable genetic intervention study by targeting these genes for enhancing P-I production.
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Affiliation(s)
- Neha Sharma
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234, HP, India
| | - Rajinder Singh Chauhan
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234, HP, India
| | - Hemant Sood
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234, HP, India.
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Budzinski IGF, Moon DH, Morosini JS, Lindén P, Bragatto J, Moritz T, Labate CA. Integrated analysis of gene expression from carbon metabolism, proteome and metabolome, reveals altered primary metabolism in Eucalyptus grandis bark, in response to seasonal variation. BMC Plant Biol 2016; 16:149. [PMID: 27364638 PMCID: PMC4929727 DOI: 10.1186/s12870-016-0839-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 06/22/2016] [Indexed: 05/09/2023]
Abstract
BACKGROUND Seasonal variation is presumed to play an important role in the regulation of tree growth, especially for Eucalyptus grandis, a fast-growing tree. This variation may induce changes in the whole tree at transcriptional, protein and metabolite levels. Bark represents an important group of tissues that protect trees from desiccation and pathogen attack, and it has been identified as potential feedstock for lignocellulosic derived biofuels. Despite the growing interest, little is known about the molecular mechanisms that regulates bark metabolism, particularly in tropical countries. RESULTS In this study we report the changes observed in the primary metabolism of E. grandis bark during two contrasting seasons in Brazil, summer (wet) and winter (dry), through the combination of transcripts (RT-qPCR), proteome (2-DE gels) and metabolome (GC-MS) analysis, in an integrated manner. Twenty-four genes, involved in carbon metabolism, were analyzed in the two seasons. Eleven were up-regulated in summer, three were up-regulated in winter and ten did not show statistical differences in the expression pattern. The proteomic analysis using 2-DE gels showed 77 proteins expressing differences in abundance, with 38 spots up-regulated in summer and 37 in winter. Different metabolites significantly accumulated during winter. CONCLUSIONS This study revealed a metabolic reconfiguration in the primary metabolism of E. grandis bark, triggered by seasonal variation. Transcripts and protein data suggests that during winter carbohydrate formation seems to be favored by tree metabolism. Glucose, fructose and sucrose accumulated at significant levels during the winter.
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Affiliation(s)
- Ilara Gabriela Frasson Budzinski
- />Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP 13418-900 Brasil
| | - David H. Moon
- />Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP 13418-900 Brasil
| | - Júlia Silva Morosini
- />Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP 13418-900 Brasil
| | - Pernilla Lindén
- />Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, SE-901 83 Sweden
| | - Juliano Bragatto
- />Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP 13418-900 Brasil
| | - Thomaz Moritz
- />Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, SE-901 83 Sweden
| | - Carlos Alberto Labate
- />Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP 13418-900 Brasil
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Córdoba J, Molina-Cano JL, Martínez-Carrasco R, Morcuende R, Pérez P. Functional and transcriptional characterization of a barley mutant with impaired photosynthesis. Plant Sci 2016; 244:19-30. [PMID: 26810450 DOI: 10.1016/j.plantsci.2015.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/14/2015] [Accepted: 12/18/2015] [Indexed: 06/05/2023]
Abstract
Chemical mutagenesis induces variations that may assist in the identification of targets for adaptation to growth under atmospheric CO2 enrichment. The aim of this work was to characterize the limitations causing reduced photosynthetic capacity in G132 mutagenized barley (Hordeum vulgare L. cv. Graphic) grown in a glasshouse. Compared to the wild type (WT) G132 showed increased transcript levels for the PSII light harvesting complex, but lower levels of chlorophyll, transcripts for protochlorophyllide oxidoreductase A and psbQ, and PSII quantum efficiency in young leaves. Rubisco limitation had an overriding influence on G132 photosynthesis, and was due to strong and selective decreases in Rubisco protein and activity. These reductions were accompanied by enhanced Rubisco transcripts, but increased levels of a Rubisco degradation product. G132 showed lower levels of carbohydrates, amino acids and corresponding transcripts, and proteins, but not of nitrate. Many of the measured parameters recovered in the mutant as development progressed, or decreased less than in the WT, indicating that senescence was delayed. G132 had a longer growth period than the WT and similar final plant dry matter. The reduced resource investment in Rubisco of G132 may prove useful for studies on barley adaptation to elevated CO2 and climate change.
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Affiliation(s)
- Javier Córdoba
- Institute of Natural Resources and Agrobiology of Salamanca, IRNASA-CSIC, Cordel de Merinas 40, E-37008 Salamanca, Spain; IRTA (Institute for Food and Agricultural Research and Technology), Field Crops, Av. Alcalde Rovira i Roure, 191, E-25198 Lérida, Spain
| | - José-Luis Molina-Cano
- IRTA (Institute for Food and Agricultural Research and Technology), Field Crops, Av. Alcalde Rovira i Roure, 191, E-25198 Lérida, Spain
| | - Rafael Martínez-Carrasco
- Institute of Natural Resources and Agrobiology of Salamanca, IRNASA-CSIC, Cordel de Merinas 40, E-37008 Salamanca, Spain
| | - Rosa Morcuende
- Institute of Natural Resources and Agrobiology of Salamanca, IRNASA-CSIC, Cordel de Merinas 40, E-37008 Salamanca, Spain
| | - Pilar Pérez
- Institute of Natural Resources and Agrobiology of Salamanca, IRNASA-CSIC, Cordel de Merinas 40, E-37008 Salamanca, Spain.
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50
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Han S, Liu Y, Xie L, Zhu B, Hu Y. Comparative expression profiling of genes involved in primary metabolism in high-yield and wild-type strains of Acremonium chrysogenum. Antonie Van Leeuwenhoek 2015; 109:357-69. [PMID: 26708072 DOI: 10.1007/s10482-015-0638-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 12/17/2015] [Indexed: 11/26/2022]
Abstract
Cephalosporin C (CPC) productivity of Acremonium chrysogenum has been improved significantly through classical strain improvement programs. Here, we used transcription and metabolite profiling to address mechanisms underlying CPC production in a high yield (HY) strain. Transcription and metabolite profiling indicated that enzymes involved in amino acid production are higher in abundance in the HY strain. Moreover, results indicate a higher flow of precursors from the glycolysis and gluconeogenesis pathways to serine synthesis at the late stage of fermentation in the HY strain. In addition, less pyruvate would enter the TCA cycle thus favoring valine synthesis. Amino acid production would also benefit from a more active pentose phosphate pathway and γ-amino butyric acid shunt both generating NADPH. Moreover the glyoxylate pathway seems to be more active in the HY strain. These results may provide new leads for CPC strain improvement in industry.
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Affiliation(s)
- Shu Han
- Shanghai Institute of Pharmaceutical Industry, 1320 Beijing Road (W), Shanghai, 200040, China
- China State Institute of Pharmaceutical Industry, Zhangjiang Institute, 285 Gebaini Road, Shanghai, 201203, China
| | - Yan Liu
- China State Institute of Pharmaceutical Industry, Zhangjiang Institute, 285 Gebaini Road, Shanghai, 201203, China
| | - Liping Xie
- China State Institute of Pharmaceutical Industry, Zhangjiang Institute, 285 Gebaini Road, Shanghai, 201203, China
| | - Baoquan Zhu
- Shanghai Institute of Pharmaceutical Industry, 1320 Beijing Road (W), Shanghai, 200040, China
| | - Youjia Hu
- China State Institute of Pharmaceutical Industry, Zhangjiang Institute, 285 Gebaini Road, Shanghai, 201203, China.
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