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Aroca A, García-Díaz I, García-Calderón M, Gotor C, Márquez AJ, Betti M. Photorespiration: regulation and new insights on the potential role of persulfidation. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6023-6039. [PMID: 37486799 PMCID: PMC10575701 DOI: 10.1093/jxb/erad291] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/21/2023] [Indexed: 07/26/2023]
Abstract
Photorespiration has been considered a 'futile' cycle in C3 plants, necessary to detoxify and recycle the metabolites generated by the oxygenating activity of Rubisco. However, several reports indicate that this metabolic route plays a fundamental role in plant metabolism and constitutes a very interesting research topic. Many open questions still remain with regard to photorespiration. One of these questions is how the photorespiratory process is regulated in plants and what factors contribute to this regulation. In this review, we summarize recent advances in the regulation of the photorespiratory pathway with a special focus on the transcriptional and post-translational regulation of photorespiration and the interconnections of this process with nitrogen and sulfur metabolism. Recent findings on sulfide signaling and protein persulfidation are also described.
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Affiliation(s)
- Angeles Aroca
- Instituto de Bioquímica Vegetal y Fotosíntesis (Universidad de Sevilla, Consejo Superior de Investigaciones Científicas), Américo Vespucio 49, 41092 Sevilla, Spain
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, C/Profesor García González, 1, 41012 Sevilla, Spain
| | - Inmaculada García-Díaz
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, C/Profesor García González, 1, 41012 Sevilla, Spain
| | - Margarita García-Calderón
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, C/Profesor García González, 1, 41012 Sevilla, Spain
| | - Cecilia Gotor
- Instituto de Bioquímica Vegetal y Fotosíntesis (Universidad de Sevilla, Consejo Superior de Investigaciones Científicas), Américo Vespucio 49, 41092 Sevilla, Spain
| | - Antonio J Márquez
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, C/Profesor García González, 1, 41012 Sevilla, Spain
| | - Marco Betti
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, C/Profesor García González, 1, 41012 Sevilla, Spain
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2
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Drapal M, Enfissi EMA, Almeida J, Rapacz E, Nogueira M, Fraser PD. The potential of metabolomics in assessing global compositional changes resulting from the application of CRISPR/Cas9 technologies. Transgenic Res 2023; 32:265-278. [PMID: 37166587 DOI: 10.1007/s11248-023-00347-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 04/03/2023] [Indexed: 05/12/2023]
Abstract
Exhaustive analysis of genetically modified crops over multiple decades has increased societal confidence in the technology. New Plant Breeding Techniques are now emerging with improved precision and the ability to generate products containing no foreign DNA and mimic/replicate conventionally bred varieties. In the present study, metabolomic analysis was used to compare (i) tobacco genotypes with and without the CRISPR associated protein 9 (Cas9), (ii) tobacco lines with the edited and non-edited DE-ETIOLATED-1 gene without phenotype and (iii) leaf and fruit tissue from stable non-edited tomato progeny with and without the Cas9. In all cases, multivariate analysis based on the difference test using LC-HRMS/MS and GC-MS data indicated no significant difference in their metabolomes. The variations in metabolome composition that were evident could be associated with the processes of tissue culture regeneration and/or transformation (e.g. interaction with Agrobacterium). Metabolites responsible for the variance included quantitative changes of abundant, well characterised metabolites such as phenolics (e.g. chlorogenic acid) and several common sugars such as fructose. This study provides fundamental data on the characterisation of gene edited crops, that are important for the evaluation of the technology and its assessment. The approach also suggests that metabolomics could contribute to routine product-based analysis of crops/foods generated from New Plant Breeding approaches.
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Affiliation(s)
- Margit Drapal
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Eugenia M A Enfissi
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | | | - Elzbieta Rapacz
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Marilise Nogueira
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Paul D Fraser
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK.
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3
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Chen MHY, Kendall IP, Evershed RP, Bogaard A, Styring AK. Reconstructing herbivore diets: a multivariate statistical approach to interpreting amino acid nitrogen isotope values. Oecologia 2023; 201:599-608. [PMID: 36786885 DOI: 10.1007/s00442-023-05320-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 01/12/2023] [Indexed: 02/15/2023]
Abstract
Recent studies have demonstrated that there exists significant variability in amino acid (AA) δ15N values of terrestrial plants, discriminating among plant types (i.e., legume seeds, grasses, tree leaves) as well as tissues of the same plant. For the first time, we investigate the potential of the spacing between the δ15N values of different AAs to differentiate between plant types and thus elucidate their relative importance in herbivore diet. Using principal component analysis, we show that it is possible to distinguish among five plant categories-cereal grains, rachis, legume seeds, herbaceous plants, and woody plants-whose consumption has different implications for understanding herbivore ecology and management practices. Furthermore, we were able to correctly classify the herbaceous plant diet of modern cattle using AA δ15N values of their tooth dentine adjusted for trophic enrichment. The AA δ15N patterns of wild and domestic herbivores from archaeological sites seem to be consistent with diets comprised predominantly of herbaceous plants, but there is variation in AA δ15N values among individuals that may reflect differing inputs of other plant types. The variation in AA δ15N values does not necessarily reflect the variation in herbivore bulk collagen δ13C and δ15N values, indicating that AA δ15N values have the potential to provide additional insights into plant dietary sources compared to bulk tissue isotope values alone. Future work should focus on defining trophic enrichment factors for a wider range of terrestrial herbivores and expanding libraries of primary producer AA δ15N values.
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Affiliation(s)
- Mickey H Y Chen
- School of Archaeology, University of Oxford, 34-36 Beaumont Street, Oxford, OX1 2PG, UK.
| | - Iain P Kendall
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Richard P Evershed
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Amy Bogaard
- School of Archaeology, University of Oxford, 34-36 Beaumont Street, Oxford, OX1 2PG, UK
| | - Amy K Styring
- School of Archaeology, University of Oxford, 34-36 Beaumont Street, Oxford, OX1 2PG, UK.
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4
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Ko J, Ryu JE, Noh SW, Choi HK. Melatonin Treatment Enhances the Growth and Productivity of Useful Metabolites in the In Vitro Culture of Spirodela polyrhiza. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:1748-1757. [PMID: 36647270 DOI: 10.1021/acs.jafc.2c07147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Spirodela polyrhiza (Araceae family) is a duckweed species that serves as a potential resource for feed, food, bioremediation, and pharmaceutical applications. In this study, we assessed the effects of different concentrations of melatonin (0, 0.1, 1, and 10 μM) on the growth of S. polyrhiza during in vitro culture and the metabolic profiles and productivities of useful metabolites using gas chromatography-mass spectrometry coupled with multivariable statistical analysis. We found that exogenous melatonin significantly improved the total dry weight and altered the metabolic profiles of S. polyrhiza cultures. Melatonin significantly enhanced the cellular production of useful metabolites, such as γ-aminobutyric acid, dopamine, threonine, valine, and phytosterols. The volumetric productivities (mg/L) of γ-aminobutyric acid, dopamine, campesterol, β-sitosterol, and stigmasterol were the highest in the presence of 10 μM melatonin on day 12. Moreover, the productivities of ascorbic acid and serotonin were the highest in the presence of 1 μM melatonin on day 12. Therefore, melatonin could be used to enhance the production of biomass and useful metabolites during large-scale S. polyrhiza cultivation in cosmetic, food/feed, and pharmaceutical industries.
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Affiliation(s)
- JuHee Ko
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Ji Eun Ryu
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Soon-Wook Noh
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyung-Kyoon Choi
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
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5
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García-Gómez ML, Reyes-Hernández BJ, Sahoo DP, Napsucialy-Mendivil S, Quintana-Armas AX, Pedroza-García JA, Shishkova S, Torres-Martínez HH, Pacheco-Escobedo MA, Dubrovsky JG. A mutation in THREONINE SYNTHASE 1 uncouples proliferation and transition domains of the root apical meristem: experimental evidence and in silico proposed mechanism. Development 2022; 149:278438. [PMID: 36278862 PMCID: PMC9796171 DOI: 10.1242/dev.200899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 10/10/2022] [Indexed: 11/11/2022]
Abstract
A continuum from stem to transit-amplifying to a differentiated cell state is a common theme in multicellular organisms. In the plant root apical meristem (RAM), transit-amplifying cells are organized into two domains: cells from the proliferation domain (PD) are displaced to the transition domain (TD), suggesting that both domains are necessarily coupled. Here, we show that in the Arabidopsis thaliana mto2-2 mutant, in which threonine (Thr) synthesis is affected, the RAM lacks the PD. Through a combination of cell length profile analysis, mathematical modeling and molecular markers, we establish that the PD and TD can be uncoupled. Remarkably, although the RAM of mto2-2 is represented solely by the TD, the known factors of RAM maintenance and auxin signaling are expressed in the mutant. Mathematical modeling predicts that the stem cell niche depends on Thr metabolism and that, when disturbed, the normal continuum of cell states becomes aborted.
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Affiliation(s)
- Monica L. García-Gómez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad, 2001, Cuernavaca 62250, Mexico
| | - Blanca J. Reyes-Hernández
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad, 2001, Cuernavaca 62250, Mexico
| | - Debee P. Sahoo
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad, 2001, Cuernavaca 62250, Mexico
| | - Selene Napsucialy-Mendivil
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad, 2001, Cuernavaca 62250, Mexico
| | - Aranza X. Quintana-Armas
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad, 2001, Cuernavaca 62250, Mexico
| | - José A. Pedroza-García
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad, 2001, Cuernavaca 62250, Mexico
| | - Svetlana Shishkova
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad, 2001, Cuernavaca 62250, Mexico
| | - Héctor H. Torres-Martínez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad, 2001, Cuernavaca 62250, Mexico
| | - Mario A. Pacheco-Escobedo
- Facultad de Ciencias de la Salud, Universidad Tecnológica de México – UNITEC MÉXICO – Campus Atizapán, Av. Calacoaya 7, Atizapán de Zaragoza, Estado de México, 52970, Mexico
| | - Joseph G. Dubrovsky
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad, 2001, Cuernavaca 62250, Mexico,Author for correspondence ()
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Johnston C, García Navarrete LT, Ortiz E, Romsdahl TB, Guzha A, Chapman KD, Grotewold E, Alonso AP. Effective Mechanisms for Improving Seed Oil Production in Pennycress ( Thlaspi arvense L.) Highlighted by Integration of Comparative Metabolomics and Transcriptomics. FRONTIERS IN PLANT SCIENCE 2022; 13:943585. [PMID: 35909773 PMCID: PMC9330397 DOI: 10.3389/fpls.2022.943585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
Pennycress is a potentially lucrative biofuel crop due to its high content of long-chain unsaturated fatty acids, and because it uses non-conventional pathways to achieve efficient oil production. However, metabolic engineering is required to improve pennycress oilseed content and make it an economically viable source of aviation fuel. Research is warranted to determine if further upregulation of these non-conventional pathways could improve oil production within the species even more, which would indicate these processes serve as promising metabolic engineering targets and could provide the improvement necessary for economic feasibility of this crop. To test this hypothesis, we performed a comparative biomass, metabolomic, and transcriptomic analyses between a high oil accession (HO) and low oil accession (LO) of pennycress to assess potential factors required to optimize oil content. An evident reduction in glycolysis intermediates, improved oxidative pentose phosphate pathway activity, malate accumulation in the tricarboxylic acid cycle, and an anaplerotic pathway upregulation were noted in the HO genotype. Additionally, higher levels of threonine aldolase transcripts imply a pyruvate bypass mechanism for acetyl-CoA production. Nucleotide sugar and ascorbate accumulation also were evident in HO, suggesting differential fate of associated carbon between the two genotypes. An altered transcriptome related to lipid droplet (LD) biosynthesis and stability suggests a contribution to a more tightly-packed LD arrangement in HO cotyledons. In addition to the importance of central carbon metabolism augmentation, alternative routes of carbon entry into fatty acid synthesis and modification, as well as transcriptionally modified changes in LD regulation, are key aspects of metabolism and storage associated with economically favorable phenotypes of the species.
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Affiliation(s)
- Christopher Johnston
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, United States
| | | | - Emmanuel Ortiz
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, United States
| | - Trevor B. Romsdahl
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, United States
| | - Athanas Guzha
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, United States
| | - Kent D. Chapman
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, United States
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Ana Paula Alonso
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, United States
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Hejri S, Salimi A, Ali Malboobi M, Fatehi F, Yousefiara M. Investigation of Possible Changes Induced by RNA Silencing in Some Leaf Metabolites of Transgenic Sugar Beet Events. FOOD CHEMISTRY: MOLECULAR SCIENCES 2022; 4:100073. [PMID: 35415694 PMCID: PMC8991520 DOI: 10.1016/j.fochms.2022.100073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/13/2021] [Accepted: 01/07/2022] [Indexed: 11/27/2022]
Abstract
Metabolite contents of transgenic sugar beets, S3 and S6, resistant to rhizomania through RNA silencing mechanism, were compared to wild type plant as a part of a risk assessment study. The alteration of S6 transgenic sugar beet metabolites was low and probably due to micro-environmental or natural individual differences. The alteration of S3 transgenic sugar beet metabolites were significant but still within the natural range and, also, beneficial because of high contents of some amino acids, especially essential ones.
Sugar beet is vulnerable to rhizomania as the most destructive viral disease. Two selected events of transgenic sugar beet carrying cassettes inducing RNA silencing mechanism, 219-T3:S3-13.2 (S3) and 6018-T3:S6-44 (S6), were shown to inhibit propagation of Beet Necrotic Yellow Vein Virus, the causative agent. As a method for signifying the substantial equivalence, we analyzed the levels of some metabolites through LC-MS in order to demonstrate possible unintended changes in the leaves of the transgenic events. There was no significant difference in the concentrations of examined key metabolites but cis-aconitate and fructose-1,6-bisphosphatase which were decreased in S3. Also, ATP was reduced in both genetically modified sugar beets. Among free amino acids, only glycine level in S6 was increased compared to the wild plant, while the production levels of 5 and 12 ones were increased in S3 compared to S6 event and the wild type plants, respectively.
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Othibeng K, Nephali L, Myoli A, Buthelezi N, Jonker W, Huyser J, Tugizimana F. Metabolic Circuits in Sap Extracts Reflect the Effects of a Microbial Biostimulant on Maize Metabolism under Drought Conditions. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040510. [PMID: 35214843 PMCID: PMC8877938 DOI: 10.3390/plants11040510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 05/17/2023]
Abstract
The use of microbial biostimulants in the agricultural sector is increasingly gaining momentum and drawing scientific attention to decode the molecular interactions between the biostimulants and plants. Although these biostimulants have been shown to improve plant health and development, the underlying molecular phenomenology remains enigmatic. Thus, this study is a metabolomics work to unravel metabolic circuits in sap extracts from maize plants treated with a microbial biostimulant, under normal and drought conditions. The biostimulant, which was a consortium of different Bacilli strains, was applied at the planting stage, followed by drought stress application. The maize sap extracts were collected at 5 weeks after emergence, and the extracted metabolites were analyzed on liquid chromatography-mass spectrometry platforms. The acquired data were mined using chemometrics and bioinformatics tools. The results showed that under both well-watered and drought stress conditions, the application of the biostimulant led to differential changes in the profiles of amino acids, hormones, TCA intermediates, phenolics, steviol glycosides and oxylipins. These metabolic changes spanned several biological pathways and involved a high correlation of the biochemical as well as structural metabolic relationships that coordinate the maize metabolism. The hypothetical model, postulated from this study, describes metabolic events induced by the microbial biostimulant for growth promotion and enhanced defences. Such understanding of biostimulant-induced changes in maize sap pinpoints to the biochemistry and molecular mechanisms that govern the biostimulant-plant interactions, which contribute to ongoing efforts to generate actionable knowledge of the molecular and physiological mechanisms that define modes of action of biostimulants.
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Affiliation(s)
- Kgalaletso Othibeng
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (K.O.); (L.N.); (A.M.); (N.B.)
| | - Lerato Nephali
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (K.O.); (L.N.); (A.M.); (N.B.)
| | - Akhona Myoli
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (K.O.); (L.N.); (A.M.); (N.B.)
| | - Nombuso Buthelezi
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (K.O.); (L.N.); (A.M.); (N.B.)
| | - Willem Jonker
- International Research and Development Division, Omnia Group, Johannesburg 2021, South Africa; (W.J.); (J.H.)
| | - Johan Huyser
- International Research and Development Division, Omnia Group, Johannesburg 2021, South Africa; (W.J.); (J.H.)
| | - Fidele Tugizimana
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (K.O.); (L.N.); (A.M.); (N.B.)
- International Research and Development Division, Omnia Group, Johannesburg 2021, South Africa; (W.J.); (J.H.)
- Correspondence: or ; Tel.: +27-011-559-7784
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Decouard B, Bailly M, Rigault M, Marmagne A, Arkoun M, Soulay F, Caïus J, Paysant-Le Roux C, Louahlia S, Jacquard C, Esmaeel Q, Chardon F, Masclaux-Daubresse C, Dellagi A. Genotypic Variation of Nitrogen Use Efficiency and Amino Acid Metabolism in Barley. FRONTIERS IN PLANT SCIENCE 2022; 12:807798. [PMID: 35185958 PMCID: PMC8854266 DOI: 10.3389/fpls.2021.807798] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/02/2021] [Indexed: 06/01/2023]
Abstract
Owing to the large genetic diversity of barley and its resilience under harsh environments, this crop is of great value for agroecological transition and the need for reduction of nitrogen (N) fertilizers inputs. In the present work, we investigated the diversity of a North African barley genotype collection in terms of growth under limiting N (LN) or ample N (HN) supply and in terms of physiological traits including amino acid content in young seedlings. We identified a Moroccan variety, Laanaceur, accumulating five times more lysine in its leaves than the others under both N nutritional regimes. Physiological characterization of the barley collection showed the genetic diversity of barley adaptation strategies to LN and highlighted a genotype x environment interaction. In all genotypes, N limitation resulted in global biomass reduction, an increase in C concentration, and a higher resource allocation to the roots, indicating that this organ undergoes important adaptive metabolic activity. The most important diversity concerned leaf nitrogen use efficiency (LNUE), root nitrogen use efficiency (RNUE), root nitrogen uptake efficiency (RNUpE), and leaf nitrogen uptake efficiency (LNUpE). Using LNUE as a target trait reflecting barley capacity to deal with N limitation, this trait was positively correlated with plant nitrogen uptake efficiency (PNUpE) and RNUpE. Based on the LNUE trait, we determined three classes showing high, moderate, or low tolerance to N limitation. The transcriptomic approach showed that signaling, ionic transport, immunity, and stress response were the major functions affected by N supply. A candidate gene encoding the HvNRT2.10 transporter was commonly up-regulated under LN in the three barley genotypes investigated. Genes encoding key enzymes required for lysine biosynthesis in plants, dihydrodipicolinate synthase (DHPS) and the catabolic enzyme, the bifunctional Lys-ketoglutarate reductase/saccharopine dehydrogenase are up-regulated in Laanaceur and likely account for a hyperaccumulation of lysine in this genotype. Our work provides key physiological markers of North African barley response to low N availability in the early developmental stages.
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Affiliation(s)
- Bérengère Decouard
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Marlène Bailly
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Martine Rigault
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Anne Marmagne
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Mustapha Arkoun
- Agro Innovation International - Laboratoire Nutrition Végétale, TIMAC AGRO International SAS, Saint Malo, France
| | - Fabienne Soulay
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - José Caïus
- Université Paris-Saclay, CNRS, INRAE, University of Évry Val d′Essonne, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Christine Paysant-Le Roux
- Université Paris-Saclay, CNRS, INRAE, University of Évry Val d′Essonne, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Said Louahlia
- Natural Resources and Environment Lab, Faculté Polydiscipliniare de Taza, Université Sidi Mohamed Ben Abdellah, Taza, Morocco
| | - Cédric Jacquard
- Université de Reims Champagne Ardenne, RIBP EA 4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, Reims, France
| | - Qassim Esmaeel
- Université de Reims Champagne Ardenne, RIBP EA 4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, Reims, France
| | - Fabien Chardon
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Céline Masclaux-Daubresse
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Alia Dellagi
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
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10
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Zhu F, Alseekh S, Koper K, Tong H, Nikoloski Z, Naake T, Liu H, Yan J, Brotman Y, Wen W, Maeda H, Cheng Y, Fernie AR. Genome-wide association of the metabolic shifts underpinning dark-induced senescence in Arabidopsis. THE PLANT CELL 2022; 34:557-578. [PMID: 34623442 PMCID: PMC8774053 DOI: 10.1093/plcell/koab251] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 10/05/2021] [Indexed: 05/31/2023]
Abstract
Dark-induced senescence provokes profound metabolic shifts to recycle nutrients and to guarantee plant survival. To date, research on these processes has largely focused on characterizing mutants deficient in individual pathways. Here, we adopted a time-resolved genome-wide association-based approach to characterize dark-induced senescence by evaluating the photochemical efficiency and content of primary and lipid metabolites at the beginning, or after 3 or 6 days in darkness. We discovered six patterns of metabolic shifts and identified 215 associations with 81 candidate genes being involved in this process. Among these associations, we validated the roles of four genes associated with glycine, galactinol, threonine, and ornithine levels. We also demonstrated the function of threonine and galactinol catabolism during dark-induced senescence. Intriguingly, we determined that the association between tyrosine contents and TYROSINE AMINOTRANSFERASE 1 influences enzyme activity of the encoded protein and transcriptional activity of the gene under normal and dark conditions, respectively. Moreover, the single-nucleotide polymorphisms affecting the expression of THREONINE ALDOLASE 1 and the amino acid transporter gene AVT1B, respectively, only underlie the variation in threonine and glycine levels in the dark. Taken together, these results allow us to present a very detailed model of the metabolic aspects of dark-induced senescence, as well as the process itself.
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Affiliation(s)
- Feng Zhu
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm 14476, Germany
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm 14476, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Kaan Koper
- Department of Botany, University of Wisconsin–Madison, Madison, Wisconsin 53706, USA
| | - Hao Tong
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm 14476, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam 14476, Germany
| | - Zoran Nikoloski
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm 14476, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam 14476, Germany
| | - Thomas Naake
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm 14476, Germany
| | - Haijun Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna 1030, Austria
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yariv Brotman
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm 14476, Germany
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Weiwei Wen
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Hiroshi Maeda
- Department of Botany, University of Wisconsin–Madison, Madison, Wisconsin 53706, USA
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Xu L, Li Z, Zhuang B, Zhou F, Li Z, Pan X, Xi H, Zhao W, Liu H. Enrofloxacin perturbs nitrogen transformation and assimilation in rice seedlings (Oryza sativa L.). THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 802:149900. [PMID: 34525725 DOI: 10.1016/j.scitotenv.2021.149900] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/21/2021] [Accepted: 08/21/2021] [Indexed: 06/13/2023]
Abstract
The extensive use of antibiotics worldwide has led to phytotoxicity and high risks to humans. Although research on the physiological toxicity of antibiotics is extensive, its influence on plant nitrogen uptake and assimilation remains unclear. The effect of enrofloxacin on nitrogen transformation and assimilation in rice (Oryza sativa L.) seedlings was investigated in this study. Enrofloxacin had no significant effect on rice growth, nitrogen assimilation and metabolism at low concentration, while significant changes were observed in high concentration. The growth of rice seedlings was inhibited, nitrate uptake was enhanced and nitrogen content increased significantly in both shoots and roots in enrofloxacin (800 μg L-1) treatment. Furthermore, enrofloxacin promoted the activity of enzymes related to nitrogen assimilation, including nitrate reductase, nitrite reductase, glutamine synthetase, glutamate synthase, and glutamate dehydrogenase. High enzyme activity resulted in an increase in intermediate products and protein content, suggesting that rice seedlings may detoxify enrofloxacin stress through amino acid binding and nitro-oxidative stress might be one of the reasons of phenotype change. Gas chromatography-mass spectrometry results revealed that different types of metabolites in both shoots and roots increased with enrofloxacin stress. Specifically, glycine, serine, and threonine metabolism; aminoacyl-tRNA biosynthesis; alanine, aspartate, and glutamate metabolism; butanoate metabolism; glyoxylate and dicarboxylate metabolism in shoot; and tyrosine metabolism and citrate cycle in root were affected. Moreover, a significant correlation between nitrogen content, nitrogen assimilation enzyme activity, and metabolite content was observed. Collectively, these findings reveal the potential risks of using reclaimed wastewater irrigation and/or antibiotic-containing animal fertilizers on crops.
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Affiliation(s)
- Linglin Xu
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, Zhejiang Province, China
| | - Zhiheng Li
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, Zhejiang Province, China
| | - Biyan Zhuang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, Zhejiang Province, China
| | - Fumin Zhou
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, Zhejiang Province, China
| | - Zejun Li
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, Zhejiang Province, China
| | - Xiaoru Pan
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, Zhejiang Province, China
| | - Hao Xi
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, Zhejiang Province, China
| | - Wenlu Zhao
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, Zhejiang Province, China
| | - Huijun Liu
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, Zhejiang Province, China; Instrumental Analysis Center of Zhejiang Gongshang University, Hangzhou 310018, Zhejiang Province, China.
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12
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Ali Q, Mazhar MW, Ishtiaq M, Hussain AI, Bhatti KH, Maqbool M, Hussain T, Khanum H, Sardar T, Mazhar M. Efficacy of Zn-Aspartate in comparison with ZnSO4 and L-Aspartate in amelioration of drought stress in maize by modulating antioxidant defence; osmolyte accumulation and photosynthetic attributes. PLoS One 2021; 16:e0260662. [PMID: 34941898 PMCID: PMC8700056 DOI: 10.1371/journal.pone.0260662] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 11/14/2021] [Indexed: 12/01/2022] Open
Abstract
Human population is exceeding beyond the carrying capacity of earth resources and stresses like water shortage faced by the plants is jeopardizing the food security. Current research study was aimed to investigate the potentials of Zn-Aspartate (Zn-Asp), Zn-Sulphate (ZnSO4) and L-Aspartate (L-Asp) to be used as osmolytes and role of various levels of these chemicals in combating drought stress in maize plants in Punjab, Pakistan. Study was performed on two plots corresponding to drought and controlled environments. The lamina of maize plants was sprinkled row wise with various treatments including No spray (NS), water sprinkle (WS), sprinkle with ZnSO4 0.25% and 0.50%, sprinkle with Zn-Asp 0.25% and 0.50% and Foliar sprinkle of L-Asp 0.5% and 1%, respectively. Role of major osmoprotectants and secondary metabolites was analyzed and positive changes were found in total soluble sugars (41.16), flavonoids (5387.74), tocopherol content (9089.18), ascorbic acid (645.27) and anthocyanin (14.84) conc. which assists in mitigating drought menace on maize. Shoot mineral ions (Ca, K, Zn, P, Mg and N) status of water stressed maize plants was also analyzed and it was found that application experimental dose enhanced their availability to crop. Physio-biochemical studies were performed on antioxidants enzymes like superoxide dismutase (SOD), peroxidase (POD), carotenoid content (CC), malondialdehyde, hydrogen peroxide, aspartate and free amino acid contents. The activity of SOD was increased by 28.5% and activity of POD was increased by 33.33% due to foliar applied 0.5% Zn-Asp under drought stress. Photosynthetic pigments (chlorophyll A, B and total chlorophyll content) analysis was also carried out in this study. It was found that conc. of different chlorophylls pigments increased (chl-A: 2.24, chl-B: 25.12, total chl: 24.30) which enhanced photosynthetic activity culminating into better growth and yield). The level of malondialdehyde and hydrogen peroxide decreased by 43.9% and 32.8% respectively on treatment with 0.5% Zn-Asp proving the efficacy of the treatment in drought amelioration. Study reveals that Zn-Asp induced modulations are far better than conventional sulphate salts in mitigating water scarce environment. Current study recommends the use of the Zn-Asp to meet the global food and agricultural challenges as compared to ZnSO4 and L-Asp due to its better drought amelioration properties. This research provides valuable informations which can used for future research and practical use in agriculture fields by indigenous and other people to enhance yield of maize to meet the food necessities of country.
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Affiliation(s)
- Qasim Ali
- Department of Botany, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Waqas Mazhar
- Department of Botany, Mirpur University of Science & Technology (MUST), Mirpur, Pakistan
| | - Muhammad Ishtiaq
- Department of Botany, Mirpur University of Science & Technology (MUST), Mirpur, Pakistan
- * E-mail:
| | | | | | - Mehwish Maqbool
- Department of Botany, Mirpur University of Science & Technology (MUST), Mirpur, Pakistan
| | - Tanveer Hussain
- Department of Botany, Mirpur University of Science & Technology (MUST), Mirpur, Pakistan
| | - Humaira Khanum
- Department of Botany, Mirpur University of Science & Technology (MUST), Mirpur, Pakistan
| | - Tauqeer Sardar
- Department of Botany, Mirpur University of Science & Technology (MUST), Mirpur, Pakistan
| | - Mubashir Mazhar
- Department of Botany, Mirpur University of Science & Technology (MUST), Mirpur, Pakistan
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Joshi V, Nimmakayala P, Song Q, Abburi V, Natarajan P, Levi A, Crosby K, Reddy UK. Genome-wide association study and population structure analysis of seed-bound amino acids and total protein in watermelon. PeerJ 2021; 9:e12343. [PMID: 34722000 PMCID: PMC8533027 DOI: 10.7717/peerj.12343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 09/28/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Watermelon seeds are a powerhouse of value-added traits such as proteins, free amino acids, vitamins, and essential minerals, offering a paleo-friendly dietary option. Despite the availability of substantial genetic variation, there is no sufficient information on the natural variation in seed-bound amino acids or proteins across the watermelon germplasm. This study aimed to analyze the natural variation in watermelon seed amino acids and total protein and explore underpinning genetic loci by genome-wide association study (GWAS). METHODS The study evaluated the distribution of seed-bound free amino acids and total protein in 211 watermelon accessions of Citrullus spp, including 154 of Citrullus lanatus, 54 of Citrullus mucosospermus (egusi) and three of Citrullus amarus. We used the GWAS approach to associate seed phenotypes with 11,456 single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing (GBS). RESULTS Our results demonstrate a significant natural variation in different free amino acids and total protein content across accessions and geographic regions. The accessions with high protein content and proportion of essential amino acids warrant its use for value-added benefits in the food and feed industries via biofortification. The GWAS analysis identified 188 SNPs coinciding with 167 candidate genes associated with watermelon seed-bound amino acids and total protein. Clustering of SNPs associated with individual amino acids found by principal component analysis was independent of the speciation or cultivar groups and was not selected during the domestication of sweet watermelon. The identified candidate genes were involved in metabolic pathways associated with amino acid metabolism, such as Argininosuccinate synthase, explaining 7% of the variation in arginine content, which validate their functional relevance and potential for marker-assisted analysis selection. This study provides a platform for exploring potential gene loci involved in seed-bound amino acids metabolism, useful in genetic analysis and development of watermelon varieties with superior seed nutritional values.
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Affiliation(s)
- Vijay Joshi
- Department of Horticultural Sciences, Texas A&M University, Uvalde, Texas, United States
- Texas A&M AgriLife Research and Extension Center, Uvalde, Texas, United States
| | - Padma Nimmakayala
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, Charleston, West Virginia, United States
| | - Qiushuo Song
- Department of Horticultural Sciences, Texas A&M University, Uvalde, Texas, United States
| | - Venkata Abburi
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, Charleston, West Virginia, United States
| | - Purushothaman Natarajan
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, Charleston, West Virginia, United States
| | - Amnon Levi
- Vegetable Laboratory, USDA-ARS, Charleston, South Carolina, United States
| | - Kevin Crosby
- Department of Horticultural Sciences, Texas A&M University, Uvalde, Texas, United States
| | - Umesh K. Reddy
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, Charleston, West Virginia, United States
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Sahoo DP, Van Winkle LJ, Díaz de la Garza RI, Dubrovsky JG. Interkingdom Comparison of Threonine Metabolism for Stem Cell Maintenance in Plants and Animals. Front Cell Dev Biol 2021; 9:672545. [PMID: 34557481 PMCID: PMC8454773 DOI: 10.3389/fcell.2021.672545] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 08/11/2021] [Indexed: 01/12/2023] Open
Abstract
In multicellular organisms, tissue generation, maintenance, and homeostasis depend on stem cells. Cellular metabolic status is an essential component of different differentiated states, from stem to fully differentiated cells. Threonine (Thr) metabolism has emerged as a critical factor required to maintain pluripotent/multipotent stem cells in both plants and animals. Thus, both kingdoms conserved or converged upon this fundamental feature of stem cell function. Here, we examine similarities and differences in Thr metabolism-dependent mechanisms supporting stem cell maintenance in these two kingdoms. We then consider common features of Thr metabolism in stem cell maintenance and predict and speculate that some knowledge about Thr metabolism and its role in stem cell function in one kingdom may apply to the other. Finally, we outline future research directions to explore these hypotheses.
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Affiliation(s)
- Debee Prasad Sahoo
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Lon J. Van Winkle
- Department of Biochemistry, Midwestern University, Downers Grove, IL, United States
- Department of Medical Humanities, Rocky Vista University, Parker, CO, United States
| | | | - Joseph G. Dubrovsky
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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15
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Dellero Y, Mauve C, Jossier M, Hodges M. The Impact of Photorespiratory Glycolate Oxidase Activity on Arabidopsis thaliana Leaf Soluble Amino Acid Pool Sizes during Acclimation to Low Atmospheric CO 2 Concentrations. Metabolites 2021; 11:metabo11080501. [PMID: 34436442 PMCID: PMC8399254 DOI: 10.3390/metabo11080501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 01/17/2023] Open
Abstract
Photorespiration is a metabolic process that removes toxic 2-phosphoglycolate produced by the oxygenase activity of ribulose-1,5-bisphosphate carboxylase/oxygenase. It is essential for plant growth under ambient air, and it can play an important role under stress conditions that reduce CO2 entry into the leaf thus enhancing photorespiration. The aim of the study was to determine the impact of photorespiration on Arabidopsis thaliana leaf amino acid metabolism under low atmospheric CO2 concentrations. To achieve this, wild-type plants and photorespiratory glycolate oxidase (gox) mutants were given either short-term (4 h) or long-term (1 to 8 d) low atmospheric CO2 concentration treatments and leaf amino acid levels were measured and analyzed. Low CO2 treatments rapidly decreased net CO2 assimilation rate and triggered a broad reconfiguration of soluble amino acids. The most significant changes involved photorespiratory Gly and Ser, aromatic and branched-chain amino acids as well as Ala, Asp, Asn, Arg, GABA and homoSer. While the Gly/Ser ratio increased in all Arabidopsis lines between air and low CO2 conditions, low CO2 conditions led to a higher increase in both Gly and Ser contents in gox1 and gox2.2 mutants when compared to wild-type and gox2.1 plants. Results are discussed with respect to potential limiting enzymatic steps with a special emphasis on photorespiratory aminotransferase activities and the complexity of photorespiration.
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Affiliation(s)
- Younès Dellero
- Institute for Genetics, Environment and Plant Protection (IGEPP), National Institute for Research for Agriculture, Food and Environment (INRAE), Institut Agro, Univ Rennes, 35653 Le Rheu, France
- Correspondence: (Y.D.); (M.H.)
| | - Caroline Mauve
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, National Committee of Scientific Research (CNRS), National Institute for Research for Agriculture, Food and Environment (INRAE), Université d’Evry, Université de Paris, 91190 Gif-sur-Yvette, France; (C.M.); (M.J.)
| | - Mathieu Jossier
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, National Committee of Scientific Research (CNRS), National Institute for Research for Agriculture, Food and Environment (INRAE), Université d’Evry, Université de Paris, 91190 Gif-sur-Yvette, France; (C.M.); (M.J.)
| | - Michael Hodges
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, National Committee of Scientific Research (CNRS), National Institute for Research for Agriculture, Food and Environment (INRAE), Université d’Evry, Université de Paris, 91190 Gif-sur-Yvette, France; (C.M.); (M.J.)
- Correspondence: (Y.D.); (M.H.)
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16
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Tsogtbaatar E, Cocuron JC, Alonso AP. Non-conventional pathways enable pennycress (Thlaspi arvense L.) embryos to achieve high efficiency of oil biosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3037-3051. [PMID: 32006014 PMCID: PMC7260723 DOI: 10.1093/jxb/eraa060] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/03/2020] [Indexed: 05/22/2023]
Abstract
Pennycress (Thlaspi arvense L.) accumulates oil up to 35% of the total seed biomass, and its overall fatty acid composition is suitable for aviation fuel. However, for this plant to become economically viable, its oil production needs to be improved. In vivo culture conditions that resemble the development of pennycress embryos in planta were developed based on the composition of the liquid endosperm. Then, substrate uptake rates and biomass accumulation were measured from cultured pennycress embryos, revealing a biosynthetic efficiency of 93%, which is one of the highest in comparison with other oilseeds to date. Additionally, the ratio of carbon in oil to CO2 indicated that non-conventional pathways are likely to be responsible for such a high carbon conversion efficiency. To identify the reactions enabling this phenomenon, parallel labeling experiments with 13C-labeled substrates were conducted in pennycress embryos. The main findings of these labeling experiments include: (i) the occurrence of the oxidative reactions of the pentose phosphate pathway in the cytosol; (ii) the reversibility of isocitrate dehydrogenase; (iii) the operation of the plastidic NADP-dependent malic enzyme; and (iv) the refixation of CO2 by Rubisco. These reactions are key providers of carbon and reductant for fatty acid synthesis and elongation.
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Affiliation(s)
| | | | - Ana Paula Alonso
- BioDiscovery Institute, University of North Texas, Denton, TX, USA
- Department of Biological Sciences, University of North Texas, Denton, TX, USA
- Correspondence:
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D'Angelo M, Zanor MI, Burgos E, Asprelli PD, Boggio SB, Carrari F, Peralta IE, Valle EM. Fruit metabolic and transcriptional programs differentiate among Andean tomato (Solanum lycopersicum L.) accessions. PLANTA 2019; 250:1927-1940. [PMID: 31529400 DOI: 10.1007/s00425-019-03274-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 09/05/2019] [Indexed: 06/10/2023]
Abstract
Andean tomatoes differed from the wild ancestor in the metabolic composition and the expression of genes related with mitochondrial functions, and environmental stresses, making them potentially suitable for breeding programmes. Traditional landraces or "criollo" tomatoes (Solanum lycopersicum L.) from Andean areas of Argentina, selected for their fruit quality, were analysed in this study. We explored the metabolome and transcriptome of the ripe fruit in nine landrace accessions representing the seven genetic groups and compared them to the mature fruit of the wild progenitor Solanum pimpinellifolium. The content of branched- (isoleucine and valine) and aromatic (phenylalanine and tryptophan) amino acids, citrate and sugars were significantly different in the fruit of several "criollo" tomatoes compared to S. pimpinellifolium. The transcriptomic profile of the ripe fruit showed several genes significantly and highly regulated in all varieties compared to S. pimpinellifolium, like genes encoding histones and mitochondrial proteins. Additionally, network analysis including transcripts and metabolites identified major hubs with the largest number of connections such as constitutive photomorphogenic protein 1 (a RING finger-type ubiquitin E3 ligase), five Zn finger transcription factors, ascorbate peroxidase, acetolactate synthase, and sucrose non-fermenting 1 kinase. Co-expression analysis of these genes revealed a potential function in acquiring tomato fruit quality during domestication.
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Affiliation(s)
- Matilde D'Angelo
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR), Rosario, Argentina
- Animal Nutrition and Welfare Service, Animal and Food Science Department, Universitat Autónoma de Barcelona, 08193, Bellaterra, Spain
| | - María I Zanor
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR), Rosario, Argentina
| | - Estanislao Burgos
- Instituto de Fisiología Biología Molecular y Neurociencias (IFIBYNE-CONICET-UBA), Buenos Aires, Argentina
| | - Pablo D Asprelli
- Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Silvana B Boggio
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR), Rosario, Argentina
| | - Fernando Carrari
- Instituto de Fisiología Biología Molecular y Neurociencias (IFIBYNE-CONICET-UBA), Buenos Aires, Argentina
| | - Iris E Peralta
- Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Mendoza, Argentina
- IADIZA CCT-CONICET, Mendoza, Argentina
| | - Estela M Valle
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR), Rosario, Argentina.
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18
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Reyes-Hernández BJ, Shishkova S, Amir R, Quintana-Armas AX, Napsucialy-Mendivil S, Cervantes-Gamez RG, Torres-Martínez HH, Montiel J, Wood CD, Dubrovsky JG. Root stem cell niche maintenance and apical meristem activity critically depend on THREONINE SYNTHASE1. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3835-3849. [PMID: 30972413 DOI: 10.1093/jxb/erz165] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 03/22/2019] [Indexed: 05/23/2023]
Abstract
Indeterminate root growth depends on the stem cell niche (SCN) and root apical meristem (RAM) maintenance whose regulation permits plasticity in root system formation. Using a forward genetics approach, we isolated the moots koom1 ('short root' in Mayan) mutant that shows complete primary RAM exhaustion and abolished SCN activity. We identified that this phenotype is caused by a point mutation in the METHIONINE OVERACCUMULATOR2 (MTO2) gene that encodes THREONINE SYNTHASE1 and renamed the mutant as mto2-2. The amino acid profile showed drastic changes, most notorious of which was accumulation of methionine. In non-allelic mto1-1 (Arabidopsis thaliana cystathionine gamma-synthetase1) and mto3-1 (S-adenosylmethionine synthetase) mutants, both with an increased methionine level, the RAM size was similar to that of the wild type, suggesting that methionine overaccumulation itself did not cause RAM exhaustion in mto2 mutants. When mto2-2 RAM is not yet completely exhausted, exogenous threonine induced de novo SCN establishment and root growth recovery. The threonine-dependent RAM re-establishment in mto2-2 suggests that threonine is a limiting factor for RAM maintenance. In the root, MTO2 was predominantly expressed in the RAM. The essential role of threonine in mouse embryonic stem cells and in RAM maintenance suggests that common regulatory mechanisms may operate in plant and animal SCN maintenance.
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Affiliation(s)
- Blanca Jazmín Reyes-Hernández
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico
| | - Svetlana Shishkova
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico
| | - Rachel Amir
- Laboratory of Plant Science, MIGAL-Galilee Research Institute, Kiryat Shmona, Israel
- Tel-Hai College, Upper Galilee, Israel
| | - Aranza Xhaly Quintana-Armas
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico
| | - Selene Napsucialy-Mendivil
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico
| | - Rocio Guadalupe Cervantes-Gamez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico
| | - Héctor Hugo Torres-Martínez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico
| | - Jesús Montiel
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico
| | - Christopher D Wood
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico
| | - Joseph G Dubrovsky
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico
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Matityahu I, Godo I, Hacham Y, Amir R. The level of threonine in tobacco seeds is limited by substrate availability, while the level of methionine is limited also by the activity of cystathionine γ-synthase. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 283:195-201. [PMID: 31128689 DOI: 10.1016/j.plantsci.2019.02.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/25/2019] [Accepted: 02/28/2019] [Indexed: 06/09/2023]
Abstract
Methionine and threonine are two essential amino acids whose low levels limit the nutritional quality of seeds. The current objective was to define factors that regulate and might increase their levels in seeds. Feeding experiments carried out on receptacles of developing tobacco (Nicotiana tabacum) capsules showed that 1 mM of S-methylmethionine increased the level of methionine to contents similar to 2.5 mM of homoserine, an intermediate metabolite of the aspartate family of amino acids. The latter also increased the level of threonine. Based on these findings, we generated tobacco seeds that expressed a combination of bacterial feedback-insensitive aspartate kinase (bAK), which was previously reported to have a high level of threonine/methionine, and feedback-insensitive cystathionine γ-synthase (CGS), the regulatory enzyme of the methionine biosynthesis pathway. Plants expressing this latter gene previously showed having higher levels of methionine. The results of total amino acids analysis showed that the level of threonine was highest in the bAK line, which has moderate levels of methionine and lysine, while the highest level of methionine was found in seeds expressing both heterologous genes. The results suggest that the level of threonine in tobacco seeds is limited by the substrate, while that of methionine is limited also by the activity of CGS.
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Affiliation(s)
- I Matityahu
- Laboratory of Plant Science, Migal - Galilee Technology Center, P.O. Box 831, Kiryat Shmona 12100, Israel
| | - I Godo
- Laboratory of Plant Science, Migal - Galilee Technology Center, P.O. Box 831, Kiryat Shmona 12100, Israel
| | - Y Hacham
- Laboratory of Plant Science, Migal - Galilee Technology Center, P.O. Box 831, Kiryat Shmona 12100, Israel; Tel-Hai College, Upper Galilee 11016, Israel
| | - R Amir
- Laboratory of Plant Science, Migal - Galilee Technology Center, P.O. Box 831, Kiryat Shmona 12100, Israel; Tel-Hai College, Upper Galilee 11016, Israel.
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20
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Kendall IP, Woodward P, Clark JP, Styring AK, Hanna JV, Evershed RP. Compound-specific δ 15N values express differences in amino acid metabolism in plants of varying lignin content. PHYTOCHEMISTRY 2019; 161:130-138. [PMID: 30826700 DOI: 10.1016/j.phytochem.2019.01.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/27/2018] [Accepted: 01/15/2019] [Indexed: 06/09/2023]
Abstract
Amino acid δ15N values of foliage of various plant taxa, grown at the experimental farm stations of North Wyke, UK and Bad Lauchstädt, Germany were determined by GC-C-IRMS. The difference between δ15N values of glutamate (Glx) and phenylalanine (Phe) were found to differ significantly between woody and herbaceous plants, with mean Δ15NGlx-Phe (i.e. δ15NPhe - δ15NGlx) values of -9.3 ± 1.6‰ and -5.8 ± 2.1‰, respectively. These differences in values are hypothesised to be due to the involvement of Phe in the phenylpropanoid pathway, by which lignin and other phenolic secondary metabolites are produced, leading to isotopic fractionation and enrichment of the remaining Phe pool available for protein biosynthesis. This results in the more negative Δ15NGlx-Phe values observed in woody plants relative to herbaceous plants, as the former are assumed to produce more lignin. To test this assumption, plant leaf tissue lignin concentrations were estimated by solid state 13C cross-polarisation, magic-angle-spinning (CPMAS) NMR spectroscopy for a subset of plants, which showed that tree foliage has a higher concentration of lignin (12.6 wt%) than herbaceous foliage (6.3 wt%). The correlation of lignin concentration with Δ15NGlx-Phe values demonstrates that the difference in these values with plant type is indeed due to differential production of lignin. The ability to estimate the lignin content of plants from amino acid δ15N values will, to give one example, allow refinement of estimates of herbivore diet in present and past ecosystems, enabling more accurate environmental niche modelling.
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Affiliation(s)
- Iain P Kendall
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - Peter Woodward
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - Joshua P Clark
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
| | - Amy K Styring
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK; Present Address: Institut für Archäologische Wissenschaften, Goethe-Universität Frankfurt Am Main, Frankfurt, Germany
| | - John V Hanna
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
| | - Richard P Evershed
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
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21
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Ke M, Qu Q, Peijnenburg WJGM, Li X, Zhang M, Zhang Z, Lu T, Pan X, Qian H. Phytotoxic effects of silver nanoparticles and silver ions to Arabidopsis thaliana as revealed by analysis of molecular responses and of metabolic pathways. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 644:1070-1079. [PMID: 30743820 DOI: 10.1016/j.scitotenv.2018.07.061] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 07/02/2018] [Accepted: 07/05/2018] [Indexed: 06/09/2023]
Abstract
The acute (3 days) and chronic (whole life history) responses of Arabidopsis thaliana following exposure to silver nanoparticles (AgNPs) and Ag+ ions (AgNO3) in respectively a hydroponic medium and in soil were studied. After 3 days of hydroponic exposure, AgNPs (1.0 and 2.5 mg/L) exerted more severe inhibitory effects on plant (shoot and root) growth and photosynthesis than the same concentrations of Ag+ ions. In soil cultivation, the photoperiod, the autonomous, and the vernalization pathways were down-regulated to 0.15- to 0.5-fold of the control after 12.5 mg/kg AgNPs treatment. This exposure caused a decrease of approximately 25%-40% as compared to the control of the transcription of flowering key genes including AP1, LFY, FT and SOC1, and finally resulted in a delayed flowering time of 5 days. Only autonomous and vernalization pathways were inhibited by Ag+ ion treatment and ultimately the time of flowering in treated plants was delayed by 3 days. The energy production related metabolic pathways in the tricarboxylic acid cycle and in sugar metabolism were stimulated stronger by AgNPs than by Ag+ ion treatment, thus releasing more energy and accelerating the physiological metabolic responses against stress in the AgNPs treatment while subsequently reducing the plant growth and yield at the maturation stage. Importantly, shikimate-phenylpropanoid biosynthesis, and tryptophan and galactose metabolisms were regulated only by the AgNPs treatment, which was a specific effect of nanoparticles. This work provides a systematic understanding at the molecular, physiological as well as metabolic level of the effects of AgNPs and Ag+ ions in A. thaliana.
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Affiliation(s)
- Mingjing Ke
- College of Environment, Zhejiang University of Technology, Hangzhou, PR China
| | - Qian Qu
- College of Environment, Zhejiang University of Technology, Hangzhou, PR China
| | - W J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, 2300 RA Leiden, The Netherlands; National Institute of Public Health and the Environment (RIVM), Center for Safety of Substances and Products, P.O. Box 1, Bilthoven, The Netherlands
| | - Xingxing Li
- College of Environment, Zhejiang University of Technology, Hangzhou, PR China
| | - Meng Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, PR China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, PR China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, PR China
| | - Xiangliang Pan
- College of Environment, Zhejiang University of Technology, Hangzhou, PR China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, PR China; Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Chinese Academy of Sciences, Urumqi, PR China.
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22
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Wang W, Xu M, Wang G, Galili G. New insights into the metabolism of aspartate-family amino acids in plant seeds. PLANT REPRODUCTION 2018; 31:203-211. [PMID: 29399717 DOI: 10.1007/s00497-018-0322-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 01/18/2018] [Indexed: 05/03/2023]
Abstract
Aspartate-family amino acids. Aspartate (Asp)-family pathway, via several metabolic branches, leads to four key essential amino acids: Lys, Met, Thr, and Ile. Among these, Lys and Met have received the most attention, as they are the most limiting amino acid in cereals and legumes crops, respectively. The metabolic pathways of these four essential amino acids and their interactions with regulatory networks have been well characterized. Using this knowledge, extensive efforts have been devoted to augmenting the levels of these amino acids in various plant organs, especially seeds, which serve as the main source of human food and livestock feed. Seeds store a number of storage proteins, which are utilized as nutrient and energy resources. Storage proteins are composed of amino acids, to guarantee the continuation of plant progeny. Thus, understanding the seed metabolism, especially with respect to the accumulation of aspartate-derived amino acids Lys and Met, is a crucial factor for sustainable agriculture. In this review, we summarized the Asp-family pathway, with some new examples of accumulated Asp-family amino acids, particularly Lys and Met, in plant seeds. We also discuss the recent advances in understanding the roles of Asp-family amino acids during seed development.
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Affiliation(s)
- Wenyi Wang
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
- Department of Plant Science, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Mengyun Xu
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Guoping Wang
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.
| | - Gad Galili
- Department of Plant Science, Weizmann Institute of Science, 76100, Rehovot, Israel.
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23
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Xia J, Zhao Y, Burks P, Pauly M, Brown PJ. A sorghum NAC gene is associated with variation in biomass properties and yield potential. PLANT DIRECT 2018; 2:e00070. [PMID: 31245734 PMCID: PMC6508854 DOI: 10.1002/pld3.70] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/12/2018] [Accepted: 06/19/2018] [Indexed: 05/13/2023]
Abstract
Sorghum bicolor is a C4 grass widely cultivated for grain, forage, sugar, and biomass. The sorghum Dry Stalk (D) locus controls a qualitative difference between juicy green (dd) and dry white (D-) stalks and midribs, and co-localizes with a quantitative trait locus for sugar yield. Here, we apply fine-mapping and genome-wide association study (GWAS) to identify a candidate gene underlying D, and use nearly isogenic lines (NILs) to characterize the transcriptional, compositional, and agronomic effects of variation at the D locus. The D locus was fine-mapped to a 36 kb interval containing four genes. One of these genes is a NAC transcription factor that contains a stop codon in the NAC domain in the recessive (dd) parent. Allelic variation at D affects grain yield, sugar yield, and biomass composition in NILs. Green midrib (dd) NILs show reductions in lignin in stalk tissue and produce higher sugar and grain yields under well-watered field conditions. Increased yield potential in dd NILs is associated with increased stalk mass and moisture, higher biomass digestibility, and an extended period of grain filling. Transcriptome profiling of midrib tissue at the 4-6 leaf stages, when NILs first become phenotypically distinct, reveals that dd NILs have increased expression of a miniature zinc finger (MIF) gene. MIF genes dimerize with and suppress zinc finger homeodomain (ZF-HD) transcription factors, and a ZF-HD gene is associated with midrib color variation in a GWAS analysis across 1,694 diverse sorghum inbreds. A premature stop codon in a NAC gene is the most likely candidate polymorphism underlying the sorghum D locus. More detailed understanding of the sorghum D locus could help improve agronomic potential in cereals.
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Affiliation(s)
- Jingnu Xia
- Department of Crop SciencesUniversity of Illinois at Urbana ChampaignUrbanaIllinois
- Present address:
Department of BiochemistryUniversity of OxfordOxfordUK
| | - Yunjun Zhao
- Department of Plant and Microbial BiologyUniversity of California, BerkeleyBerkeleyCalifornia
- Present address:
Brookhaven National LabUptonNew York
| | - Payne Burks
- Department of Crop SciencesUniversity of Illinois at Urbana ChampaignUrbanaIllinois
- Present address:
Chromatin Inc.LubbockTexas
| | - Markus Pauly
- Department of Plant and Microbial BiologyUniversity of California, BerkeleyBerkeleyCalifornia
- Present address:
Heinrich‐Heine UniversityDuesseldorfGermany
| | - Patrick J. Brown
- Department of Crop SciencesUniversity of Illinois at Urbana ChampaignUrbanaIllinois
- Present address:
University of California, DavisDavisCalifornia
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24
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Sajitz-Hermstein M, Töpfer N, Kleessen S, Fernie AR, Nikoloski Z. iReMet-flux: constraint-based approach for integrating relative metabolite levels into a stoichiometric metabolic models. Bioinformatics 2017; 32:i755-i762. [PMID: 27587698 DOI: 10.1093/bioinformatics/btw465] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
MOTIVATION Understanding the rerouting of metabolic reaction fluxes upon perturbations has the potential to link changes in molecular state of a cellular system to alteration of growth. Yet, differential flux profiling on a genome-scale level remains one of the biggest challenges in systems biology. This is particularly relevant in plants, for which fluxes in autotrophic growth necessitate time-consuming instationary labeling experiments and costly computations, feasible for small-scale networks. RESULTS Here we present a computationally and experimentally facile approach, termed iReMet-Flux, which integrates relative metabolomics data in a metabolic model to predict differential fluxes at a genome-scale level. Our approach and its variants complement the flux estimation methods based on radioactive tracer labeling. We employ iReMet-Flux with publically available metabolic profiles to predict reactions and pathways with altered fluxes in photo-autotrophically grown Arabidopsis and four photorespiratory mutants undergoing high-to-low CO2 acclimation. We also provide predictions about reactions and pathways which are most strongly regulated in the investigated experiments. The robustness and variability analyses, tailored to the formulation of iReMet-Flux, demonstrate that the findings provide biologically relevant information that is validated with external measurements of net CO2 exchange and biomass production. Therefore, iReMet-Flux paves the wave for mechanistic dissection of the interplay between pathways of primary and secondary metabolisms at a genome-scale. AVAILABILITY AND IMPLEMENTATION The source code is available from the authors upon request. CONTACT nikoloski@mpimp-golm.mpg.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Nadine Töpfer
- Department of Plant and Environmental Sciences, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | | | - Alisdair R Fernie
- Central Metabolism Group, Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam 14476, Germany
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25
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Dynamics of H3K4me3 Chromatin Marks Prevails over H3K27me3 for Gene Regulation during Flower Morphogenesis in Arabidopsis thaliana. EPIGENOMES 2017. [DOI: 10.3390/epigenomes1020008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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26
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Xing A, Last RL. A Regulatory Hierarchy of the Arabidopsis Branched-Chain Amino Acid Metabolic Network. THE PLANT CELL 2017; 29:1480-1499. [PMID: 28522547 PMCID: PMC5502462 DOI: 10.1105/tpc.17.00186] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/12/2017] [Accepted: 05/11/2017] [Indexed: 05/18/2023]
Abstract
The branched-chain amino acids (BCAAs) Ile, Val, and Leu are essential nutrients that humans and other animals obtain from plants. However, total and relative amounts of plant BCAAs rarely match animal nutritional needs, and improvement requires a better understanding of the mechanistic basis for BCAA homeostasis. We present an in vivo regulatory model of BCAA homeostasis derived from analysis of feedback-resistant Arabidopsis thaliana mutants for the three allosteric committed enzymes in the biosynthetic network: threonine deaminase (also named l-O-methylthreonine resistant 1 [OMR1]), acetohydroxyacid synthase small subunit 2 (AHASS2), and isopropylmalate synthase 1 (IPMS1). In this model, OMR1 exerts primary control on Ile accumulation and functions independently of AHAS and IPMS AHAS and IPMS regulate Val and Leu homeostasis, where AHAS affects total Val+Leu and IPMS controls partitioning between these amino acids. In addition, analysis of feedback-resistant and loss-of-function single and double mutants revealed that each AHAS and IPMS isoenzyme contributes to homeostasis rather than being functionally redundant. The characterized feedback resistance mutations caused increased free BCAA levels in both seedlings and seeds. These results add to our understanding of the basis of in vivo BCAA homeostasis and inform approaches to improve the amount and balance of these essential nutrients in crops.
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Affiliation(s)
- Anqi Xing
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319
| | - Robert L Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824-1319
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27
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Dethloff F, Orf I, Kopka J. Rapid in situ 13C tracing of sucrose utilization in Arabidopsis sink and source leaves. PLANT METHODS 2017; 13:87. [PMID: 29075313 PMCID: PMC5648436 DOI: 10.1186/s13007-017-0239-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 10/10/2017] [Indexed: 05/08/2023]
Abstract
BACKGROUND Conventional metabolomics approaches face the problem of hidden metabolic phenotypes where only fluxes are altered but pool sizes stay constant. Metabolic flux experiments are used to detect such hidden flux phenotypes. These experiments are, however, time consuming, may be cost intensive, and involve specialists for modeling. We fill the gap between conventional metabolomics and flux modeling. We present rapid stable isotope tracing assays and analysis strategies of 13C labeling data. For this purpose, we combine the conventional metabolomics approach that detects significant relative changes of metabolite pool sizes with analyses of differential utilization of 13C labeled carbon. As a test case, we use uniformly labeled 13C-sucrose. RESULTS We present petiole and hypocotyl feeding assays for the rapid in situ feeding (≤ 4 h) of isotopically labeled metabolic precursor to whole Arabidopsis thaliana rosettes. The assays are assessed by conventional gas chromatography-mass spectrometry based metabolite profiling that was extended by joined differential analysis of 13C-labeled sub-pools and of 13C enrichment of metabolites relative to the enrichment of 13C-sucrose within each sample. We apply these analyses to the sink to source transition continuum of leaves from single A. thaliana rosettes and characterize the associated relative changes of metabolite pools, as well as previously hidden changes of sucrose-derived carbon partitioning. We compared the contribution of sucrose as a carbon source in predominantly sink to predominantly source leaves and identified a set of primary metabolites with differential carbon utilization during sink to source transition. CONCLUSION The presented feeding assays and data evaluation strategies represent a rapid and easy-to-use tool box for enhanced metabolomics studies that combine differential pool size analysis with screening for differential carbon utilization from defined stable isotope labeled metabolic precursors.
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Affiliation(s)
- Frederik Dethloff
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804 Munich, Germany
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Isabel Orf
- French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer, Israel
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Joachim Kopka
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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28
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Van Dingenen J, Blomme J, Gonzalez N, Inzé D. Plants grow with a little help from their organelle friends. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:6267-6281. [PMID: 27815330 DOI: 10.1093/jxb/erw399] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Chloroplasts and mitochondria are indispensable for plant development. They not only provide energy and carbon sources to cells, but also have evolved to become major players in a variety of processes such as amino acid metabolism, hormone biosynthesis and cellular signalling. As semi-autonomous organelles, they contain a small genome that relies largely on nuclear factors for its maintenance and expression. An intensive crosstalk between the nucleus and the organelles is therefore essential to ensure proper functioning, and the nuclear genes encoding organellar proteins involved in photosynthesis and oxidative phosphorylation are obviously crucial for plant growth. Organ growth is determined by two main cellular processes: cell proliferation and cell expansion. Here, we review how plant growth is affected in mutants of organellar proteins that are differentially expressed during leaf and root development. Our findings indicate a clear role for organellar proteins in plant organ growth, primarily during cell proliferation. However, to date, the role of the nuclear-encoded organellar proteins in the cellular processes driving organ growth has not been investigated in much detail. We therefore encourage researchers to extend their phenotypic characterization beyond macroscopic features in order to get a better view on how chloroplasts and mitochondria regulate the basic processes of cell proliferation and cell expansion, essential to driving growth.
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Affiliation(s)
- Judith Van Dingenen
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Jonas Blomme
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Nathalie Gonzalez
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
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29
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Lynch AH, Kruger NJ, Hedges REM, McCullagh JSO. Variability in the carbon isotope composition of individual amino acids in plant proteins from different sources: 1 Leaves. PHYTOCHEMISTRY 2016; 125:27-34. [PMID: 26948983 DOI: 10.1016/j.phytochem.2016.01.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 01/14/2016] [Accepted: 01/19/2016] [Indexed: 06/05/2023]
Abstract
The natural carbon isotope composition of individual amino acids from plant leaf proteins has been measured to establish potential sources of variability. The plant leaves studied, taken from a range of plant groups (forbs, trees, grasses, and freshwater aquatic plants), showed no significant influence of either season or environment (water and light availability) on their Δδ(13)C values. Plant groups did, however, differ in carbon isotope composition, although no consistent differences were identified at the species level. A discriminant analysis model was constructed which allowed leaves from (1) nettles, (2) Pooideae, (3) other Poales, (4) trees and (5) freshwater higher plants to be distinguished from each other on the basis of their natural abundance (13)C/(12)C ratios of individual amino acids. Differences in carbon isotope composition are known to be retained, to some extent, in the tissues of their consumers, and hence an understanding of compound-specific variation in (13)C/(12)C fractional abundance in plants has the potential to provide dietary insights of value in archaeological and ecological studies.
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Affiliation(s)
- Anthony H Lynch
- Laboratory for Archaeology and the History of Art, South Parks Road, University of Oxford, Oxford OX1 3QY, UK; Department of Chemistry, Mansfield Road, University of Oxford, Oxford OX1 3TA, UK
| | - Nicholas J Kruger
- Department of Plant Sciences, South Parks Road, University of Oxford, Oxford OX1 3RB, UK
| | - Robert E M Hedges
- Laboratory for Archaeology and the History of Art, South Parks Road, University of Oxford, Oxford OX1 3QY, UK
| | - James S O McCullagh
- Department of Chemistry, Mansfield Road, University of Oxford, Oxford OX1 3TA, UK.
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30
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Galili G, Amir R, Fernie AR. The Regulation of Essential Amino Acid Synthesis and Accumulation in Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2016; 67:153-78. [PMID: 26735064 DOI: 10.1146/annurev-arplant-043015-112213] [Citation(s) in RCA: 166] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Although amino acids are critical for all forms of life, only proteogenic amino acids that humans and animals cannot synthesize de novo and therefore must acquire in their diets are classified as essential. Nine amino acids-lysine, methionine, threonine, phenylalanine, tryptophan, valine, isoleucine, leucine, and histidine-fit this definition. Despite their nutritional importance, several of these amino acids are present in limiting quantities in many of the world's major crops. In recent years, a combination of reverse genetic and biochemical approaches has been used to define the genes encoding the enzymes responsible for synthesizing, degrading, and regulating these amino acids. In this review, we describe recent advances in our understanding of the metabolism of the essential amino acids, discuss approaches for enhancing their levels in plants, and appraise efforts toward their biofortification in crop plants.
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Affiliation(s)
- Gad Galili
- Department of Plant Science, Weizmann Institute of Science, Rehovot 76100, Israel;
| | - Rachel Amir
- Laboratory of Plant Science, MIGAL-Galilee Research Institute, Kiryat Shmona 11016, Israel;
| | - Alisdair R Fernie
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam-Golm, Germany;
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31
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Doidy J, Li Y, Neymotin B, Edwards MB, Varala K, Gresham D, Coruzzi GM. "Hit-and-Run" transcription: de novo transcription initiated by a transient bZIP1 "hit" persists after the "run". BMC Genomics 2016; 17:92. [PMID: 26843062 PMCID: PMC4738784 DOI: 10.1186/s12864-016-2410-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 01/21/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Dynamic transcriptional regulation is critical for an organism's response to environmental signals and yet remains elusive to capture. Such transcriptional regulation is mediated by master transcription factors (TF) that control large gene regulatory networks. Recently, we described a dynamic mode of TF regulation named "hit-and-run". This model proposes that master TF can interact transiently with a set of targets, but the transcription of these transient targets continues after the TF dissociation from the target promoter. However, experimental evidence validating active transcription of the transient TF-targets is still lacking. RESULTS Here, we show that active transcription continues after transient TF-target interactions by tracking de novo synthesis of RNAs made in response to TF nuclear import. To do this, we introduced an affinity-labeled 4-thiouracil (4tU) nucleobase to specifically isolate newly synthesized transcripts following conditional TF nuclear import. Thus, we extended the TARGET system (Transient Assay Reporting Genome-wide Effects of Transcription factors) to include 4tU-labeling and named this new technology TARGET-tU. Our proof-of-principle example is the master TF Basic Leucine Zipper 1 (bZIP1), a central integrator of metabolic signaling in plants. Using TARGET-tU, we captured newly synthesized mRNAs made in response to bZIP1 nuclear import at a time when bZIP1 is no longer detectably bound to its target. Thus, the analysis of de novo transcripomics demonstrates that bZIP1 may act as a catalyst TF to initiate a transcriptional complex ("hit"), after which active transcription by RNA polymerase continues without the TF being bound to the gene promoter ("run"). CONCLUSION Our findings provide experimental proof for active transcription of transient TF-targets supporting a "hit-and-run" mode of action. This dynamic regulatory model allows a master TF to catalytically propagate rapid and broad transcriptional responses to changes in environment. Thus, the functional read-out of de novo transcripts produced by transient TF-target interactions allowed us to capture new models for genome-wide transcriptional control.
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Affiliation(s)
- Joan Doidy
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA.
| | - Ying Li
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA.
| | - Benjamin Neymotin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA.
| | - Molly B Edwards
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA.
| | - Kranthi Varala
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA.
| | - David Gresham
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA.
| | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA.
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Hildebrandt TM, Nunes Nesi A, Araújo WL, Braun HP. Amino Acid Catabolism in Plants. MOLECULAR PLANT 2015; 8:1563-79. [PMID: 26384576 DOI: 10.1016/j.molp.2015.09.005] [Citation(s) in RCA: 546] [Impact Index Per Article: 60.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 09/07/2015] [Accepted: 09/08/2015] [Indexed: 05/19/2023]
Abstract
Amino acids have various prominent functions in plants. Besides their usage during protein biosynthesis, they also represent building blocks for several other biosynthesis pathways and play pivotal roles during signaling processes as well as in plant stress response. In general, pool sizes of the 20 amino acids differ strongly and change dynamically depending on the developmental and physiological state of the plant cell. Besides amino acid biosynthesis, which has already been investigated in great detail, the catabolism of amino acids is of central importance for adjusting their pool sizes but so far has drawn much less attention. The degradation of amino acids can also contribute substantially to the energy state of plant cells under certain physiological conditions, e.g. carbon starvation. In this review, we discuss the biological role of amino acid catabolism and summarize current knowledge on amino acid degradation pathways and their regulation in the context of plant cell physiology.
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Affiliation(s)
- Tatjana M Hildebrandt
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany.
| | - Adriano Nunes Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil.
| | - Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
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Peng C, Uygun S, Shiu SH, Last RL. The Impact of the Branched-Chain Ketoacid Dehydrogenase Complex on Amino Acid Homeostasis in Arabidopsis. PLANT PHYSIOLOGY 2015; 169:1807-20. [PMID: 25986129 PMCID: PMC4634046 DOI: 10.1104/pp.15.00461] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/15/2015] [Indexed: 05/05/2023]
Abstract
The branched-chain amino acids (BCAAs) Leu, Ile, and Val are among nine essential amino acids that must be obtained from the diet of humans and other animals, and can be nutritionally limiting in plant foods. Despite genetic evidence of its importance in regulating seed amino acid levels, the full BCAA catabolic network is not completely understood in plants, and limited information is available regarding its regulation. In this study, transcript coexpression analyses revealed positive correlations among BCAA catabolism genes in stress, development, diurnal/circadian, and light data sets. A core subset of BCAA catabolism genes, including those encoding putative branched-chain ketoacid dehydrogenase subunits, is highly expressed during the night in plants on a diel cycle and in prolonged darkness. Mutants defective in these subunits accumulate higher levels of BCAAs in mature seeds, providing genetic evidence for their function in BCAA catabolism. In addition, prolonged dark treatment caused the mutants to undergo senescence early and overaccumulate leaf BCAAs. These results extend the previous evidence that BCAAs can be catabolized and serve as respiratory substrates at multiple steps. Moreover, comparison of amino acid profiles between mature seeds and dark-treated leaves revealed differences in amino acid accumulation when BCAA catabolism is perturbed. Together, these results demonstrate the consequences of blocking BCAA catabolism during both normal growth conditions and under energy-limited conditions.
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Affiliation(s)
- Cheng Peng
- Department of Plant Biology (C.P., S.-H.S., R.L.L.), Department of Energy Plant Research Laboratory (C.P., S.U.), Genetics Program (S.U., S.-H.S.), and Department of Biochemistry and Molecular Biology (R.L.L.), Michigan State University, East Lansing, Michigan 48824
| | - Sahra Uygun
- Department of Plant Biology (C.P., S.-H.S., R.L.L.), Department of Energy Plant Research Laboratory (C.P., S.U.), Genetics Program (S.U., S.-H.S.), and Department of Biochemistry and Molecular Biology (R.L.L.), Michigan State University, East Lansing, Michigan 48824
| | - Shin-Han Shiu
- Department of Plant Biology (C.P., S.-H.S., R.L.L.), Department of Energy Plant Research Laboratory (C.P., S.U.), Genetics Program (S.U., S.-H.S.), and Department of Biochemistry and Molecular Biology (R.L.L.), Michigan State University, East Lansing, Michigan 48824
| | - Robert L Last
- Department of Plant Biology (C.P., S.-H.S., R.L.L.), Department of Energy Plant Research Laboratory (C.P., S.U.), Genetics Program (S.U., S.-H.S.), and Department of Biochemistry and Molecular Biology (R.L.L.), Michigan State University, East Lansing, Michigan 48824
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Tzin V, Fernandez-Pozo N, Richter A, Schmelz EA, Schoettner M, Schäfer M, Ahern KR, Meihls LN, Kaur H, Huffaker A, Mori N, Degenhardt J, Mueller LA, Jander G. Dynamic Maize Responses to Aphid Feeding Are Revealed by a Time Series of Transcriptomic and Metabolomic Assays. PLANT PHYSIOLOGY 2015; 169:1727-43. [PMID: 26378100 PMCID: PMC4634079 DOI: 10.1104/pp.15.01039] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 09/15/2015] [Indexed: 05/18/2023]
Abstract
As a response to insect attack, maize (Zea mays) has inducible defenses that involve large changes in gene expression and metabolism. Piercing/sucking insects such as corn leaf aphid (Rhopalosiphum maidis) cause direct damage by acquiring phloem nutrients as well as indirect damage through the transmission of plant viruses. To elucidate the metabolic processes and gene expression changes involved in maize responses to aphid attack, leaves of inbred line B73 were infested with corn leaf aphids for 2 to 96 h. Analysis of infested maize leaves showed two distinct response phases, with the most significant transcriptional and metabolic changes occurring in the first few hours after the initiation of aphid feeding. After 4 d, both gene expression and metabolite profiles of aphid-infested maize reverted to being more similar to those of control plants. Although there was a predominant effect of salicylic acid regulation, gene expression changes also indicated prolonged induction of oxylipins, although not necessarily jasmonic acid, in aphid-infested maize. The role of specific metabolic pathways was confirmed using Dissociator transposon insertions in maize inbred line W22. Mutations in three benzoxazinoid biosynthesis genes, Bx1, Bx2, and Bx6, increased aphid reproduction. In contrast, progeny production was greatly decreased by a transposon insertion in the single W22 homolog of the previously uncharacterized B73 terpene synthases TPS2 and TPS3. Together, these results show that maize leaves shift to implementation of physical and chemical defenses within hours after the initiation of aphid feeding and that the production of specific metabolites can have major effects in maize-aphid interactions.
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Affiliation(s)
- Vered Tzin
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (V.T., N.F.-P., K.R.A., L.N.M., H.K., L.A.M., G.J.);Martin Luther University Halle, Wittenberg Institute for Pharmacy, D-06108 Halle, Germany (A.R., J.D.);Division of Biological Sciences, University of California, La Jolla, California 92093 (E.A.S., A.H.);Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (M.Scho., M.Schä.); andGraduate School of Agriculture, Kyoto University, Kyoto 808-8502, Japan (N.M.)
| | - Noe Fernandez-Pozo
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (V.T., N.F.-P., K.R.A., L.N.M., H.K., L.A.M., G.J.);Martin Luther University Halle, Wittenberg Institute for Pharmacy, D-06108 Halle, Germany (A.R., J.D.);Division of Biological Sciences, University of California, La Jolla, California 92093 (E.A.S., A.H.);Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (M.Scho., M.Schä.); andGraduate School of Agriculture, Kyoto University, Kyoto 808-8502, Japan (N.M.)
| | - Annett Richter
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (V.T., N.F.-P., K.R.A., L.N.M., H.K., L.A.M., G.J.);Martin Luther University Halle, Wittenberg Institute for Pharmacy, D-06108 Halle, Germany (A.R., J.D.);Division of Biological Sciences, University of California, La Jolla, California 92093 (E.A.S., A.H.);Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (M.Scho., M.Schä.); andGraduate School of Agriculture, Kyoto University, Kyoto 808-8502, Japan (N.M.)
| | - Eric A Schmelz
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (V.T., N.F.-P., K.R.A., L.N.M., H.K., L.A.M., G.J.);Martin Luther University Halle, Wittenberg Institute for Pharmacy, D-06108 Halle, Germany (A.R., J.D.);Division of Biological Sciences, University of California, La Jolla, California 92093 (E.A.S., A.H.);Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (M.Scho., M.Schä.); andGraduate School of Agriculture, Kyoto University, Kyoto 808-8502, Japan (N.M.)
| | - Matthias Schoettner
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (V.T., N.F.-P., K.R.A., L.N.M., H.K., L.A.M., G.J.);Martin Luther University Halle, Wittenberg Institute for Pharmacy, D-06108 Halle, Germany (A.R., J.D.);Division of Biological Sciences, University of California, La Jolla, California 92093 (E.A.S., A.H.);Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (M.Scho., M.Schä.); andGraduate School of Agriculture, Kyoto University, Kyoto 808-8502, Japan (N.M.)
| | - Martin Schäfer
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (V.T., N.F.-P., K.R.A., L.N.M., H.K., L.A.M., G.J.);Martin Luther University Halle, Wittenberg Institute for Pharmacy, D-06108 Halle, Germany (A.R., J.D.);Division of Biological Sciences, University of California, La Jolla, California 92093 (E.A.S., A.H.);Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (M.Scho., M.Schä.); andGraduate School of Agriculture, Kyoto University, Kyoto 808-8502, Japan (N.M.)
| | - Kevin R Ahern
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (V.T., N.F.-P., K.R.A., L.N.M., H.K., L.A.M., G.J.);Martin Luther University Halle, Wittenberg Institute for Pharmacy, D-06108 Halle, Germany (A.R., J.D.);Division of Biological Sciences, University of California, La Jolla, California 92093 (E.A.S., A.H.);Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (M.Scho., M.Schä.); andGraduate School of Agriculture, Kyoto University, Kyoto 808-8502, Japan (N.M.)
| | - Lisa N Meihls
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (V.T., N.F.-P., K.R.A., L.N.M., H.K., L.A.M., G.J.);Martin Luther University Halle, Wittenberg Institute for Pharmacy, D-06108 Halle, Germany (A.R., J.D.);Division of Biological Sciences, University of California, La Jolla, California 92093 (E.A.S., A.H.);Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (M.Scho., M.Schä.); andGraduate School of Agriculture, Kyoto University, Kyoto 808-8502, Japan (N.M.)
| | - Harleen Kaur
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (V.T., N.F.-P., K.R.A., L.N.M., H.K., L.A.M., G.J.);Martin Luther University Halle, Wittenberg Institute for Pharmacy, D-06108 Halle, Germany (A.R., J.D.);Division of Biological Sciences, University of California, La Jolla, California 92093 (E.A.S., A.H.);Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (M.Scho., M.Schä.); andGraduate School of Agriculture, Kyoto University, Kyoto 808-8502, Japan (N.M.)
| | - Alisa Huffaker
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (V.T., N.F.-P., K.R.A., L.N.M., H.K., L.A.M., G.J.);Martin Luther University Halle, Wittenberg Institute for Pharmacy, D-06108 Halle, Germany (A.R., J.D.);Division of Biological Sciences, University of California, La Jolla, California 92093 (E.A.S., A.H.);Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (M.Scho., M.Schä.); andGraduate School of Agriculture, Kyoto University, Kyoto 808-8502, Japan (N.M.)
| | - Naoki Mori
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (V.T., N.F.-P., K.R.A., L.N.M., H.K., L.A.M., G.J.);Martin Luther University Halle, Wittenberg Institute for Pharmacy, D-06108 Halle, Germany (A.R., J.D.);Division of Biological Sciences, University of California, La Jolla, California 92093 (E.A.S., A.H.);Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (M.Scho., M.Schä.); andGraduate School of Agriculture, Kyoto University, Kyoto 808-8502, Japan (N.M.)
| | - Joerg Degenhardt
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (V.T., N.F.-P., K.R.A., L.N.M., H.K., L.A.M., G.J.);Martin Luther University Halle, Wittenberg Institute for Pharmacy, D-06108 Halle, Germany (A.R., J.D.);Division of Biological Sciences, University of California, La Jolla, California 92093 (E.A.S., A.H.);Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (M.Scho., M.Schä.); andGraduate School of Agriculture, Kyoto University, Kyoto 808-8502, Japan (N.M.)
| | - Lukas A Mueller
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (V.T., N.F.-P., K.R.A., L.N.M., H.K., L.A.M., G.J.);Martin Luther University Halle, Wittenberg Institute for Pharmacy, D-06108 Halle, Germany (A.R., J.D.);Division of Biological Sciences, University of California, La Jolla, California 92093 (E.A.S., A.H.);Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (M.Scho., M.Schä.); andGraduate School of Agriculture, Kyoto University, Kyoto 808-8502, Japan (N.M.)
| | - Georg Jander
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (V.T., N.F.-P., K.R.A., L.N.M., H.K., L.A.M., G.J.);Martin Luther University Halle, Wittenberg Institute for Pharmacy, D-06108 Halle, Germany (A.R., J.D.);Division of Biological Sciences, University of California, La Jolla, California 92093 (E.A.S., A.H.);Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (M.Scho., M.Schä.); andGraduate School of Agriculture, Kyoto University, Kyoto 808-8502, Japan (N.M.)
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Dellero Y, Lamothe-Sibold M, Jossier M, Hodges M. Arabidopsis thaliana ggt1 photorespiratory mutants maintain leaf carbon/nitrogen balance by reducing RuBisCO content and plant growth. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015. [PMID: 26216646 DOI: 10.1111/tpj.12945] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Metabolic and physiological analyses of glutamate:glyoxylate aminotransferase 1 (GGT1) mutants were performed at the global leaf scale to elucidate the mechanisms involved in their photorespiratory growth phenotype. Air-grown ggt1 mutants showed retarded growth and development, that was not observed at high CO2 (3000 μL L(-1) ). When compared to wild-type (WT) plants, air-grown ggt1 plants exhibited glyoxylate accumulation, global changes in amino acid amounts including a decrease in serine content, lower organic acid levels, and modified ATP/ADP and NADP(+) /NADPH ratios. When compared to WT plants, their net CO2 assimilation rates (An ) were 50% lower and this mirrored decreases in ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) contents. High CO2 -grown ggt1 plants transferred to air revealed a rapid decrease of An and photosynthetic electron transfer rate while maintaining a high energetic state. Short-term (a night period and 4 h of light) transferred ggt1 leaves accumulated glyoxylate and exhibited low serine contents, while other amino acid levels were not modified. RuBisCO content, activity and activation state were not altered after a short-term transfer while the ATP/ADP ratio was lowered in ggt1 rosettes. However, plant growth and RuBisCO levels were both reduced in ggt1 leaves after a long-term (12 days) acclimation to air from high CO2 when compared to WT plants. The data are discussed with respect to a reduced photorespiratory carbon recycling in the mutants. It is proposed that the low An limits nitrogen-assimilation, this decreases leaf RuBisCO content until plants attain a new homeostatic state that maintains a constant C/N balance and leads to smaller, slower growing plants.
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Affiliation(s)
- Younès Dellero
- Institute of Plant Sciences Paris-Saclay, UMR 9213/UMR1403, CNRS/INRA, Université Paris Sud, Université d'Evry, Université Paris-Diderot, Bâtiment 630, Orsay Cedex, 91405, France
| | - Marlène Lamothe-Sibold
- Institute of Plant Sciences Paris-Saclay, UMR 9213/UMR1403, CNRS/INRA, Université Paris Sud, Université d'Evry, Université Paris-Diderot, Bâtiment 630, Orsay Cedex, 91405, France
| | - Mathieu Jossier
- Institute of Plant Sciences Paris-Saclay, UMR 9213/UMR1403, CNRS/INRA, Université Paris Sud, Université d'Evry, Université Paris-Diderot, Bâtiment 630, Orsay Cedex, 91405, France
| | - Michael Hodges
- Institute of Plant Sciences Paris-Saclay, UMR 9213/UMR1403, CNRS/INRA, Université Paris Sud, Université d'Evry, Université Paris-Diderot, Bâtiment 630, Orsay Cedex, 91405, France
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Colling J, Tohge T, De Clercq R, Brunoud G, Vernoux T, Fernie AR, Makunga NP, Goossens A, Pauwels L. Overexpression of the Arabidopsis thaliana signalling peptide TAXIMIN1 affects lateral organ development. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5337-49. [PMID: 26071531 PMCID: PMC4526920 DOI: 10.1093/jxb/erv291] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Lateral organ boundary formation is highly regulated by transcription factors and hormones such as auxins and brassinosteroids. However, in contrast to many other developmental processes in plants, no role for signalling peptides in the regulation of this process has been reported yet. The first characterization of the secreted cysteine-rich TAXIMIN (TAX) signalling peptides in Arabidopsis is presented here. TAX1 overexpression resulted in minor alterations in the primary shoot and root metabolome, abnormal fruit morphology, and fusion of the base of cauline leaves to stems forming a decurrent leaf attachment. The phenotypes at the paraclade junction match TAX1 promoter activity in this region and are similar to loss of LATERAL ORGAN FUSION (LOF) transcription factor function. Nevertheless, TAX1 expression was unchanged in lof1lof2 paraclade junctions and, conversely, LOF gene expression was unchanged in TAX1 overexpressing plants, suggesting TAX1 may act independently. This study identifies TAX1 as the first plant signalling peptide influencing lateral organ separation and implicates the existence of a peptide signal cascade regulating this process in Arabidopsis.
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Affiliation(s)
- Janine Colling
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, (VIB), Technologiepark 927, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium Institute for Plant Biotechnology, Department of Genetics, Stellenbosch University, Stellenbosch, 7602, South Africa
| | - Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Rebecca De Clercq
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, (VIB), Technologiepark 927, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
| | - Geraldine Brunoud
- Laboratoire de Reproduction et Développement des Plantes, CNRS, INRA, ENS Lyon, Lyon, France
| | - Teva Vernoux
- Laboratoire de Reproduction et Développement des Plantes, CNRS, INRA, ENS Lyon, Lyon, France
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Nokwanda P Makunga
- Institute for Plant Biotechnology, Department of Genetics, Stellenbosch University, Stellenbosch, 7602, South Africa Department of Botany and Zoology, Stellenbosch University, Stellenbosch, 7602, South Africa
| | - Alain Goossens
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, (VIB), Technologiepark 927, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
| | - Laurens Pauwels
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, (VIB), Technologiepark 927, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
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37
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Zhang C, Pang Q, Jiang L, Wang S, Yan X, Chen S, He Y. Dihydroxyacid dehydratase is important for gametophyte development and disruption causes increased susceptibility to salinity stress in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:879-88. [PMID: 25399005 PMCID: PMC4321549 DOI: 10.1093/jxb/eru449] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Dihydroxyacid dehydratase (DHAD) catalyses a key step in the branched-chain amino acid (BCAA) biosynthetic pathway that exists in numerous organisms, including bacteria, fungi, and plants, but not humans. In Arabidopsis thaliana, DHAD is encoded by a single gene (AT3G23940), but its biological function in controlling plant development remains uncharacterized. In this study, we showed that DHAD is highly expressed in most vegetative and reproductive tissues. It is an essential gene, and complete disruption caused partial sterility in both male and female gametophyte phases. In addition, reduced expression of DHAD in knockdown mutants resulted in a reduction in the accumulation of all three BCAAs in roots and, as a consequence, led to a shorter root phenotype, which could be restored by an exogenous supplement of free BCAAs. Interestingly, the knockdown mutants became hypersensitive to salt stress, not to heavy metal stress, implying that BCAAs may act as osmolytes in salt tolerance. This would be the second amino acid shown to confer such a function in addition to the well-documented proline. Our results provide evidence that BCAA biosynthesis plays important roles in gametophyte and root development, and BCAA homeostasis contributes to the adaptation of Arabidopsis to salinity stress.
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Affiliation(s)
- Chun Zhang
- National Maize Improvement Centre of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Qiuying Pang
- Alkali Soil Natural Environmental Science Centre, Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Luguang Jiang
- National Maize Improvement Centre of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Shoucai Wang
- National Maize Improvement Centre of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Xiufeng Yan
- Alkali Soil Natural Environmental Science Centre, Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Sixue Chen
- Department of Biology, Genetics Institute, and Plant Molecular & Cellular Biology Program, University of Florida, Gainesville, Florida, USA
| | - Yan He
- National Maize Improvement Centre of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
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38
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Toubiana D, Batushansky A, Tzfadia O, Scossa F, Khan A, Barak S, Zamir D, Fernie AR, Nikoloski Z, Fait A. Combined correlation-based network and mQTL analyses efficiently identified loci for branched-chain amino acid, serine to threonine, and proline metabolism in tomato seeds. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:121-33. [PMID: 25359542 DOI: 10.1111/tpj.12717] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 10/22/2014] [Indexed: 05/20/2023]
Abstract
Correlation-based network analysis (CNA) of the metabolic profiles of seeds of a tomato introgression line mapping population revealed a clique of proteinogenic amino acids: Gly, Ile, Pro, Ser, Thr, and Val. Correlations between profiles of these amino acids exhibited a statistically significant average correlation coefficient of 0.84 as compared with an average correlation coefficient of 0.39 over the 16 119 other metabolite cliques containing six metabolites. In silico removal of cliques was used to quantify their importance in determining seminal network properties, highlighting the strong effects of the amino acid clique. Quantitative trait locus analysis revealed co-localization for the six amino acids on chromosome 2, 4 and 10. Sequence analysis identified a unique set of 10 genes on chromosome 2 only, which were associated with amino acid metabolism and specifically the metabolism of Ser-Gly and their conversion into branched-chain amino acids. Metabolite profiling of a set of sublines, with introgressions on chromosome 2, identified a significant change in the abundance of the six amino acids in comparison with M82. Expression analysis of candidate genes affecting Ser metabolism matched the observation from the metabolite data, suggesting a coordinated behavior of the level of these amino acids at the genetic level. Analysis of transcription factor binding sites in the promoter regions of the identified genes suggested combinatorial response to light and the circadian clock.
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Affiliation(s)
- David Toubiana
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990, Midreshet Ben-Gurion, Israel
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Galili G, Avin-Wittenberg T, Angelovici R, Fernie AR. The role of photosynthesis and amino acid metabolism in the energy status during seed development. FRONTIERS IN PLANT SCIENCE 2014; 5:447. [PMID: 25232362 PMCID: PMC4153028 DOI: 10.3389/fpls.2014.00447] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 08/19/2014] [Indexed: 05/07/2023]
Abstract
Seeds are the major organs responsible for the evolutionary upkeep of angiosperm plants. Seeds accumulate significant amounts of storage compounds used as nutrients and energy reserves during the initial stages of seed germination. The accumulation of storage compounds requires significant amounts of energy, the generation of which can be limited due to reduced penetration of oxygen and light particularly into the inner parts of seeds. In this review, we discuss the adjustment of seed metabolism to limited energy production resulting from the suboptimal penetration of oxygen into the seed tissues. We also discuss the role of photosynthesis during seed development and its contribution to the energy status of developing seeds. Finally, we describe the contribution of amino acid metabolism to the seed energy status, focusing on the Asp-family pathway that leads to the synthesis and catabolism of Lys, Thr, Met, and Ile.
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Affiliation(s)
- Gad Galili
- Department of Plant Sciences, The Weizmann Institute of ScienceRehovot, Israel
| | | | - Ruthie Angelovici
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast Lansing, MI, USA
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
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Dumont J, Keski-Saari S, Keinänen M, Cohen D, Ningre N, Kontunen-Soppela S, Baldet P, Gibon Y, Dizengremel P, Vaultier MN, Jolivet Y, Oksanen E, Le Thiec D. Ozone affects ascorbate and glutathione biosynthesis as well as amino acid contents in three Euramerican poplar genotypes. TREE PHYSIOLOGY 2014; 34:253-266. [PMID: 24682617 DOI: 10.1093/treephys/tpu004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Ozone is an air pollutant that causes oxidative stress by generation of reactive oxygen species (ROS) within the leaf. The capacity to detoxify ROS and repair ROS-induced damage may contribute to ozone tolerance. Ascorbate and glutathione are known to be key players in detoxification. Ozone effects on their biosynthesis and on amino acid metabolism were investigated in three Euramerican poplar genotypes (Populus deltoides Bartr. × Populus nigra L.) differing in ozone sensitivity. Total ascorbate and glutathione contents were increased in response to ozone in all genotypes, with the most resistant genotype (Carpaccio) showing an increase of up to 70%. Reduced ascorbate (ASA) concentration at least doubled in the two most resistant genotypes (Carpaccio and Cima), whereas the most sensitive genotype (Robusta) seemed unable to regenerate ASA from oxidized ascorbate (DHA), leading to an increase of 80% of the oxidized form. Increased ascorbate (ASA + DHA) content correlated with the increase in gene expression in its biosynthetic pathway, especially the putative gene of GDP-l-galactose phosphorylase VTC2. Increased cysteine availability combined with increased expression of γ-glutamylcysteine synthetase (GSH1) and glutathione synthetase (GSH2) genes allows higher glutathione biosynthesis in response to ozone, particularly in Carpaccio. In addition, ozone caused a remobilization of amino acids with a decreased pool of total amino acids and an increase of Cys and putrescine, especially in Carpaccio. In addition, the expression of genes encoding threonine aldolase was strongly induced only in the most tolerant genotype, Carpaccio. Reduced ascorbate levels could partly explain the sensitivity to ozone for Robusta but not for Cima. Reduced ascorbate level alone is not sufficient to account for ozone tolerance in poplar, and it is necessary to consider several other factors including glutathione content.
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Benstein RM, Ludewig K, Wulfert S, Wittek S, Gigolashvili T, Frerigmann H, Gierth M, Flügge UI, Krueger S. Arabidopsis phosphoglycerate dehydrogenase1 of the phosphoserine pathway is essential for development and required for ammonium assimilation and tryptophan biosynthesis. THE PLANT CELL 2013; 25:5011-29. [PMID: 24368794 PMCID: PMC3904002 DOI: 10.1105/tpc.113.118992] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/26/2013] [Accepted: 12/06/2013] [Indexed: 05/17/2023]
Abstract
In plants, two independent serine biosynthetic pathways, the photorespiratory and glycolytic phosphoserine (PS) pathways, have been postulated. Although the photorespiratory pathway is well characterized, little information is available on the function of the PS pathway in plants. Here, we present a detailed characterization of phosphoglycerate dehydrogenases (PGDHs) as components of the PS pathway in Arabidopsis thaliana. All PGDHs localize to plastids and possess similar kinetic properties, but they differ with respect to their sensitivity to serine feedback inhibition. Furthermore, analysis of pgdh1 and phosphoserine phosphatase mutants revealed an embryo-lethal phenotype and PGDH1-silenced lines were inhibited in growth. Metabolic analyses of PGDH1-silenced lines grown under ambient and high CO2 conditions indicate a direct link between PS biosynthesis and ammonium assimilation. In addition, we obtained several lines of evidence for an interconnection between PS and tryptophan biosynthesis, because the expression of PGDH1 and phosphoserine aminotransferase1 is regulated by MYB51 and MYB34, two activators of tryptophan biosynthesis. Moreover, the concentration of tryptophan-derived glucosinolates and auxin were reduced in PGDH1-silenced plants. In essence, our results provide evidence for a vital function of PS biosynthesis for plant development and metabolism.
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Van Bochaute P, Novoa A, Ballet S, Rognes SE, Angenon G. Regulatory mechanisms after short- and long-term perturbed lysine biosynthesis in the aspartate pathway: the need for isogenes in Arabidopsis thaliana. PHYSIOLOGIA PLANTARUM 2013; 149:449-460. [PMID: 23556418 DOI: 10.1111/ppl.12053] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 02/22/2013] [Accepted: 03/12/2013] [Indexed: 06/02/2023]
Abstract
The aspartate-derived amino acid pathway in plants is an intensively studied metabolic pathway, because of the biosynthesis of the four essential amino acids lysine, threonine, isoleucine and methionine. The pathway is mainly controlled by the key regulatory enzymes aspartate kinase (AK; EC 2.7.2.4), homoserine dehydrogenase (HSDH; EC 1.1.1.3) and 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7), formerly referred to as dihydrodipicolinate synthase (DHDPS). They are encoded by isoenzyme families and it is not known why such families are evolutionarily maintained. To gain more insight into the specific roles and regulation of the isoenzymes, we inhibited DHDPS in Arabidopsis thaliana with the chemical compound (N,N-dimethylglycinatoboranyloxycarbonylmethyl)-dimethylamine-borane (DDAB) and compared the short-term effects on the biochemical and biomolecular level to the long-term adaptations in dhdps knockout mutants. We found that DHDPS2 plays a crucial role in controlling lysine biosynthesis, thereby stabilizing flux through the whole aspartate pathway. Moreover, DHDPS2 was also shown to influence the threonine level to a large extent. In addition, the lysine-sensitive AKs, AKLYS1 and AKLYS3 control the short- and long-term responses to perturbed lysine biosynthesis in Arabidopsis thaliana.
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Affiliation(s)
- Pieter Van Bochaute
- Laboratory of Plant Genetics, Institute for Molecular Biology and Biotechnology, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050, Brussels, Belgium
| | - Alexandre Novoa
- Department of Chemistry, Faculty of Science, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050, Brussels, Belgium
| | - Steven Ballet
- Department of Chemistry, Faculty of Science, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050, Brussels, Belgium
| | - Sven Erik Rognes
- Department of Molecular Biosciences, University of Oslo, P.O. Box 1041, Blindern, 0316, Oslo, Norway
| | - Geert Angenon
- Laboratory of Plant Genetics, Institute for Molecular Biology and Biotechnology, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050, Brussels, Belgium
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Rippa S, Zhao Y, Merlier F, Charrier A, Perrin Y. The carnitine biosynthetic pathway in Arabidopsis thaliana shares similar features with the pathway of mammals and fungi. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2012; 60:109-14. [PMID: 22922110 DOI: 10.1016/j.plaphy.2012.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 08/02/2012] [Indexed: 05/01/2023]
Abstract
Carnitine is an essential quaternary ammonium amino acid that occurs in the microbial, plant and animal kingdoms. The role and synthesis of this compound are very well documented in bacteria, fungi and mammals. On the contrary, although the presence of carnitine in plant tissue has been reported four decades ago and information about its biological implication are available, nothing is known about its synthesis in plants. We designed experiments to determine if the carnitine biosynthetic pathway in Arabidopsis thaliana is similar to the pathway in mammals and in the fungi Neurospora crassa and Candida albicans. We first checked for the presence of trimetyllysine (TML) and γ-butyrobetaine (γ-BB), two precursors of carnitine in fungi and in mammals, using liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS). Both compounds were shown to be present in plant extracts at concentrations in the picomole range per mg of dry weight. We next synthesized deuterium-labeled TML and transferred A. thaliana seedlings on growth medium supplemented with 1 mM of the deuterated precursor. LC-ESI-MS/MS analysis of plant extracts clearly highlighted the synthesis of deuterium labeled γ-BB and labeled carnitine in deuterated-TML fed plants. The similarities between plant, fungal and mammalian pathways provide very useful information to search homologies between genomes. As a matter of fact the analysis of A. thaliana protein database provides homology for several enzymes responsible for carnitine synthesis in fungi and mammals. The study of mutants affected in the corresponding genes would be very useful to elucidate the plant carnitine biosynthetic pathway and to investigate further the role of carnitine in plant physiology.
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Affiliation(s)
- Sonia Rippa
- Génie Enzymatique et Cellulaire (GEC), UMR 6022 CNRS, Université de Technologie de Compiègne, Centre de Recherche Royallieu, BP 20529, 60205 Compiègne Cedex, France
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Avin-Wittenberg T, Tzin V, Angelovici R, Less H, Galili G. Deciphering energy-associated gene networks operating in the response of Arabidopsis plants to stress and nutritional cues. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:954-66. [PMID: 22288575 DOI: 10.1111/j.1365-313x.2012.04926.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plants need to continuously adjust their transcriptome in response to various stresses that lead to inhibition of photosynthesis and the deprivation of cellular energy. This adjustment is triggered in part by a coordinated re-programming of the energy-associated transcriptome to slow down photosynthesis and activate other energy-promoting gene networks. Therefore, understanding the stress-related transcriptional networks of genes belonging to energy-associated pathways is of major importance for engineering stress tolerance. In a bioinformatics approach developed by our group, termed 'gene coordination', we previously divided genes encoding for enzymes and transcription factors in Arabidopsis thaliana into three clusters, displaying altered coordinated transcriptional behaviors in response to multiple biotic and abiotic stresses (Plant Cell, 23, 2011, 1264). Enrichment analysis indicated further that genes controlling energy-associated metabolism operate as a compound network in response to stress. In the present paper, we describe in detail the network association of genes belonging to six central energy-associated pathways in each of these three clusters described in our previous paper. Our results expose extensive stress-associated intra- and inter-pathway interactions between genes from these pathways, indicating that genes encoding proteins involved in energy-associated metabolism are expressed in a highly coordinated manner. We also provide examples showing that this approach can be further utilized to elucidate candidate genes for stress tolerance and functions of isozymes.
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Affiliation(s)
- Tamar Avin-Wittenberg
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
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Huang T, Rehak L, Jander G. meta-Tyrosine in Festuca rubra ssp. commutata (Chewings fescue) is synthesized by hydroxylation of phenylalanine. PHYTOCHEMISTRY 2012; 75:60-6. [PMID: 22192329 DOI: 10.1016/j.phytochem.2011.09.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Revised: 08/11/2011] [Accepted: 09/05/2011] [Indexed: 05/18/2023]
Abstract
m-Tyrosine is a non-protein amino acid that is structurally similar to the common protein amino acids p-tyrosine and phenylalanine. Copious amounts of m-tyrosine can be found in root exudates of the fine fescue cultivar, Festuca rubra L. ssp. commutata (Chewings fescue). The phytotoxicity of m-tyrosine may contribute to the allelopathic potential of F. rubra. m-Tyrosine in Euphorbia myrsinites (donkey-tail spurge), was previously shown to be synthesized via transamination of m-hydroxyphenylpyruvate. Here we show that m-tyrosine biosynthesis in F. rubra occurs through direct hydroxylation of phenylalanine in the root tips, perhaps through the activity of a cytochrome P450 enzyme. Hence, E. myrsinites and F. rubra, the only two plant species known to produce m-tyrosine, use distinct biosynthetic pathways that likely arose independently in evolutionary history.
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Affiliation(s)
- Tengfang Huang
- Boyce Thompson Institute for Plant Research, 1 Tower Road, Ithaca, NY 14853, USA
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Serine hydroxymethyltransferase: A model enzyme for mechanistic, structural, and evolutionary studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1489-96. [DOI: 10.1016/j.bbapap.2010.10.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Revised: 10/25/2010] [Accepted: 10/29/2010] [Indexed: 11/18/2022]
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Degu A, Hatew B, Nunes-Nesi A, Shlizerman L, Zur N, Katz E, Fernie AR, Blumwald E, Sadka A. Inhibition of aconitase in citrus fruit callus results in a metabolic shift towards amino acid biosynthesis. PLANTA 2011; 234:501-13. [PMID: 21528417 DOI: 10.1007/s00425-011-1411-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2011] [Accepted: 03/28/2011] [Indexed: 05/08/2023]
Abstract
Citrate, a major determinant of citrus fruit quality, accumulates early in fruit development and declines towards maturation. The isomerization of citrate to isocitrate, catalyzed by aconitase is a key step in acid metabolism. Inhibition of mitochondrial aconitase activity early in fruit development contributes to acid accumulation, whereas increased cytosolic activity of aconitase causes citrate decline. It was previously hypothesized that the block in mitochondrial aconitase activity, inducing acid accumulation, is caused by citramalate. Here, we investigated the effect of citramalate and of another aconitase inhibitor, oxalomalate, on aconitase activity and regulation in callus originated from juice sacs. These compounds significantly increased citrate content and reduced the enzyme's activity, while slightly inducing its protein level. Citramalate inhibited the mitochondrial, but not cytosolic form of the enzyme. Its external application to mandarin fruits resulted in inhibition of aconitase activity, with a transient increase in fruit acidity detected a few weeks later. The endogenous level of citramalate was analyzed in five citrus varieties: its pattern of accumulation challenged the notion of its action as an endogenous inhibitor of mitochondrial aconitase. Metabolite profiling of oxalomalate-treated cells showed significant increases in a few amino acids and organic acids. The activities of alanine transaminase, aspartate transaminase and aspartate kinase, as well as these of two γ-aminobutyrate (GABA)-shunt enzymes, succinic semialdehyde reductase (SSAR) and succinic semialdehyde dehydrogenase (SSAD) were significantly induced in oxalomalate-treated cells. It is suggested that the increase in citrate, caused by aconitase inhibition, induces amino acid synthesis and the GABA shunt, in accordance with the suggested fate of citrate during the acid decline stage in citrus fruit.
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Affiliation(s)
- Asfaw Degu
- Department of Fruit Tree Sciences, ARO, The Volcani Center, P.O. Box 6, Bet Dagan 50250, Israel
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Avin-Wittenberg T, Tzin V, Less H, Angelovici R, Galili G. A friend in need is a friend indeed: understanding stress-associated transcriptional networks of plant metabolism using cliques of coordinately expressed genes. PLANT SIGNALING & BEHAVIOR 2011; 6:1294-6. [PMID: 21847019 PMCID: PMC3258055 DOI: 10.4161/psb.6.9.16567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The response of plants to environmental cues, particularly stresses, involves the coordinated induction or repression of gene expression. In a previous study, we developed a bioinformatics approach to analyze the mutual expression pattern of genes encoding transcription factors and metabolic enzymes upon exposure of Arabidopsis plants to abiotic and biotic stresses. The analysis resulted in three gene clusters, each displaying a unique expression pattern. In the present addendum, we address the composition of each of these three clusters in regard to the functional identity of their encoded proteins as enzymes or transcription factors.
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Stuttmann J, Hubberten HM, Rietz S, Kaur J, Muskett P, Guerois R, Bednarek P, Hoefgen R, Parker JE. Perturbation of Arabidopsis amino acid metabolism causes incompatibility with the adapted biotrophic pathogen Hyaloperonospora arabidopsidis. THE PLANT CELL 2011; 23:2788-803. [PMID: 21784950 PMCID: PMC3226217 DOI: 10.1105/tpc.111.087684] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 06/27/2011] [Accepted: 07/07/2011] [Indexed: 05/18/2023]
Abstract
Reliance of biotrophic pathogens on living plant tissues to propagate implies strong interdependence between host metabolism and nutrient uptake by the pathogen. However, factors determining host suitability and establishment of infection are largely unknown. We describe a loss-of-inhibition allele of ASPARTATE KINASE2 and a loss-of-function allele of DIHYDRODIPICOLINATE SYNTHASE2 identified in a screen for Arabidopsis thaliana mutants with increased resistance to the obligate biotrophic oomycete Hyaloperonospora arabidopsidis (Hpa). Through different molecular mechanisms, these mutations perturb amino acid homeostasis leading to overaccumulation of the Asp-derived amino acids Met, Thr, and Ile. Although detrimental for the plant, the mutations do not cause defense activation, and both mutants retain full susceptibility to the adapted obligate biotrophic fungus Golovinomyces orontii (Go). Chemical treatments mimicking the mutants' metabolic state identified Thr as the amino acid suppressing Hpa but not Go colonization. We conclude that perturbations in amino acid homeostasis render the mutant plants unsuitable as an infection substrate for Hpa. This may be explained by deployment of the same amino acid biosynthetic pathways by oomycetes and plants. Our data show that the plant host metabolic state can, in specific ways, influence the ability of adapted biotrophic strains to cause disease.
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Affiliation(s)
- Johannes Stuttmann
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | | | - Steffen Rietz
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Jagreet Kaur
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Paul Muskett
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Raphael Guerois
- Commissariat á l’Energie Atomique, Institut de Biologie et Technologies de Saclay, Laboratoire de Biologie Structurale et Radiobiologie and Centre National de la Recherche Scientifique, Unités de Recherche Associées 2096, F-91191 Gif-sur-Yvette, France
| | - Paweł Bednarek
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany
| | - Jane E. Parker
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
- Address correspondence to
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Qi Q, Huang J, Crowley J, Ruschke L, Goldman BS, Wen L, Rapp WD. Metabolically engineered soybean seed with enhanced threonine levels: biochemical characterization and seed-specific expression of lysine-insensitive variants of aspartate kinases from the enteric bacterium Xenorhabdus bovienii. PLANT BIOTECHNOLOGY JOURNAL 2011; 9:193-204. [PMID: 20633240 DOI: 10.1111/j.1467-7652.2010.00545.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Threonine (Thr) is one of a few limiting essential amino acids (EAAs) in the animal feed industry, and its level in feed rations can impact production of important meat sources, such as swine and poultry. Threonine as well as EAAs lysine (Lys) and methionine (Met) are all synthesized via the aspartate family pathway. Here, we report a successful strategy to produce high free threonine soybean seed via identification of a feedback-resistant aspartate kinase (AK) enzyme that can be over-expressed in developing soybean seed. Towards this goal, we have purified and biochemically characterized AK from the enteric bacterium Xenorhabdus bovienii (Xb). Site-directed mutagenesis of XbAK identified two key regulatory residues Glu-257 and Thr-359 involved in lysine inhibition. Three feedback-resistant alleles, XbAK_T359I, XbAK_E257K and XbAK_E257K/T359I, have been generated. This study is the first to kinetically characterize the XbAK enzyme and provide biochemical and transgenic evidence that Glu-257 near the catalytic site is a critical residue for the allosteric regulation of AK. Furthermore, seed-specific expression of the feedback-resistant XbAK_T359I or XbAK_E257K allele results in increases of free Thr levels of up to 100-fold in R(1) soybean seed when compared to wild-type. Expression of feedback-sensitive wild-type AK did not substantially impact seed Thr content. In addition to high Thr, transgenic seed also showed substantial increases in other major free amino acid (FAA) levels, resulting in an up to 3.5-fold increase in the total FAA content. The transgenic seed was normal in appearance and germinated well under greenhouse conditions.
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Affiliation(s)
- Qungang Qi
- Monsanto Company, Chesterfield, MO, USA.
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