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Garfinkel AM, Ilker E, Miyazawa H, Schmeisser K, Tennessen JM. Historic obstacles and emerging opportunities in the field of developmental metabolism - lessons from Heidelberg. Development 2024; 151:dev202937. [PMID: 38912552 PMCID: PMC11299503 DOI: 10.1242/dev.202937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
The field of developmental metabolism is experiencing a technological revolution that is opening entirely new fields of inquiry. Advances in metabolomics, small-molecule sensors, single-cell RNA sequencing and computational modeling present new opportunities for exploring cell-specific and tissue-specific metabolic networks, interorgan metabolic communication, and gene-by-metabolite interactions in time and space. Together, these advances not only present a means by which developmental biologists can tackle questions that have challenged the field for centuries, but also present young scientists with opportunities to define new areas of inquiry. These emerging frontiers of developmental metabolism were at the center of a highly interactive 2023 EMBO workshop 'Developmental metabolism: flows of energy, matter, and information'. Here, we summarize key discussions from this forum, emphasizing modern developmental biology's challenges and opportunities.
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Affiliation(s)
- Alexandra M. Garfinkel
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
- Section of Endocrinology, Department of Internal Medicine, Yale University, New Haven, CT 06510, USA
| | - Efe Ilker
- Max Planck Institute for the Physics of Complex Systems, Dresden 01187, Germany
| | - Hidenobu Miyazawa
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Kathrin Schmeisser
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
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2
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Wu L, Chen X, Zhang P, Yan S, Zhang T, Li Y. TON1 recruiting motif 21 positively regulates the flavonoid metabolic pathway at the translational level in Arabidopsis thaliana. PLANTA 2024; 259:65. [PMID: 38329545 PMCID: PMC10853083 DOI: 10.1007/s00425-024-04337-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 01/09/2024] [Indexed: 02/09/2024]
Abstract
MAIN CONCLUSION This study reveals that TRM21 acts as a positive regulator of flavonoid biosynthesis at the translational level in Arabidopsis, impacting both secondary metabolites and genes associated with root hair growth. TRM (TONNEAU1-recruiting motif) superfamily proteins are reported to be involved in microtubule assembly. However, the functions of this protein family are just beginning to be uncovered. Here, we provide metabolomic and genetic evidence that 1 of the 34 TRM members, TRM21, positively regulates the biosynthesis of flavonoids at the translational level in Arabidopsis thaliana. A loss-of-function mutation in TRM21 led to root hair growth defects and stunted plant growth, accompanied by significant alterations in secondary metabolites, particularly a marked reduction in flavonoid content. Interestingly, our study revealed that the transcription levels of genes involved in the flavonoid biosynthesis pathway remained unchanged in the trm21 mutants, but there was a significant downregulation in the translation levels of certain genes [flavanone 3-hydroxylase (F3H), dihydroflavonol-4-reductase (DFR), anthocyanidin reductase (ANR), flavanone 3'-hydroxylase (F3'H), flavonol synthase (FLS), chalcone synthase (CHS)]. Additionally, the translation levels of some genes related to root hair growth [RHO-related GTPases of plant 2 (ROP2), root hair defective 6 (RHD6), root hair defective 2 (RHD2)] were also reduced in the trm21 mutants. Taken together, these results indicate that TRM21 functions as a positive regulator of flavonoid biosynthesis at the translational level in Arabidopsis.
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Affiliation(s)
- Ling Wu
- College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan Province, China
- Syoung Cosmetics Manufacturing Co., Ltd., Changsha, 410000, Hunan Province, China
| | - Xuan Chen
- Changsha Yuelu Experimental High School, Changsha, 410000, Hunan Province, China
| | - Ping Zhang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan Province, China
| | - Shaowei Yan
- Syoung Cosmetics Manufacturing Co., Ltd., Changsha, 410000, Hunan Province, China
| | - Tingzhi Zhang
- Syoung Cosmetics Manufacturing Co., Ltd., Changsha, 410000, Hunan Province, China
| | - Yuanyuan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, Hunan Province, China.
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3
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Minen RI, Thirumalaikumar VP, Skirycz A. Proteinogenic dipeptides, an emerging class of small-molecule regulators. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102395. [PMID: 37311365 DOI: 10.1016/j.pbi.2023.102395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 06/15/2023]
Abstract
Proteinogenic dipeptides, with few known exceptions, are products of protein degradation. Dipeptide levels respond to the changes in the environment, often in a dipeptide-specific manner. What drives this specificity is currently unknown; what likely contributes is the activity of the different peptidases that cleave off the terminal dipeptide from the longer peptides. Dipeptidases that degrade dipeptides to amino acids, and the turnover rates of the "substrate" proteins/peptides. Plants can both uptake dipeptides from the soil, but dipeptides are also found in root exudates. Dipeptide transporters, members of the proton-coupled peptide transporters NTR1/PTR family, contribute to nitrogen reallocation between the sink and source tissues. Besides their role in nitrogen distribution, it becomes increasingly clear that dipeptides may also serve regulatory, dipeptide-specific functions. Dipeptides are found in protein complexes affecting the activity of their protein partners. Moreover, dipeptide supplementation leads to cellular phenotypes reflected in changes in plant growth and stress tolerance. Herein we will review the current understanding of dipeptides' metabolism, transport, and functions and discuss significant challenges and future directions for the comprehensive characterization of this fascinating but underrated group of small-molecule compounds.
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Affiliation(s)
| | | | - Aleksandra Skirycz
- Boyce Thompson Institute, 14853, Ithaca, NY, USA; Cornell University, 14853, Ithaca, NY, USA.
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4
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Figueroa NE, Franz P, Luzarowski M, Martinez-Seidel F, Moreno JC, Childs D, Ziemblicka A, Sampathkumar A, Andersen TG, Tsiavaliaris G, Chodasiewicz M, Skirycz A. Protein interactome of 3',5'-cAMP reveals its role in regulating the actin cytoskeleton. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1214-1230. [PMID: 37219088 DOI: 10.1111/tpj.16313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 05/24/2023]
Abstract
Identification of protein interactors is ideally suited for the functional characterization of small molecules. 3',5'-cAMP is an evolutionary ancient signaling metabolite largely uncharacterized in plants. To tap into the physiological roles of 3',5'-cAMP, we used a chemo-proteomics approach, thermal proteome profiling (TPP), for the unbiased identification of 3',5'-cAMP protein targets. TPP measures shifts in the protein thermal stability upon ligand binding. Comprehensive proteomics analysis yielded a list of 51 proteins significantly altered in their thermal stability upon incubation with 3',5'-cAMP. The list contained metabolic enzymes, ribosomal subunits, translation initiation factors, and proteins associated with the regulation of plant growth such as CELL DIVISION CYCLE 48. To functionally validate obtained results, we focused on the role of 3',5'-cAMP in regulating the actin cytoskeleton suggested by the presence of actin among the 51 identified proteins. 3',5'-cAMP supplementation affected actin organization by inducing actin-bundling. Consistent with these results, the increase in 3',5'-cAMP levels, obtained either by feeding or by chemical modulation of 3',5'-cAMP metabolism, was sufficient to partially rescue the short hypocotyl phenotype of the actin2 actin7 mutant, severely compromised in actin level. The observed rescue was specific to 3',5'-cAMP, as demonstrated using a positional isomer 2',3'-cAMP, and true for the nanomolar 3',5'-cAMP concentrations reported for plant cells. In vitro characterization of the 3',5'-cAMP-actin pairing argues against a direct interaction between actin and 3',5'-cAMP. Alternative mechanisms by which 3',5'-cAMP would affect actin dynamics, such as by interfering with calcium signaling, are discussed. In summary, our work provides a specific resource, 3',5'-cAMP interactome, as well as functional insight into 3',5'-cAMP-mediated regulation in plants.
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Affiliation(s)
- Nicolás E Figueroa
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Peter Franz
- Institute for Biophysical Chemistry, Hannover Medical School, Carl-Neuberg-Straße 1, Hannover, 30625, Germany
| | - Marcin Luzarowski
- Max-Planck-Institute of Molecular Plant Physiology, Am Muhlenberg 1, Potsdam-Golm, 14476, Germany
- Core facility for Mass Spectrometry and Proteomics, Zentrum fur Molekulare Biologie der Universitat Heidelberg, Im Neuenheimer Feld 329, Heidelberg, 69120, Germany
| | - Federico Martinez-Seidel
- Max-Planck-Institute of Molecular Plant Physiology, Am Muhlenberg 1, Potsdam-Golm, 14476, Germany
- School of BioSciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Juan C Moreno
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Max-Planck-Institute of Molecular Plant Physiology, Am Muhlenberg 1, Potsdam-Golm, 14476, Germany
| | - Dorothee Childs
- European Molecular Biology Laboratory (EMBL) Heidelberg, Heidelberg, 69117, Germany
| | - Aleksandra Ziemblicka
- Max-Planck-Institute of Molecular Plant Physiology, Am Muhlenberg 1, Potsdam-Golm, 14476, Germany
| | - Arun Sampathkumar
- Max-Planck-Institute of Molecular Plant Physiology, Am Muhlenberg 1, Potsdam-Golm, 14476, Germany
| | - Tonni Grube Andersen
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Georgios Tsiavaliaris
- Institute for Biophysical Chemistry, Hannover Medical School, Carl-Neuberg-Straße 1, Hannover, 30625, Germany
| | - Monika Chodasiewicz
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Max-Planck-Institute of Molecular Plant Physiology, Am Muhlenberg 1, Potsdam-Golm, 14476, Germany
| | - Aleksandra Skirycz
- Max-Planck-Institute of Molecular Plant Physiology, Am Muhlenberg 1, Potsdam-Golm, 14476, Germany
- Boyce Thompson Institute (BTI), Cornell University, 533 Tower Rd., Ithaca, New York, 14853, USA
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Deng P, Yin R, Wang H, Chen L, Cao X, Xu X. Comparative analyses of functional traits based on metabolome and economic traits variation of Bletilla striata: Contribution of intercropping. FRONTIERS IN PLANT SCIENCE 2023; 14:1147076. [PMID: 37008465 PMCID: PMC10064063 DOI: 10.3389/fpls.2023.1147076] [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: 01/18/2023] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
The intercropping practice has been regarded as a practical land-use selection to improve the management benefits of Bletilla striata plantations. The reports about the variety of economic and functional traits of Bletilla pseudobulb under intercropping systems were limited. The present study investigated the variation of economic and functional traits of Bletilla pseudobulb under different intercropping systems (the deep-rooted intercropping system: B. striata - Cyclocarya paliurus, CB; and the shallow-rooted intercropping system: B. striata - Phyllostachys edulis, PB). The functional traits were analyzed through non-targeted metabolomics based on GC-MS. The results indicated that the PB intercropping system significantly decreased the yield of Bletilla pseudobulb while significantly increasing the total phenol and flavonoids compared with the control (CK). However, there were no significant differences in all economic traits between CB and CK. The functional traits among CB, PB, and CK were separated and exhibited significant differences. Under different intercropping systems, B. striata may adopt different functional strategies in response to interspecific competition. The functional node metabolites (D-galactose, cellobiose, raffinose, D-fructose, maltose, and D-ribose) were up-regulated in CB, while the functional node metabolites (L-valine, L-leucine, L-isoleucine, methionine, L-lysine, serine, D-glucose, cellobiose, trehalose, maltose, D-ribose, palatinose, raffinose, xylobiose, L-rhamnose, melezitose, and maltotriose) were up-regulated in PB. The correlation between economic and functional traits depends on the degree of environmental stress. Artificial neural network models (ANNs) accurately predicted the variation in economic traits via the combination of functional node metabolites in PB. The correlation analysis of environmental factors indicated that Ns (including TN, NH4 +-, and NO3 --), SRI (solar radiation intensity), and SOC were the main factors that affected the economic traits (yield, total phenol, and total flavonoids). TN, SRI, and SOC were the main factors affecting the functional traits of the Bletilla pseudobulb. These findings strengthen our understanding of the variation of economic and functional traits of Bletilla pseudobulb under intercropping and clarify the main limiting environmental factors under B. striata intercropping systems.
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Affiliation(s)
- Pengfei Deng
- School of Forestry & Landscape Architecture, Anhui Agricultural University, Hefei, Anhui, China
| | - Ruoyong Yin
- School of Forestry & Landscape Architecture, Anhui Agricultural University, Hefei, Anhui, China
| | - Huiling Wang
- School of Forestry & Landscape Architecture, Anhui Agricultural University, Hefei, Anhui, China
- School of Architecture & Planning, Anhui Jianzhu University, Hefei, Anhui, China
| | - Leiru Chen
- School of Forestry & Landscape Architecture, Anhui Agricultural University, Hefei, Anhui, China
| | - Xiaoqing Cao
- School of Forestry & Landscape Architecture, Anhui Agricultural University, Hefei, Anhui, China
| | - Xiaoniu Xu
- School of Forestry & Landscape Architecture, Anhui Agricultural University, Hefei, Anhui, China
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6
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Schlossarek D, Zhang Y, Sokolowska EM, Fernie AR, Luzarowski M, Skirycz A. Don't let go: co-fractionation mass spectrometry for untargeted mapping of protein-metabolite interactomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:904-914. [PMID: 36575913 DOI: 10.1111/tpj.16084] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 12/20/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
The chemical complexity of metabolomes goes hand in hand with their functional diversity. Small molecules have many essential roles, many of which are executed by binding and modulating the function of a protein partner. The complex and dynamic protein-metabolite interaction (PMI) network underlies most if not all biological processes, but remains under-characterized. Herein, we highlight how co-fractionation mass spectrometry (CF-MS), a well-established approach to map protein assemblies, can be used for proteome and metabolome identification of the PMIs. We will review recent CF-MS studies, discuss the main advantages and limitations, summarize the available CF-MS guidelines, and outline future challenges and opportunities.
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Affiliation(s)
- Dennis Schlossarek
- Depeartment One, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Youjun Zhang
- Depeartment One, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Ewelina M Sokolowska
- Depeartment One, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Alisdair R Fernie
- Depeartment One, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Marcin Luzarowski
- Center for Molecular Biology Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Aleksandra Skirycz
- Depeartment One, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
- Boyce Thompson Institute, Ithaca, NY, 14850, USA
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14850, USA
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7
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Figueroa NE, Hernandez-Sanchez IE, Maruri-Lopez I, Chodasiewicz M. Affinity Purification Protocol Starting with a Small Molecule as Bait. Methods Mol Biol 2023; 2554:11-19. [PMID: 36178617 DOI: 10.1007/978-1-0716-2624-5_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Protein-metabolite interactions (PMIs) are fundamental for several biological processes. Even though PMI studies have increased in recent years, our knowledge is still limited. The screening of PMIs using small molecules as bait will broaden our ability to uncover novel PMIs, setting the basis for establishing their biological relevance. Here, we describe a protocol that allows the identification of multiple protein partners for one ligand. This protocol describes a straightforward methodology that can be adapted to a wide variety of organisms.
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Affiliation(s)
- Nicolás E Figueroa
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Itzell E Hernandez-Sanchez
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Israel Maruri-Lopez
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Monika Chodasiewicz
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
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8
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Metabarcoding and Metabolome Analyses Reveal Mechanisms of Leymus chinensis Growth Promotion by Fairy Ring of Leucocalocybe mongolica. J Fungi (Basel) 2022; 8:jof8090944. [PMID: 36135669 PMCID: PMC9505569 DOI: 10.3390/jof8090944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/03/2022] [Accepted: 09/06/2022] [Indexed: 11/17/2022] Open
Abstract
Fairy rings are a unique ecological phenomenon caused by the growth of the fungal mycelium in the soil. Fairy rings formed by Leucocalocybe mongolica (LM) are generally distributed in the Mongolian Plateau, where they promote plant growth without fertilization and alleviate fertilizer use. We previously investigated the soil factors regulating growth promotion in a fairy ring ecosystem; however, the aspects of the plant (Leymus chinensis, LC) that promote growth have not been explored. Therefore, the present study investigated the endophyte diversity and metabolome of LC in an LM fairy ring ecosystem. We analyzed the leaf and root samples of LC from the DARK (FR) and OUT (CK) zones. The fairy rings significantly improved the fungal diversity of roots and leaves and the bacterial diversity of leaves in the FR zone. Ralstonia was the dominant bacteria detected in the LC leaves. In addition, Marasmius, another fairy ring fungal genus, was also detected with a high abundance in the roots of the FR zone. Furthermore, widely targeted metabolome analysis combined with KEGG annotation identified 1011 novel metabolites from the leaves and roots of LC and seven pathways significantly regulated by the fairy ring in the FR zone. The fairy ring ecosystem significantly downregulated the flavonoid metabolism in the leaves and roots of LC. The correlation analysis found Ralstonia is a potential regulatory factor of flavonoid biosynthesis in LC. In addition, salicylic acid and jasmonic acid were found upregulated in the leaves, probably related to Marasmius enrichment. Thus, the study details plant factors associated with enhanced growth in an LM fairy ring ecosystem. These findings lay a theoretical foundation for developing the fairy ring ecosystem in an agricultural system.
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Skirycz A, Fernie AR. Past accomplishments and future challenges of the multi-omics characterization of leaf growth. PLANT PHYSIOLOGY 2022; 189:473-489. [PMID: 35325227 PMCID: PMC9157134 DOI: 10.1093/plphys/kiac136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
The advent of omics technologies has revolutionized biology and advanced our understanding of all biological processes, including major developmental transitions in plants and animals. Here, we review the vast knowledge accumulated concerning leaf growth in terms of transcriptional regulation before turning our attention to the historically less well-characterized alterations at the protein and metabolite level. We will then discuss how the advent of biochemical methods coupled with metabolomics and proteomics can provide insight into the protein-protein and protein-metabolite interactome of the growing leaves. We finally highlight the substantial challenges in detection, spatial resolution, integration, and functional validation of the omics results, focusing on metabolomics as a prerequisite for a comprehensive understanding of small-molecule regulation of plant growth.
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Affiliation(s)
- Aleksandra Skirycz
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
- Boyce Thompson Institute, Ithaca, New York 14853, USA
- Cornell University, Ithaca, New York 14853, USA
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
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10
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Dussarrat T, Prigent S, Latorre C, Bernillon S, Flandin A, Díaz FP, Cassan C, Van Delft P, Jacob D, Varala K, Joubes J, Gibon Y, Rolin D, Gutiérrez RA, Pétriacq P. Predictive metabolomics of multiple Atacama plant species unveils a core set of generic metabolites for extreme climate resilience. THE NEW PHYTOLOGIST 2022; 234:1614-1628. [PMID: 35288949 PMCID: PMC9324839 DOI: 10.1111/nph.18095] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Current crop yield of the best ideotypes is stagnating and threatened by climate change. In this scenario, understanding wild plant adaptations in extreme ecosystems offers an opportunity to learn about new mechanisms for resilience. Previous studies have shown species specificity for metabolites involved in plant adaptation to harsh environments. Here, we combined multispecies ecological metabolomics and machine learning-based generalized linear model predictions to link the metabolome to the plant environment in a set of 24 species belonging to 14 families growing along an altitudinal gradient in the Atacama Desert. Thirty-nine common compounds predicted the plant environment with 79% accuracy, thus establishing the plant metabolome as an excellent integrative predictor of environmental fluctuations. These metabolites were independent of the species and validated both statistically and biologically using an independent dataset from a different sampling year. Thereafter, using multiblock predictive regressions, metabolites were linked to climatic and edaphic stressors such as freezing temperature, water deficit and high solar irradiance. These findings indicate that plants from different evolutionary trajectories use a generic metabolic toolkit to face extreme environments. These core metabolites, also present in agronomic species, provide a unique metabolic goldmine for improving crop performances under abiotic pressure.
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Affiliation(s)
- Thomas Dussarrat
- Departamento de Genética Molecular y MicrobiologíaPontificia Universidad Católica de ChileFONDAP Center for Genome Regulation and Millenium Institute for Integrative Biology (iBio)Av Libertador Bernardo O'Higgins 340SantiagoChile
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
| | - Sylvain Prigent
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
| | - Claudio Latorre
- Departamento de EcologíaPontificia Universidad Católica de ChileAv Libertador Bernardo O'Higgins 340SantiagoChile
- Institute of Ecology and Biodiversity (IEB)Las Palmeras3425ÑuñoaSantiagoChile
| | - Stéphane Bernillon
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
| | - Amélie Flandin
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
| | - Francisca P. Díaz
- Departamento de Genética Molecular y MicrobiologíaPontificia Universidad Católica de ChileFONDAP Center for Genome Regulation and Millenium Institute for Integrative Biology (iBio)Av Libertador Bernardo O'Higgins 340SantiagoChile
| | - Cédric Cassan
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
| | - Pierre Van Delft
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
- Laboratoire de Biogenèse Membranaire, CNRSUniv. Bordeaux, UMR 5200Villenave d'OrnonFrance
| | - Daniel Jacob
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
| | - Kranthi Varala
- Department of Horticulture and Landscape ArchitecturePurdue UniversityWest LafayetteIN47907USA
- Center for Plant BiologyPurdue UniversityWest LafayetteIN47907USA
| | - Jérôme Joubes
- Laboratoire de Biogenèse Membranaire, CNRSUniv. Bordeaux, UMR 5200Villenave d'OrnonFrance
| | - Yves Gibon
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
| | - Dominique Rolin
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
| | - Rodrigo A. Gutiérrez
- Departamento de Genética Molecular y MicrobiologíaPontificia Universidad Católica de ChileFONDAP Center for Genome Regulation and Millenium Institute for Integrative Biology (iBio)Av Libertador Bernardo O'Higgins 340SantiagoChile
| | - Pierre Pétriacq
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
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11
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Dani KGS, Loreto F. Plant volatiles as regulators of hormone homeostasis. THE NEW PHYTOLOGIST 2022; 234:804-812. [PMID: 35170033 DOI: 10.1111/nph.18035] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Some canonical plant hormones such as auxins and gibberellins have precursors that are biogenic volatiles (indole, indole acetonitrile, phenylacetaldoxime and ent-kaurene). Cytokinins, abscisic acid and strigolactones are hormones comprising chemical moieties that have distinct volatile analogues, and are synthesised alongside constitutively emitted volatiles (isoprene, sesquiterpenes, lactones, benzenoids and apocarotenoid volatiles). Nonvolatile hormone analogues and biogenic volatile organic compounds (BVOCs) evolved in tandem as growth and behavioural regulators in unicellular organisms. In plants, however, nonvolatile hormones evolved as regulators of growth, development and differentiation, while endogenous BVOCs (often synthesised lifelong) became subtle regulators of hormone synthesis, availability, activity and turnover, all supported by functionally redundant components of hormone metabolism. Reciprocal changes in the abundance and activity of hormones, nitric oxide, and constitutive plant volatiles constantly bridge retrograde and anterograde signalling to maintain hormone equilibria even in unstressed plants. This is distinct from transient interference in hormone signalling by stress-induced and exogenously received volatiles.
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Affiliation(s)
- Kaidala Ganesha Srikanta Dani
- Institute of Sustainable Plant Protection, National Research Council of Italy, Via Madonna del Piano 10, Sesto Fiorentino, Florence, 50019, Italy
- Department of Biology, Agriculture and Food Sciences, National Research Council of Italy, Piazzale Aldo Moro 7, Rome, 00185, Italy
| | - Francesco Loreto
- Institute of Sustainable Plant Protection, National Research Council of Italy, Via Madonna del Piano 10, Sesto Fiorentino, Florence, 50019, Italy
- Department of Biology, University of Naples Federico II, Via Cinthia, Naples, 80126, Italy
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12
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Rico-Chávez AK, Franco JA, Fernandez-Jaramillo AA, Contreras-Medina LM, Guevara-González RG, Hernandez-Escobedo Q. Machine Learning for Plant Stress Modeling: A Perspective towards Hormesis Management. PLANTS 2022; 11:plants11070970. [PMID: 35406950 PMCID: PMC9003083 DOI: 10.3390/plants11070970] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 01/11/2023]
Abstract
Plant stress is one of the most significant factors affecting plant fitness and, consequently, food production. However, plant stress may also be profitable since it behaves hormetically; at low doses, it stimulates positive traits in crops, such as the synthesis of specialized metabolites and additional stress tolerance. The controlled exposure of crops to low doses of stressors is therefore called hormesis management, and it is a promising method to increase crop productivity and quality. Nevertheless, hormesis management has severe limitations derived from the complexity of plant physiological responses to stress. Many technological advances assist plant stress science in overcoming such limitations, which results in extensive datasets originating from the multiple layers of the plant defensive response. For that reason, artificial intelligence tools, particularly Machine Learning (ML) and Deep Learning (DL), have become crucial for processing and interpreting data to accurately model plant stress responses such as genomic variation, gene and protein expression, and metabolite biosynthesis. In this review, we discuss the most recent ML and DL applications in plant stress science, focusing on their potential for improving the development of hormesis management protocols.
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Affiliation(s)
- Amanda Kim Rico-Chávez
- Unidad de Ingeniería en Biosistemas, Facultad de Ingeniería Campus Amazcala, Universidad Autónoma de Querétaro, Carretera Chichimequillas, s/n km 1, El Marqués CP 76265, Mexico; (A.K.R.-C.); (L.M.C.-M.)
| | - Jesus Alejandro Franco
- Escuela Nacional de Estudios Superiores Unidad Juriquilla, UNAM, Querétaro CP 76230, Mexico;
| | - Arturo Alfonso Fernandez-Jaramillo
- Unidad Académica de Ingeniería Biomédica, Universidad Politécnica de Sinaloa, Carretera Municipal Libre Mazatlán Higueras km 3, Col. Genaro Estrada, Mazatlán CP 82199, Mexico;
| | - Luis Miguel Contreras-Medina
- Unidad de Ingeniería en Biosistemas, Facultad de Ingeniería Campus Amazcala, Universidad Autónoma de Querétaro, Carretera Chichimequillas, s/n km 1, El Marqués CP 76265, Mexico; (A.K.R.-C.); (L.M.C.-M.)
| | - Ramón Gerardo Guevara-González
- Unidad de Ingeniería en Biosistemas, Facultad de Ingeniería Campus Amazcala, Universidad Autónoma de Querétaro, Carretera Chichimequillas, s/n km 1, El Marqués CP 76265, Mexico; (A.K.R.-C.); (L.M.C.-M.)
- Correspondence: (R.G.G.-G.); (Q.H.-E.)
| | - Quetzalcoatl Hernandez-Escobedo
- Escuela Nacional de Estudios Superiores Unidad Juriquilla, UNAM, Querétaro CP 76230, Mexico;
- Correspondence: (R.G.G.-G.); (Q.H.-E.)
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13
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Boutet S, Barreda L, Perreau F, Totozafy JC, Mauve C, Gakière B, Delannoy E, Martin-Magniette ML, Monti A, Lepiniec L, Zanetti F, Corso M. Untargeted metabolomic analyses reveal the diversity and plasticity of the specialized metabolome in seeds of different Camelina sativa genotypes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:147-165. [PMID: 34997644 DOI: 10.1111/tpj.15662] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Stéphanie Boutet
- Institut Jean-Pierre Bourgin, Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
| | - Léa Barreda
- Institut Jean-Pierre Bourgin, Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
| | - François Perreau
- Institut Jean-Pierre Bourgin, Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
| | - Jean-Chrisologue Totozafy
- Institut Jean-Pierre Bourgin, Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
| | - Caroline Mauve
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, University of Evry, Orsay, France
- Institute of Plant Sciences Paris Saclay (IPS2), Université de Paris, CNRS, INRAE, 91405, Orsay, France
| | - Bertrand Gakière
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, University of Evry, Orsay, France
- Institute of Plant Sciences Paris Saclay (IPS2), Université de Paris, CNRS, INRAE, 91405, Orsay, France
| | - Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, University of Evry, Orsay, France
- Institute of Plant Sciences Paris Saclay (IPS2), Université de Paris, CNRS, INRAE, 91405, Orsay, France
| | - Marie-Laure Martin-Magniette
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, University of Evry, Orsay, France
- Institute of Plant Sciences Paris Saclay (IPS2), Université de Paris, CNRS, INRAE, 91405, Orsay, France
- UMR MIA-Paris, AgroParisTech, INRAE, Université Paris-Saclay, 75005, Paris, France
| | - Andrea Monti
- Department of Agricultural and Food Sciences, Alma Mater Studiorum - Università di Bologna, Viale G. Fanin 44, 40127, Bologna, Italy
| | - Loïc Lepiniec
- Institut Jean-Pierre Bourgin, Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
| | - Federica Zanetti
- Department of Agricultural and Food Sciences, Alma Mater Studiorum - Università di Bologna, Viale G. Fanin 44, 40127, Bologna, Italy
| | - Massimiliano Corso
- Institut Jean-Pierre Bourgin, Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
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Chodasiewicz M, Kerber O, Gorka M, Moreno JC, Maruri-Lopez I, Minen RI, Sampathkumar A, Nelson ADL, Skirycz A. 2',3'-cAMP treatment mimics the stress molecular response in Arabidopsis thaliana. PLANT PHYSIOLOGY 2022; 188:1966-1978. [PMID: 35043968 PMCID: PMC8968299 DOI: 10.1093/plphys/kiac013] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/01/2021] [Indexed: 05/12/2023]
Abstract
The role of the RNA degradation product 2',3'-cyclic adenosine monophosphate (2',3'-cAMP) is poorly understood. Recent studies have identified 2',3'-cAMP in plant material and determined its role in stress signaling. The level of 2',3'-cAMP increases upon wounding, in the dark, and under heat, and 2',3'-cAMP binding to an RNA-binding protein, Rbp47b, promotes stress granule (SG) assembly. To gain further mechanistic insights into the function of 2',3'-cAMP, we used a multi-omics approach by combining transcriptomics, metabolomics, and proteomics to dissect the response of Arabidopsis (Arabidopsis thaliana) to 2',3'-cAMP treatment. We demonstrated that 2',3'-cAMP is metabolized into adenosine, suggesting that the well-known cyclic nucleotide-adenosine pathway of human cells might also exist in plants. Transcriptomics analysis revealed only minor overlap between 2',3'-cAMP- and adenosine-treated plants, suggesting that these molecules act through independent mechanisms. Treatment with 2',3'-cAMP changed the levels of hundreds of transcripts, proteins, and metabolites, many previously associated with plant stress responses, including protein and RNA degradation products, glucosinolates, chaperones, and SG components. Finally, we demonstrated that 2',3'-cAMP treatment influences the movement of processing bodies, confirming the role of 2',3'-cAMP in the formation and motility of membraneless organelles.
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Affiliation(s)
| | - Olga Kerber
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Michal Gorka
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Juan C Moreno
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Israel Maruri-Lopez
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Romina I Minen
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853, USA
| | - Arun Sampathkumar
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Andrew D L Nelson
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853, USA
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15
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Yang C, Shen S, Zhou S, Li Y, Mao Y, Zhou J, Shi Y, An L, Zhou Q, Peng W, Lyu Y, Liu X, Chen W, Wang S, Qu L, Liu X, Fernie AR, Luo J. Rice metabolic regulatory network spanning the entire life cycle. MOLECULAR PLANT 2022; 15:258-275. [PMID: 34715392 DOI: 10.1016/j.molp.2021.10.005] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 09/09/2021] [Accepted: 10/21/2021] [Indexed: 05/18/2023]
Abstract
As one of the most important crops in the world, rice (Oryza sativa) is a model plant for metabolome research. Although many studies have focused on the analysis of specific tissues, the changes in metabolite abundance across the entire life cycle have not yet been determined. In this study, combining both targeted and nontargeted metabolite profiling methods, a total of 825 annotated metabolites were quantified in rice samples from different tissues covering the entire life cycle. The contents of metabolites in different tissues of rice were significantly different, with various metabolites accumulating in the plumule and radicle during seed germination. Combining these data with transcriptome data obtained from the same time period, we constructed the Rice Metabolic Regulation Network. The metabolites and co-expressed genes were further divided into 12 clusters according to their accumulation patterns, with members within each cluster displaying a uniform and clear pattern of abundance across development. Using this dataset, we established a comprehensive metabolic profile of the rice life cycle and used two independent strategies to identify novel transcription factors-namely the use of known regulatory genes as bait to screen for new networks underlying lignin metabolism and the unbiased identification of new glycerophospholipid metabolism regulators on the basis of tissue specificity. This study thus demonstrates how guilt-by-association analysis of metabolome and transcriptome data spanning the entire life cycle in cereal crops provides novel resources and tools to aid in understanding the mechanisms underlying important agronomic traits.
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Affiliation(s)
- Chenkun Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Shuangqian Shen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Shen Zhou
- College of Tropical Crops, Hainan University, Haikou 570228, China; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Yufei Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yuyuan Mao
- College of Tropical Crops, Hainan University, Haikou 570228, China; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Junjie Zhou
- College of Tropical Crops, Hainan University, Haikou 570228, China; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Yuheng Shi
- College of Tropical Crops, Hainan University, Haikou 570228, China; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Longxu An
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Qianqian Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Wenju Peng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yuanyuan Lyu
- College of Tropical Crops, Hainan University, Haikou 570228, China; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Xuemei Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shouchuang Wang
- College of Tropical Crops, Hainan University, Haikou 570228, China; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Lianghuan Qu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xianqing Liu
- College of Tropical Crops, Hainan University, Haikou 570228, China; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany; Centre of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou 570228, China; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China.
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16
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Shahi A, Mafu S. Specialized metabolites as mediators for plant-fungus crosstalk and their evolving roles. CURRENT OPINION IN PLANT BIOLOGY 2021; 64:102141. [PMID: 34814027 PMCID: PMC8671350 DOI: 10.1016/j.pbi.2021.102141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 10/10/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
Plants, fungi, and bacteria produce numerous natural products with bioactive properties essential for ecological adaptation. Because of their chemical complexity, these natural products have been adapted for diverse applications in industry. The discovery of their biosynthetic pathways has been accelerated due to improved 'omics' approaches, metabolic engineering, and the availability of genetic manipulation techniques. Ongoing research into these metabolites is not only resolving the enzymatic diversity underlying their biosynthesis but also delving into the physiological and mechanistic basis of their modes of action. This review highlights progress made in the elucidation of biosynthetic pathways and biological roles of specialized metabolites, focusing on some that play important roles at the interface of plant-fungus interactions.
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Affiliation(s)
- Ayousha Shahi
- Plant Biology Graduate Program, University of Massachusetts-Amherst, 240 Thatcher Way, Life Science Laboratories, Amherst, MA 01003, USA
| | - Sibongile Mafu
- Plant Biology Graduate Program, University of Massachusetts-Amherst, 240 Thatcher Way, Life Science Laboratories, Amherst, MA 01003, USA; Department of Biochemistry and Molecular Biology, University of Massachusetts - Amherst, 240 Thatcher Way, Life Science Laboratories, Amherst, MA 01003, USA.
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17
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Durán-Medina Y, Ruiz-Cortés BE, Guerrero-Largo H, Marsch-Martínez N. Specialized metabolism and development: An unexpected friendship. CURRENT OPINION IN PLANT BIOLOGY 2021; 64:102142. [PMID: 34856480 DOI: 10.1016/j.pbi.2021.102142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 10/12/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Plants produce a myriad of metabolites. Some of them have been regarded for a long time as secondary or specialized metabolites and are considered to have functions mostly in defense and the adaptation of plants to their environment. However, in the last years, new research has shown that these metabolites can also have roles in the regulation of plant growth and development, some acting as signals, through the interaction with hormonal pathways, and some independently of them. These reports provide a glimpse of the functional possibilities that specialized metabolites present in the modulation of plant development and encourage more research in this direction.
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Affiliation(s)
- Yolanda Durán-Medina
- Biotecnology and Biochemistry Department, Centre for Research and Advanced Studies (CINVESTAV-IPN) Irapuato Unit, Mexico
| | - Beatriz Esperanza Ruiz-Cortés
- Biotecnology and Biochemistry Department, Centre for Research and Advanced Studies (CINVESTAV-IPN) Irapuato Unit, Mexico
| | - Herenia Guerrero-Largo
- Biotecnology and Biochemistry Department, Centre for Research and Advanced Studies (CINVESTAV-IPN) Irapuato Unit, Mexico
| | - Nayelli Marsch-Martínez
- Biotecnology and Biochemistry Department, Centre for Research and Advanced Studies (CINVESTAV-IPN) Irapuato Unit, Mexico.
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18
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Lazcano-Ramírez HG, Gamboa-Becerra R, García-López IJ, Montes RAC, Díaz-Ramírez D, de la Vega OM, Ordaz-Ortíz JJ, de Folter S, Tiessen-Favier A, Winkler R, Marsch-Martínez N. Effects of the Developmental Regulator BOLITA on the Plant Metabolome. Genes (Basel) 2021; 12:genes12070995. [PMID: 34209960 PMCID: PMC8305173 DOI: 10.3390/genes12070995] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 12/13/2022] Open
Abstract
Transcription factors are important regulators of gene expression. They can orchestrate the activation or repression of hundreds or thousands of genes and control diverse processes in a coordinated way. This work explores the effect of a master regulator of plant development, BOLITA (BOL), in plant metabolism, with a special focus on specialized metabolism. For this, we used an Arabidopsis thaliana line in which the transcription factor activity can be induced. Fingerprinting metabolomic analyses of whole plantlets were performed at different times after induction. After 96 h, all induced replicas clustered as a single group, in contrast with all controls which did not cluster. Metabolomic analyses of shoot and root tissues enabled the putative identification of differentially accumulated metabolites in each tissue. Finally, the analysis of global gene expression in induced vs. non-induced root samples, together with enrichment analyses, allowed the identification of enriched metabolic pathways among the differentially expressed genes and accumulated metabolites after the induction. We concluded that the induction of BOL activity can modify the Arabidopsis metabolome. Future work should investigate whether its action is direct or indirect, and the implications of the metabolic changes for development regulation and bioprospection.
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Affiliation(s)
- Hugo Gerardo Lazcano-Ramírez
- Cell Identity Laboratory, Biotechnology and Biochemistry Department, CINVESTAV-IPN Irapuato Unit, Irapuato 36824, Mexico; (H.G.L.-R.); (D.D.-R.)
| | - Roberto Gamboa-Becerra
- Laboratory of Biochemical and Instrumental Analysis, Biotechnology and Biochemistry Department, CINVESTAV-IPN Irapuato Unit, Irapuato 36824, Mexico;
- Red de Biodiversidad y Sistemática, Instituto de Ecología A.C. Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico
| | - Irving J. García-López
- Genetic Engineering Department, CINVESTAV-IPN Irapuato Unit, Irapuato 36824, Mexico; (I.J.G.-L.); (A.T.-F.)
| | - Ricardo A. Chávez Montes
- Advanced Genomics Unit (UGA-Langebio), CINVESTAV-IPN, Irapuato 36824, Mexico; (R.A.C.M.); (O.M.d.l.V.); (J.J.O.-O.); (S.d.F.)
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX 79409, USA
| | - David Díaz-Ramírez
- Cell Identity Laboratory, Biotechnology and Biochemistry Department, CINVESTAV-IPN Irapuato Unit, Irapuato 36824, Mexico; (H.G.L.-R.); (D.D.-R.)
| | - Octavio Martínez de la Vega
- Advanced Genomics Unit (UGA-Langebio), CINVESTAV-IPN, Irapuato 36824, Mexico; (R.A.C.M.); (O.M.d.l.V.); (J.J.O.-O.); (S.d.F.)
| | - José Juan Ordaz-Ortíz
- Advanced Genomics Unit (UGA-Langebio), CINVESTAV-IPN, Irapuato 36824, Mexico; (R.A.C.M.); (O.M.d.l.V.); (J.J.O.-O.); (S.d.F.)
| | - Stefan de Folter
- Advanced Genomics Unit (UGA-Langebio), CINVESTAV-IPN, Irapuato 36824, Mexico; (R.A.C.M.); (O.M.d.l.V.); (J.J.O.-O.); (S.d.F.)
| | - Axel Tiessen-Favier
- Genetic Engineering Department, CINVESTAV-IPN Irapuato Unit, Irapuato 36824, Mexico; (I.J.G.-L.); (A.T.-F.)
| | - Robert Winkler
- Laboratory of Biochemical and Instrumental Analysis, Biotechnology and Biochemistry Department, CINVESTAV-IPN Irapuato Unit, Irapuato 36824, Mexico;
- Correspondence: (R.W.); (N.M.-M.); Tel.: +52-(462)-623-9635 (R.W.); +52-462-623-9671 (N.M.-M.)
| | - Nayelli Marsch-Martínez
- Cell Identity Laboratory, Biotechnology and Biochemistry Department, CINVESTAV-IPN Irapuato Unit, Irapuato 36824, Mexico; (H.G.L.-R.); (D.D.-R.)
- Correspondence: (R.W.); (N.M.-M.); Tel.: +52-(462)-623-9635 (R.W.); +52-462-623-9671 (N.M.-M.)
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19
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Venegas-Molina J, Molina-Hidalgo FJ, Clicque E, Goossens A. Why and How to Dig into Plant Metabolite-Protein Interactions. TRENDS IN PLANT SCIENCE 2021; 26:472-483. [PMID: 33478816 DOI: 10.1016/j.tplants.2020.12.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/08/2020] [Accepted: 12/14/2020] [Indexed: 06/12/2023]
Abstract
Interaction between metabolites and proteins drives cellular regulatory processes within and between organisms. Recent reports highlight that numerous plant metabolites embrace multiple biological activities, beyond a sole role as substrates, products, or cofactors of enzymes, or as defense or growth-regulatory compounds. Though several technologies have been developed to identify and characterize metabolite-protein interactions, the systematic implementation of such methods in the plant field remains limited. Here, we discuss the plant metabolic space, with a specific focus on specialized metabolites and their roles, and review the technologies to study their interaction with proteins. We approach it both from a plant's perspective, to increase our understanding of plant metabolite-dependent regulatory networks, and from a human perspective, to empower agrochemical and drug discoveries.
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Affiliation(s)
- Jhon Venegas-Molina
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Francisco J Molina-Hidalgo
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Elke Clicque
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium.
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20
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Pang Z, Chen J, Wang T, Gao C, Li Z, Guo L, Xu J, Cheng Y. Linking Plant Secondary Metabolites and Plant Microbiomes: A Review. FRONTIERS IN PLANT SCIENCE 2021; 12:621276. [PMID: 33737943 PMCID: PMC7961088 DOI: 10.3389/fpls.2021.621276] [Citation(s) in RCA: 209] [Impact Index Per Article: 69.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/08/2021] [Indexed: 05/09/2023]
Abstract
Plant secondary metabolites (PSMs) play many roles including defense against pathogens, pests, and herbivores; response to environmental stresses, and mediating organismal interactions. Similarly, plant microbiomes participate in many of the above-mentioned processes directly or indirectly by regulating plant metabolism. Studies have shown that plants can influence their microbiome by secreting various metabolites and, in turn, the microbiome may also impact the metabolome of the host plant. However, not much is known about the communications between the interacting partners to impact their phenotypic changes. In this article, we review the patterns and potential underlying mechanisms of interactions between PSMs and plant microbiomes. We describe the recent developments in analytical approaches and methods in this field. The applications of these new methods and approaches have increased our understanding of the relationships between PSMs and plant microbiomes. Though the current studies have primarily focused on model organisms, the methods and results obtained so far should help future studies of agriculturally important plants and facilitate the development of methods to manipulate PSMs-microbiome interactions with predictive outcomes for sustainable crop productions.
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Affiliation(s)
- Zhiqiang Pang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jia Chen
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Tuhong Wang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Chunsheng Gao
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Zhimin Li
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Litao Guo
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jianping Xu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Yi Cheng
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
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21
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Szepesi Á. Halotropism: Phytohormonal Aspects and Potential Applications. FRONTIERS IN PLANT SCIENCE 2020; 11:571025. [PMID: 33042187 PMCID: PMC7527526 DOI: 10.3389/fpls.2020.571025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/02/2020] [Indexed: 05/15/2023]
Abstract
Halotropism is a sodium specific tropic movement of roots in order to obtain the optimal salt concentration for proper growth and development. Numerous results suggest that halotropic events are under the control and regulation of complex plant hormone pathway. This minireview collects some recent evidences about sodium sensing during halotropism and the hormonal regulation of halotropic responses in glycophytes. The precise hormonal mechanisms by which halophytes plant roots perceive salt stress and translate this perception into adaptive, directional growth forward increased salt concentrations are not well understood. This minireview aims to gather recently deciphered information about halotropism focusing potential hormonal aspects both in glycophytes and halophytes. Advances in our understanding of halotropic responses in different plant species could help these plants to be used for sustainable agriculture and other future applications.
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Affiliation(s)
- Ágnes Szepesi
- Department of Plant Biology, Institute of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
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22
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Li W, Gupta A, Tian H, Nguyen KH, Tran CD, Watanabe Y, Tian C, Li K, Yang Y, Guo J, Luo Y, Miao Y, Phan Tran LS. Different strategies of strigolactone and karrikin signals in regulating the resistance of Arabidopsis thaliana to water-deficit stress. PLANT SIGNALING & BEHAVIOR 2020; 15:1789321. [PMID: 32669036 PMCID: PMC8550175 DOI: 10.1080/15592324.2020.1789321] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/19/2020] [Accepted: 06/20/2020] [Indexed: 05/21/2023]
Abstract
Strigolactone and karrikin receptors, DWARF14 (D14) and KARRIKIN INSENSITIVE 2 (KAI2), respectively, have been shown to positively regulate drought resistance in Arabidopsis thaliana by modulating abscisic acid responsiveness, anthocyanin accumulation, stomatal closure, cell membrane integrity and cuticle formation. Here, we aim to identify genes specifically or commonly regulated by D14 and KAI2 under water scarcity, using comparative analysis of the transcriptome data of the A. thaliana d14-1 and kai2-2 mutants under dehydration conditions. In comparison with wild-type, under dehydration conditions, the expression levels of genes related to photosynthesis and the metabolism of glucosinolates and trehalose were significantly changed in both d14-1 and kai2-2 mutant plants, whereas the transcript levels of genes related to the metabolism of cytokinins and brassinosteroids were significantly altered in the d14-1 mutant plants only. These results suggest that cytokinin and brassinosteroid metabolism might be specifically regulated by the D14 pathway, whereas photosynthesis and metabolism of glucosinolates and trehalose are potentially regulated by both D14 and KAI2 pathways in plant response to water scarcity.
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Affiliation(s)
- Weiqiang Li
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, China
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Henan Joint International Laboratory for Crop Multi-Omics Research, Henan University, Kaifeng, China
| | - Aarti Gupta
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
| | - Hongtao Tian
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, China
| | - Kien Huu Nguyen
- Agricultural Genetics Institute, Vietnam Academy of Agricultural Sciences, Hanoi, Vietnam
| | - Cuong Duy Tran
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Agricultural Genetics Institute, Vietnam Academy of Agricultural Sciences, Hanoi, Vietnam
| | - Yasuko Watanabe
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Kun Li
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, China
- Henan Joint International Laboratory for Crop Multi-Omics Research, Henan University, Kaifeng, China
| | - Yong Yang
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, China
| | - Jinggong Guo
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, China
- Henan Joint International Laboratory for Crop Multi-Omics Research, Henan University, Kaifeng, China
| | - Yin Luo
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Yuchen Miao
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, China
- Henan Joint International Laboratory for Crop Multi-Omics Research, Henan University, Kaifeng, China
- CONTACT Yuchen Miao Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng475001, China
| | - Lam-Son Phan Tran
- Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang, Vietnam; Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Lam-Son Phan Tran ; Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang, Vietnam; Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Yokohama 230-0045, Japan
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