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Zhang J, Meng Q, Wang Q, Zhang H, Tian H, Wang T, Xu F, Yan X, Luo M. Cotton sphingosine kinase GhLCBK1 participates in fiber cell elongation by affecting sphingosine-1-phophate and auxin synthesis. Int J Biol Macromol 2024; 267:131323. [PMID: 38574912 DOI: 10.1016/j.ijbiomac.2024.131323] [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: 02/05/2024] [Revised: 03/30/2024] [Accepted: 03/30/2024] [Indexed: 04/06/2024]
Abstract
Sphingolipids serve as essential components of biomembrane and possess significant bioactive properties. Sphingosine-1-phophate (S1P) plays a key role in plant resistance to stress, but its specific impact on plant growth and development remains to be fully elucidated. Cotton fiber cells are an ideal material for investigating the growth and maturation of plant cells. In this study, we examined the content and composition of sphingosine (Sph) and S1P throughout the progression of fiber cell development. The content of S1P elevated gradually during fiber elongation but declined during the transition stage. Exogenous application of S1P promoted fiber elongation while using of FTY720 (an antagonist of S1P), and DMS (an inhibitor of LCBK) hindered fiber elongation. Cotton Long Chain Base Kinase 1 (GhLCBK1) was notably expressed during the fiber elongation stage, containing all conserved domains of LCBK protein and localized in the endoplasmic reticulum. Overexpression GhLCBK1 increased the S1P content and promoted fiber elongation while retarded secondary cell wall (SCW) deposition. Conversely, downregulation of GhLCBK1 reduced the S1P levels, and suppressed fiber elongation, and accelerated SCW deposition. Transcriptome analysis revealed that upregulating GhLCBK1 or applying S1P induced the expression of GhEXPANSIN and auxin related genes. Furthermore, the levels of IAA were elevated and reduced in the fibers when up-regulating or down-regulating GhLCBK1, respectively. Our investigation demonstrated that GhLCBK1 and its product S1P facilitated the elongation of fiber cells by affecting auxin biosynthesis. This study contributes novel insights into the intricate regulatory pathways involved in fiber cell elongation, identifying GhLCBK1 as a potential target gene and laying the groundwork for enhancing fiber quality via genetic manipulation.
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Affiliation(s)
- Jian Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Qian Meng
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Qiaoling Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Hongju Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Huidan Tian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Tiantian Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Fan Xu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Xingying Yan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Ming Luo
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China.
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2
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Mahood EH, Bennett AA, Komatsu K, Kruse LH, Lau V, Rahmati Ishka M, Jiang Y, Bravo A, Louie K, Bowen BP, Harrison MJ, Provart NJ, Vatamaniuk OK, Moghe GD. Information theory and machine learning illuminate large-scale metabolomic responses of Brachypodium distachyon to environmental change. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:463-481. [PMID: 36880270 DOI: 10.1111/tpj.16160] [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: 05/20/2022] [Revised: 02/06/2023] [Accepted: 02/19/2023] [Indexed: 05/10/2023]
Abstract
Plant responses to environmental change are mediated via changes in cellular metabolomes. However, <5% of signals obtained from liquid chromatography tandem mass spectrometry (LC-MS/MS) can be identified, limiting our understanding of how metabolomes change under biotic/abiotic stress. To address this challenge, we performed untargeted LC-MS/MS of leaves, roots, and other organs of Brachypodium distachyon (Poaceae) under 17 organ-condition combinations, including copper deficiency, heat stress, low phosphate, and arbuscular mycorrhizal symbiosis. We found that both leaf and root metabolomes were significantly affected by the growth medium. Leaf metabolomes were more diverse than root metabolomes, but the latter were more specialized and more responsive to environmental change. We found that 1 week of copper deficiency shielded the root, but not the leaf metabolome, from perturbation due to heat stress. Machine learning (ML)-based analysis annotated approximately 81% of the fragmented peaks versus approximately 6% using spectral matches alone. We performed one of the most extensive validations of ML-based peak annotations in plants using thousands of authentic standards, and analyzed approximately 37% of the annotated peaks based on these assessments. Analyzing responsiveness of each predicted metabolite class to environmental change revealed significant perturbations of glycerophospholipids, sphingolipids, and flavonoids. Co-accumulation analysis further identified condition-specific biomarkers. To make these results accessible, we developed a visualization platform on the Bio-Analytic Resource for Plant Biology website (https://bar.utoronto.ca/efp_brachypodium_metabolites/cgi-bin/efpWeb.cgi), where perturbed metabolite classes can be readily visualized. Overall, our study illustrates how emerging chemoinformatic methods can be applied to reveal novel insights into the dynamic plant metabolome and stress adaptation.
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Affiliation(s)
- Elizabeth H Mahood
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Alexandra A Bennett
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Karyn Komatsu
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
| | - Lars H Kruse
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Vincent Lau
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
| | - Maryam Rahmati Ishka
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute, Ithaca, NY, USA
| | - Yulin Jiang
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | | | - Katherine Louie
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Lawrence Berkeley National Laboratory, Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Benjamin P Bowen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Lawrence Berkeley National Laboratory, Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | | | - Nicholas J Provart
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
| | - Olena K Vatamaniuk
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Gaurav D Moghe
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
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3
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Perlikowski D, Skirycz A, Marczak Ł, Lechowicz K, Augustyniak A, Michaelis Ä, Kosmala A. Metabolism of crown tissue is crucial for drought tolerance and recovery after stress cessation in Lolium/Festuca forage grasses. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:396-414. [PMID: 36214776 DOI: 10.1093/jxb/erac398] [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: 07/13/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
A process of plant recovery after drought cessation is a complex trait which has not been fully recognized. The most important organ associated with this phenomenon in monocots, including forage grasses, is the crown tissue located between shoots and roots. The crown tissue is a meristematic crossroads for metabolites and other compounds between these two plant organs. Here, for the first time, we present a metabolomic and lipidomic study focused on the crown tissue under drought and recovery in forage grasses, important for agriculture in European temperate regions. The plant materials involve high (HDT) and low drought-tolerant (LDT) genotypes of Festuca arundinacea, and Lolium multiflorum/F. arundinacea introgression forms. The obtained results clearly demonstrated that remodeling patterns of the primary metabolome and lipidome in the crown under drought and recovery were different between HDT and LDT plants. Furthermore, HDT plants accumulated higher contents of primary metabolites under drought in the crown tissue, especially carbohydrates which could function as osmoprotectants and storage materials. On the other hand, LDT plants characterized by higher membranes damage under drought, simultaneously accumulated membrane phospholipids in the crown and possessed the capacity to recover their metabolic functions after stress cessation to the levels observed in HDT plants.
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Affiliation(s)
- Dawid Perlikowski
- Plant Physiology Team, Institute of Plant Genetics Polish Academy of Sciences, Strzeszyńska 34, Poznan 60-479, Poland
| | - Aleksandra Skirycz
- Department of Molecular Physiology, Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
- Boyce Thompson Institute, 533 Tower Rd, Ithaca, NY 14853, USA
| | - Łukasz Marczak
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, Poznan 61-704, Poland
| | - Katarzyna Lechowicz
- Plant Physiology Team, Institute of Plant Genetics Polish Academy of Sciences, Strzeszyńska 34, Poznan 60-479, Poland
| | - Adam Augustyniak
- Plant Physiology Team, Institute of Plant Genetics Polish Academy of Sciences, Strzeszyńska 34, Poznan 60-479, Poland
- Centre for Advanced Technology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 10, Poznan 61-614, Poland
| | - Änna Michaelis
- Department of Molecular Physiology, Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Arkadiusz Kosmala
- Plant Physiology Team, Institute of Plant Genetics Polish Academy of Sciences, Strzeszyńska 34, Poznan 60-479, Poland
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4
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Lin XY, Zhang NN, Yao BH, Zhang X, Liu WY, Zhang WQ, Zhang JH, Wei GH, Chen J. Interactions between hydrogen sulphide and rhizobia modulate the physiological and metabolism process during water deficiency-induced oxidative defense in soybean. PLANT, CELL & ENVIRONMENT 2022; 45:3249-3274. [PMID: 36043459 DOI: 10.1111/pce.14431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 08/23/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
Hydrogen sulphide (H2 S), a new gas signal molecule, participates in the regulation of various abiotic stresses in plants. However, how the tandem working of H2 S and rhizobia affects the adaptation of soybean to water deficiency is still unclear. In this study, we investigated the adaptation mechanism of H2 S and rhizobia in soybean to water deficiency. Our results revealed that H2 S and rhizobia jointly enhanced the leaf chlorophyll content and relative water content in plants, and caused an increase in the biomass of soybean seedlings under water deficiency. Besides, in the absence of water, H2 S enhanced the biomass by affecting the number of nodules and nitrogenase activity during vegetative growth. The expression of nodulation marker genes including early nodulin 40 (GmENOD40), ERF required for nodulation (GmERN) and nodulation inception genes (GmNIN1a, GmNIN2a and GmNIN2b) were upregulated by H2 S and rhizobia in the nodules. Moreover, the combined effect of H2 S and rhizobia was proved to affect the enzyme activities and gene expression level of antioxidants, as well as osmotic protective substance content and related gene expression levels under water deficiency in soybean seedlings. In addition, the metabolomic results suggested that the combined effect of H2 S and rhizobia remarkably promoted the contents of lipids and lipid-like molecules. Our results indicated that H2 S and rhizobia synergistically reduced the oxidative damage caused by water deficiency through increasing the accumulation of metabolites and strengthening the plant antioxidant capacity.
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Affiliation(s)
- Xue-Yuan Lin
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Ni-Na Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Bai-Hui Yao
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Xin Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Wu-Yu Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Wei-Qin Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Jian-Hua Zhang
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Ge-Hong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Juan Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
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5
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Santos TCB, Dingjan T, Futerman AH. The sphingolipid anteome: implications for evolution of the sphingolipid metabolic pathway. FEBS Lett 2022; 596:2345-2363. [PMID: 35899376 DOI: 10.1002/1873-3468.14457] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/10/2022] [Accepted: 07/19/2022] [Indexed: 11/09/2022]
Abstract
Modern cell membranes contain a bewildering complexity of lipids, among them sphingolipids (SLs). Advances in mass spectrometry have led to the realization that the number and combinatorial complexity of lipids, including SLs, is much greater than previously appreciated. SLs are generated de novo by four enzymes, namely serine palmitoyltransferase, 3-ketodihydrosphingosine reductase, ceramide synthase and dihydroceramide Δ4-desaturase 1. Some of these enzymes depend on the availability of specific substrates and cofactors, which are themselves supplied by other complex metabolic pathways. The evolution of these four enzymes is poorly understood and likely depends on the co-evolution of the metabolic pathways that supply the other essential reaction components. Here, we introduce the concept of the 'anteome', from the Latin ante ('before') to describe the network of metabolic ('omic') pathways that must have converged in order for these pathways to co-evolve and permit SL synthesis. We also suggest that current origin of life and evolutionary models lack appropriate experimental support to explain the appearance of this complex metabolic pathway and its anteome.
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Affiliation(s)
- Tania C B Santos
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Tamir Dingjan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Anthony H Futerman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
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6
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Vaghela P, Das AK, Trivedi K, Anand KV, Shinde P, Ghosh A. Characterization and metabolomics profiling of Kappaphycus alvarezii seaweed extract. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102774] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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7
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Sphingolipids at Plasmodesmata: Structural Components and Functional Modulators. Int J Mol Sci 2022; 23:ijms23105677. [PMID: 35628487 PMCID: PMC9145688 DOI: 10.3390/ijms23105677] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 11/16/2022] Open
Abstract
Plasmodesmata (PD) are plant-specific channels connecting adjacent cells to mediate intercellular communication of molecules essential for plant development and defense. The typical PD are organized by the close apposition of the plasma membrane (PM), the desmotubule derived from the endoplasmic reticulum (ER), and spoke-like elements linking the two membranes. The plasmodesmal PM (PD-PM) is characterized by the formation of unique microdomains enriched with sphingolipids, sterols, and specific proteins, identified by lipidomics and proteomics. These components modulate PD to adapt to the dynamic changes of developmental processes and environmental stimuli. In this review, we focus on highlighting the functions of sphingolipid species in plasmodesmata, including membrane microdomain organization, architecture transformation, callose deposition and permeability control, and signaling regulation. We also briefly discuss the difference between sphingolipids and sterols, and we propose potential unresolved questions that are of help for further understanding the correspondence between plasmodesmal structure and function.
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8
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Haslam TM, Feussner I. Diversity in sphingolipid metabolism across land plants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2785-2798. [PMID: 35560193 PMCID: PMC9113257 DOI: 10.1093/jxb/erab558] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/21/2021] [Indexed: 05/08/2023]
Abstract
Sphingolipids are essential metabolites found in all plant species. They are required for plasma membrane integrity, tolerance of and responses to biotic and abiotic stresses, and intracellular signalling. There is extensive diversity in the sphingolipid content of different plant species, and in the identities and roles of enzymes required for their processing. In this review, we survey results obtained from investigations of the classical genetic model Arabidopsis thaliana, from assorted dicots with less extensive genetic toolkits, from the model monocot Oryza sativa, and finally from the model bryophyte Physcomitrium patens. For each species or group, we first broadly summarize what is known about sphingolipid content. We then discuss the most insightful and puzzling features of modifications to the hydrophobic ceramides, and to the polar headgroups of complex sphingolipids. Altogether, these data can serve as a framework for our knowledge of sphingolipid metabolism across the plant kingdom. This chemical and metabolic heterogeneity underpins equally diverse functions. With greater availability of different tools for analytical measurements and genetic manipulation, our field is entering an exciting phase of expanding our knowledge of the biological functions of this persistently cryptic class of lipids.
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Affiliation(s)
- Tegan M Haslam
- University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, Justus-von-Liebig-Weg 11, D-37077, Goettingen, Germany
| | - Ivo Feussner
- University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, Justus-von-Liebig-Weg 11, D-37077, Goettingen, Germany
- University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Service Unit for Metabolomics and Lipidomics, Goettingen, Germany
- University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Department of Plant Biochemistry, Goettingen, Germany
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9
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Webster C, Figueroa‐Corona L, Méndez‐González ID, Álvarez‐Soto L, Neale DB, Jaramillo‐Correa JP, Wegrzyn JL, Vázquez‐Lobo A. Comparative analysis of differential gene expression indicates divergence in ontogenetic strategies of leaves in two conifer genera. Ecol Evol 2022; 12:e8611. [PMID: 35222971 PMCID: PMC8848466 DOI: 10.1002/ece3.8611] [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: 09/13/2021] [Revised: 12/21/2021] [Accepted: 01/23/2022] [Indexed: 11/09/2022] Open
Abstract
In land plants, heteroblasty broadly refers to a drastic change in morphology during growth through ontogeny. Juniperus flaccida and Pinus cembroides are conifers of independent lineages known to exhibit leaf heteroblasty between the juvenile and adult life stage of development. Juvenile leaves of P. cembroides develop spirally on the main stem and appear decurrent, flattened, and needle‐like; whereas adult photosynthetic leaves are triangular or semi‐circular needle‐like, and grow in whorls on secondary or tertiary compact dwarf shoots. By comparison, J. flaccida juvenile leaves are decurrent and needle‐like, and adult leaves are compact, short, and scale‐like. Comparative analyses were performed to evaluate differences in anatomy and gene expression patterns between developmental phases in both species. RNA from 12 samples was sequenced and analyzed with available software. They were assembled de novo from the RNA‐Seq reads. Following assembly, 63,741 high‐quality transcripts were functionally annotated in P. cembroides and 69,448 in J. flaccida. Evaluation of the orthologous groups yielded 4140 shared gene families among the four references (adult and juvenile from each species). Activities related to cell division and development were more abundant in juveniles than adults in P. cembroides, and more abundant in adults than juveniles in J. flaccida. Overall, there were 509 up‐regulated and 81 down‐regulated genes in the juvenile condition of P. cembroides and 14 up‐regulated and 22 down‐regulated genes in J. flaccida. Gene interaction network analysis showed evidence of co‐expression and co‐localization of up‐regulated genes involved in cell wall and cuticle formation, development, and phenylpropanoid pathway, in juvenile P. cembroides leaves. Whereas in J. flaccida, differential expression and gene interaction patterns were detected in genes involved in photosynthesis and chloroplast biogenesis. Although J. flaccida and P. cembroides both exhibit leaf heteroblastic development, little overlap was detected, and unique genes and pathways were highlighted in this study.
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Affiliation(s)
- Cynthia Webster
- Department of Ecology and Evolutionary Biology University of Connecticut Storrs Connecticut USA
| | - Laura Figueroa‐Corona
- Departamento de Ecología Evolutiva Instituto de Ecología Universidad Nacional Autónoma de México Ciudad de México Mexico
| | - Iván David Méndez‐González
- Departamento de Ecología Evolutiva Instituto de Ecología Universidad Nacional Autónoma de México Ciudad de México Mexico
- Department of Biological Sciences University of Pittsburgh Pittsburgh Pennsylvania USA
| | - Lluvia Álvarez‐Soto
- Facultad de Ciencias Biológicas Universidad Autónoma del Estado de Morelos Cuernavaca México
| | - David B. Neale
- Department of Plant Sciences University of California Davis California USA
| | - Juan Pablo Jaramillo‐Correa
- Departamento de Ecología Evolutiva Instituto de Ecología Universidad Nacional Autónoma de México Ciudad de México Mexico
| | - Jill L. Wegrzyn
- Department of Ecology and Evolutionary Biology University of Connecticut Storrs Connecticut USA
| | - Alejandra Vázquez‐Lobo
- Centro de Investigación en Biodiversidad y Conservación Universidad Autónoma del Estado de Morelos Cuernavaca México
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10
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Ali S, Gill RA, Shafique MS, Ahmar S, Kamran M, Zhang N, Riaz M, Nawaz M, Fang R, Ali B, Zhou W. Role of phytomelatonin responsive to metal stresses: An omics perspective and future scenario. FRONTIERS IN PLANT SCIENCE 2022; 13:936747. [PMID: 36147242 PMCID: PMC9486320 DOI: 10.3389/fpls.2022.936747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/08/2022] [Indexed: 05/03/2023]
Abstract
A pervasive melatonin (N-acetyl-5-methoxytryptamine) reveals a crucial role in stress tolerance and plant development. Melatonin (MT) is a unique molecule with multiple phenotypic expressions and numerous actions within the plants. It has been extensively studied in crop plants under different abiotic stresses such as drought, salinity, heat, cold, and heavy metals. Mainly, MT role is appraised as an antioxidant molecule that deals with oxidative stress by scavenging reactive oxygen species (ROS) and modulating stress related genes. It improves the contents of different antioxidant enzyme activities and thus, regulates the redox hemostasis in crop plants. In this comprehensive review, regulatory effects of melatonin in plants as melatonin biosynthesis, signaling pathway, modulation of stress related genes and physiological role of melatonin under different heavy metal stress have been reviewed in detail. Further, this review has discussed how MT regulates different genes/enzymes to mediate defense responses and overviewed the context of transcriptomics and phenomics followed by the metabolomics pathways in crop plants.
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Affiliation(s)
- Skhawat Ali
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, China
| | - Rafaqat Ali Gill
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | | | - Sunny Ahmar
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Muhammad Kamran
- School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA, Australia
| | - Na Zhang
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, China
| | - Muhammad Riaz
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Guangdong, China
| | - Muhammad Nawaz
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Rouyi Fang
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, China
| | - Basharat Ali
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
- Basharat Ali,
| | - Weijun Zhou
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, China
- *Correspondence: Weijun Zhou,
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11
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Seo SY, Kim YJ, Kim J, Nam MH, Park KY. Phytosphingosine induces systemic acquired resistance through activation of sphingosine kinase. PLANT DIRECT 2021; 5:e351. [PMID: 34622122 PMCID: PMC8483070 DOI: 10.1002/pld3.351] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 10/13/2020] [Accepted: 09/08/2021] [Indexed: 05/11/2023]
Abstract
Phytosphingosine (PHS) is a naturally occurring bioactive sphingolipid molecule. Intermediates such as sphingolipid long-chain bases (LCBs) in sphingolipid biosynthesis have been shown to have important roles as signaling molecules. PHS treatment caused rapid cell damage and upregulated the generation of reactive oxygen species (ROS) and ethylene in tobacco plants. These events were followed by the induction of sphingosine kinase (SphK) in a biphasic manner, which metabolized PHS to phytosphingosine-1-phosphate (PHS-1-P). On the other hand, a PHS treatment with a virulent pathogen, Phytophthora parasitica var. nicotianae (Ppn), alleviated the pathogen-induced cell damage and reduced the growth of Ppn. A Ppn infection increased the PHS and PHS-1-P levels significantly in the upper part of the leaves at the infection site at the later stage. In addition, Ppn increased the transcription levels of serine palmitoyltransferase (LCB1 and LCB2) for sphingolipid biosynthesis at the later stage, which was enhanced further by PHS. Moreover, the PHS treatment increased the transcription and activity of SphK, which was accompanied by prominent increases in the transcription levels of ROS-detoxifying enzymes and PR proteins in the later phase of the pathogen infection. Overall, the PHS-induced resistant effects were prominent during the necrotic stage of this hemibiotrophic infection, indicating that it is more beneficial for inhibiting the pathogenicity on necrotic cell death. Phosphorylated LCBs reduced the pathogen-induced cell damage significantly in this stage. These results suggest that the selective channeling of sphingolipids into phosphorylated forms has a pro-survival effect on plant immunity.
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Affiliation(s)
- So Yeon Seo
- Department of Biology Sunchon National University Suncheon Republic of Korea
| | - Yu Jung Kim
- Department of Biology Sunchon National University Suncheon Republic of Korea
| | - Jinwoo Kim
- Seoul Center Korea Basic Science Institute (KBSI) Seoul Republic of Korea
| | - Myung Hee Nam
- Seoul Center Korea Basic Science Institute (KBSI) Seoul Republic of Korea
| | - Ky Young Park
- Department of Biology Sunchon National University Suncheon Republic of Korea
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12
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Iacovacci J, Lin W, Griffin JL, Glen RC. IonFlow: a galaxy tool for the analysis of ionomics data sets. Metabolomics 2021; 17:91. [PMID: 34562172 PMCID: PMC8464566 DOI: 10.1007/s11306-021-01841-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 09/13/2021] [Indexed: 10/28/2022]
Abstract
INTRODUCTION Inductively coupled plasma mass spectrometry (ICP-MS) experiments generate complex multi-dimensional data sets that require specialist data analysis tools. OBJECTIVE Here we describe tools to facilitate analysis of the ionome composed of high-throughput elemental profiling data. METHODS IonFlow is a Galaxy tool written in R for ionomics data analysis and is freely accessible at https://github.com/wanchanglin/ionflow . It is designed as a pipeline that can process raw data to enable exploration and interpretation using multivariate statistical techniques and network-based algorithms, including principal components analysis, hierarchical clustering, relevance network extraction and analysis, and gene set enrichment analysis. RESULTS AND CONCLUSION The pipeline is described and tested on two benchmark data sets of the haploid S. Cerevisiae ionome and of the human HeLa cell ionome.
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Affiliation(s)
- J Iacovacci
- Department of Metabolism Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK.
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
| | - W Lin
- Department of Metabolism Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - J L Griffin
- Department of Metabolism Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- Department of Biochemistry and Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - R C Glen
- Department of Metabolism Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK.
- Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Cambridge, UK.
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13
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Exploitation of Drought Tolerance-Related Genes for Crop Improvement. Int J Mol Sci 2021; 22:ijms221910265. [PMID: 34638606 PMCID: PMC8508643 DOI: 10.3390/ijms221910265] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/15/2021] [Accepted: 09/15/2021] [Indexed: 12/03/2022] Open
Abstract
Drought has become a major threat to food security, because it affects crop growth and development. Drought tolerance is an important quantitative trait, which is regulated by hundreds of genes in crop plants. In recent decades, scientists have made considerable progress to uncover the genetic and molecular mechanisms of drought tolerance, especially in model plants. This review summarizes the evaluation criteria for drought tolerance, methods for gene mining, characterization of genes related to drought tolerance, and explores the approaches to enhance crop drought tolerance. Collectively, this review illustrates the application prospect of these genes in improving the drought tolerance breeding of crop plants.
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14
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Liu NJ, Hou LP, Bao JJ, Wang LJ, Chen XY. Sphingolipid metabolism, transport, and functions in plants: Recent progress and future perspectives. PLANT COMMUNICATIONS 2021; 2:100214. [PMID: 34746760 PMCID: PMC8553973 DOI: 10.1016/j.xplc.2021.100214] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 05/12/2021] [Accepted: 06/26/2021] [Indexed: 05/08/2023]
Abstract
Sphingolipids, which comprise membrane systems together with other lipids, are ubiquitous in cellular organisms. They show a high degree of diversity across plant species and vary in their structures, properties, and functions. Benefiting from the development of lipidomic techniques, over 300 plant sphingolipids have been identified. Generally divided into free long-chain bases (LCBs), ceramides, glycosylceramides (GlcCers) and glycosyl inositol phosphoceramides (GIPCs), plant sphingolipids exhibit organized aggregation within lipid membranes to form raft domains with sterols. Accumulating evidence has revealed that sphingolipids obey certain trafficking and distribution rules and confer unique properties to membranes. Functional studies using sphingolipid biosynthetic mutants demonstrate that sphingolipids participate in plant developmental regulation, stimulus sensing, and stress responses. Here, we present an updated metabolism/degradation map and summarize the structures of plant sphingolipids, review recent progress in understanding the functions of sphingolipids in plant development and stress responses, and review sphingolipid distribution and trafficking in plant cells. We also highlight some important challenges and issues that we may face during the process of studying sphingolipids.
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Affiliation(s)
- Ning-Jing Liu
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China
- Corresponding author
| | - Li-Pan Hou
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China
- University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Jing-Jing Bao
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China
- University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Ling-Jian Wang
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China
| | - Xiao-Ya Chen
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China
- University of Chinese Academy of Sciences, Shanghai 200032, China
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15
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Chen Q, Xu F, Wang L, Suo X, Wang Q, Meng Q, Huang L, Ma C, Li G, Luo M. Sphingolipid Profile during Cotton Fiber Growth Revealed That a Phytoceramide Containing Hydroxylated and Saturated VLCFA Is Important for Fiber Cell Elongation. Biomolecules 2021; 11:biom11091352. [PMID: 34572565 PMCID: PMC8466704 DOI: 10.3390/biom11091352] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 11/22/2022] Open
Abstract
Cotton fiber is a single-celled seed trichrome that arises from the epidermis of the ovule’s outer integument. The fiber cell displays high polar expansion and thickens but not is disrupted by cell division. Therefore, it is an ideal model for studying the growth and development of plant cells. Sphingolipids are important components of membranes and are also active molecules in cells. However, the sphingolipid profile during fiber growth and the differences in sphingolipid metabolism at different developmental stages are still unclear. In this study, we detected that there were 6 classes and 95 molecular species of sphingolipids in cotton fibers by ultrahigh performance liquid chromatography-MS/MS (UHPLC-MS/MS). Among these, the phytoceramides (PhytoCer) contained the most molecular species, and the PhytoCer content was highest, while that of sphingosine-1-phosphate (S1P) was the lowest. The content of PhytoCer, phytoceramides with hydroxylated fatty acyls (PhytoCer-OHFA), phyto-glucosylceramides (Phyto-GluCer), and glycosyl-inositol-phospho-ceramides (GIPC) was higher than that of other classes in fiber cells. With the development of fiber cells, phytosphingosine-1-phosphate (t-S1P) and PhytoCer changed greatly. The sphingolipid molecular species Ceramide (Cer) d18:1/26:1, PhytoCer t18:1/26:0, PhytoCer t18:0/26:0, PhytoCer t18:1/h20:0, PhytoCer t18:1/h26:0, PhytoCer t18:0/h26:0, and GIPC t18:0/h16:0 were significantly enriched in 10-DPA fiber cells while Cer d18:1/20:0, Cer d18:1/22:0, and GIPC t18:0/h18:0 were significantly enriched in 20-DPA fiber cells, indicating that unsaturated PhytoCer containing hydroxylated and saturated very long chain fatty acids (VLCFA) play some role in fiber cell elongation. Consistent with the content analysis results, the related genes involved in long chain base (LCB) hydroxylation and unsaturation as well as VLCFA synthesis and hydroxylation were highly expressed in rapidly elongating fiber cells. Furthermore, the exogenous application of a potent inhibitor of serine palmitoyltransferase, myriocin, severely blocked fiber cell elongation, and the exogenous application of sphingosine antagonized the inhibition of myriocin for fiber elongation. Taking these points together, we concluded that sphingolipids play crucial roles in fiber cell elongation and SCW deposition. This provides a new perspective for further studies on the regulatory mechanism of the growth and development of cotton fiber cells.
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Affiliation(s)
- Qian Chen
- Key Laboratory of Biotechnology and Crop Quality Improvement, Ministry of Agriculture/Biotechnology Research Center, Southwest University, Chongqing 400716, China; (Q.C.); (F.X.); (X.S.); (Q.W.); (Q.M.); (L.H.); (C.M.); (G.L.)
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Fan Xu
- Key Laboratory of Biotechnology and Crop Quality Improvement, Ministry of Agriculture/Biotechnology Research Center, Southwest University, Chongqing 400716, China; (Q.C.); (F.X.); (X.S.); (Q.W.); (Q.M.); (L.H.); (C.M.); (G.L.)
| | - Li Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China;
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xiaodong Suo
- Key Laboratory of Biotechnology and Crop Quality Improvement, Ministry of Agriculture/Biotechnology Research Center, Southwest University, Chongqing 400716, China; (Q.C.); (F.X.); (X.S.); (Q.W.); (Q.M.); (L.H.); (C.M.); (G.L.)
| | - Qiaoling Wang
- Key Laboratory of Biotechnology and Crop Quality Improvement, Ministry of Agriculture/Biotechnology Research Center, Southwest University, Chongqing 400716, China; (Q.C.); (F.X.); (X.S.); (Q.W.); (Q.M.); (L.H.); (C.M.); (G.L.)
| | - Qian Meng
- Key Laboratory of Biotechnology and Crop Quality Improvement, Ministry of Agriculture/Biotechnology Research Center, Southwest University, Chongqing 400716, China; (Q.C.); (F.X.); (X.S.); (Q.W.); (Q.M.); (L.H.); (C.M.); (G.L.)
| | - Li Huang
- Key Laboratory of Biotechnology and Crop Quality Improvement, Ministry of Agriculture/Biotechnology Research Center, Southwest University, Chongqing 400716, China; (Q.C.); (F.X.); (X.S.); (Q.W.); (Q.M.); (L.H.); (C.M.); (G.L.)
| | - Caixia Ma
- Key Laboratory of Biotechnology and Crop Quality Improvement, Ministry of Agriculture/Biotechnology Research Center, Southwest University, Chongqing 400716, China; (Q.C.); (F.X.); (X.S.); (Q.W.); (Q.M.); (L.H.); (C.M.); (G.L.)
| | - Guiming Li
- Key Laboratory of Biotechnology and Crop Quality Improvement, Ministry of Agriculture/Biotechnology Research Center, Southwest University, Chongqing 400716, China; (Q.C.); (F.X.); (X.S.); (Q.W.); (Q.M.); (L.H.); (C.M.); (G.L.)
| | - Ming Luo
- Key Laboratory of Biotechnology and Crop Quality Improvement, Ministry of Agriculture/Biotechnology Research Center, Southwest University, Chongqing 400716, China; (Q.C.); (F.X.); (X.S.); (Q.W.); (Q.M.); (L.H.); (C.M.); (G.L.)
- Correspondence:
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16
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Ali S, Tyagi A, Bae H. Ionomic Approaches for Discovery of Novel Stress-Resilient Genes in Plants. Int J Mol Sci 2021; 22:7182. [PMID: 34281232 PMCID: PMC8267685 DOI: 10.3390/ijms22137182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 01/03/2023] Open
Abstract
Plants, being sessile, face an array of biotic and abiotic stresses in their lifespan that endanger their survival. Hence, optimized uptake of mineral nutrients creates potential new routes for enhancing plant health and stress resilience. Recently, minerals (both essential and non-essential) have been identified as key players in plant stress biology, owing to their multifaceted functions. However, a realistic understanding of the relationship between different ions and stresses is lacking. In this context, ionomics will provide new platforms for not only understanding the function of the plant ionome during stresses but also identifying the genes and regulatory pathways related to mineral accumulation, transportation, and involvement in different molecular mechanisms under normal or stress conditions. This article provides a general overview of ionomics and the integration of high-throughput ionomic approaches with other "omics" tools. Integrated omics analysis is highly suitable for identification of the genes for various traits that confer biotic and abiotic stress tolerance. Moreover, ionomics advances being used to identify loci using qualitative trait loci and genome-wide association analysis of element uptake and transport within plant tissues, as well as genetic variation within species, are discussed. Furthermore, recent developments in ionomics for the discovery of stress-tolerant genes in plants have also been addressed; these can be used to produce more robust crops with a high nutritional value for sustainable agriculture.
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Affiliation(s)
- Sajad Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea;
| | - Anshika Tyagi
- National Institute for Plant Biotechnology, New Delhi 110012, India;
| | - Hanhong Bae
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea;
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17
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Campos ACAL, van Dijk WFA, Ramakrishna P, Giles T, Korte P, Douglas A, Smith P, Salt DE. 1,135 ionomes reveal the global pattern of leaf and seed mineral nutrient and trace element diversity in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:536-554. [PMID: 33506585 DOI: 10.1111/tpj.15177] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 01/07/2021] [Accepted: 01/20/2021] [Indexed: 05/06/2023]
Abstract
Soil is a heterogeneous reservoir of essential elements needed for plant growth and development. Plants have evolved mechanisms to balance their nutritional needs based on availability of nutrients. This has led to genetically based variation in the elemental composition, the 'ionome', of plants, both within and between species. We explore this natural variation using a panel of wild-collected, geographically widespread Arabidopsis thaliana accessions from the 1001 Genomes Project including over 1,135 accessions, and the 19 parental accessions of the Multi-parent Advanced Generation Inter-Cross (MAGIC) panel, all with full-genome sequences available. We present an experimental design pipeline for high-throughput ionomic screenings and analyses with improved normalisation procedures to account for errors and variability in conditions often encountered in large-scale, high-throughput data collection. We report quantification of the complete leaf and seed ionome of the entire collection using this pipeline and a digital tool, Ion Explorer, to interact with the dataset. We describe the pattern of natural ionomic variation across the A. thaliana species and identify several accessions with extreme ionomic profiles. It forms a valuable resource for exploratory genetic mapping studies to identify genes underlying natural variation in leaf and seed ionome and genetic adaptation of plants to soil conditions.
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Affiliation(s)
- Ana Carolina A L Campos
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
| | - William F A van Dijk
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
| | - Priya Ramakrishna
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
| | - Tom Giles
- Digital Research Service and Advanced Data Analysis Centre, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
| | - Pamela Korte
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
| | - Alex Douglas
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
| | - Pete Smith
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
| | - David E Salt
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
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18
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Watanabe T, Azuma T. Ionomic variation in leaves of 819 plant species growing in the botanical garden of Hokkaido University, Japan. JOURNAL OF PLANT RESEARCH 2021; 134:291-304. [PMID: 33511523 DOI: 10.1007/s10265-021-01254-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
Ionomics is the measurement of total metal, metalloid, and nonmetal accumulation in living organisms. Plant ionomics has been applied to various types of research in the last decade. It has been reported that the ionome of a plant is strongly affected by its evolution and by environmental factors. In this study, we analyzed the concentration of 23 elements in leaves of 819 plant species (175 families) growing in the Botanic Garden of Hokkaido University, Japan. Relative variation estimated by the coefficient of variation in foliar concentrations of essential elements among various plant species tended to be low, whereas nickel concentration showed exceptionally large relative variation. By contrast, the relative variation in nonessential elements was high, particularly in sodium, aluminum, and arsenic. The higher relative variations in these element concentrations can be explained by the occurrence of plants that are hyperaccumulators for these elements. Differences in life forms such as herbaceous/woody species, deciduous/evergreen woody species and annual/perennial herbaceous species affected the concentration of several elements in the leaves. These differences were considered to be due to the combined factors including differences in lifespan, growth rate, and cell wall thickness of the leaves. Results of principal component analyses (based on concentration data of essential and nonessential elements in leaf samples) indicated phylogenetic influences on plant ionomes at the family level in Polypodiales, Pinales, Poales, and Ericales. Furthermore, when analyzing correlations among concentrations of all elements in each order and comparing among different orders, the results also suggested that Polypodiales, Pinales, and Poales each had a specific ion homeostasis network.
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Affiliation(s)
- Toshihiro Watanabe
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kitaku, Sapporo, 0608589, Japan.
| | - Takayuki Azuma
- Field Science Center for Northern Biosphere, Botanic Garden, Hokkaido University, Kita-3, Nishi-8, Chuoku, Sapporo, 0600003, Japan
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19
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Song X, Zhu G, Hou S, Ren Y, Amjid MW, Li W, Guo W. Genome-Wide Association Analysis Reveals Loci and Candidate Genes Involved in Fiber Quality Traits Under Multiple Field Environments in Cotton ( Gossypium hirsutum). FRONTIERS IN PLANT SCIENCE 2021; 12:695503. [PMID: 34421946 PMCID: PMC8374309 DOI: 10.3389/fpls.2021.695503] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/16/2021] [Indexed: 05/17/2023]
Abstract
Fiber length, fiber strength, and fiber micronaire are the main fiber quality parameters in cotton. Thus, mining the elite and stable loci/alleles related to fiber quality traits and elucidating the relationship between the two may accelerate genetic improvement of fiber quality in cotton. Here, genome-wide association analysis (GWAS) was performed for fiber quality parameters based on phenotypic data, and 56,010 high-quality single nucleotide polymorphisms (SNPs) using 242 upland cotton accessions under 12 field environments were obtained. Phenotypic analysis exhibited that fiber length (FL) had a positive correlation with fiber strength (FS) and had a negative correlation with fiber micronaire (Mic). Genetic analysis also indicated that FL, FS, and Mic had high heritability of more than 80%. A total of 67 stable quantitative trait loci (QTLs) were identified through GWAS analysis, including 31 for FL, 21 for FS, and 22 for Mic. Of them, three pairs homologous QTLs were detected between A and D subgenomes, and seven co-located QTLs with two fiber quality parameters were found. Compared with the reported QTLs, 34 co-located with previous studies, and 33 were newly revealed. Integrated with transcriptome analysis, we selected 256, 244, and 149 candidate genes for FL, FS, and Mic, respectively. Gene Ontology (GO) analysis showed that most of the genes located in QTLs interval of the three fiber quality traits were involved in sugar biosynthesis, sugar metabolism, microtubule, and cytoskeleton organization, which played crucial roles in fiber development. Through correlation analysis between haplotypes and phenotypes, three genes (GH_A05G1494, GH_D11G3097, and GH_A05G1082) predominately expressed in fiber development stages were indicated to be potentially responsible for FL, FS, and Mic, respectively. The GH_A05G1494 encoded a protein containing SGS-domain, which is related to tubulin-binding and ubiquitin-protein ligase binding. The GH_D11G3097 encoded 20S proteasome beta subunit G1, and was involved in the ubiquitin-dependent protein catabolic process. The GH_A05G1082 encoded RAN binding protein 1 with a molecular function of GTPase activator activity. These results provide new insights and candidate loci/genes for the improvement of fiber quality in cotton.
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20
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Kovács T, Ahres M, Pálmai T, Kovács L, Uemura M, Crosatti C, Galiba G. Decreased R:FR Ratio in Incident White Light Affects the Composition of Barley Leaf Lipidome and Freezing Tolerance in a Temperature-Dependent Manner. Int J Mol Sci 2020; 21:ijms21207557. [PMID: 33066276 PMCID: PMC7593930 DOI: 10.3390/ijms21207557] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/29/2020] [Accepted: 10/08/2020] [Indexed: 02/06/2023] Open
Abstract
In cereals, C-repeat binding factor genes have been defined as key components of the light quality-dependent regulation of frost tolerance by integrating phytochrome-mediated light and temperature signals. This study elucidates the differences in the lipid composition of barley leaves illuminated with white light or white light supplemented with far-red light at 5 or 15 °C. According to LC-MS analysis, far-red light supplementation increased the amount of monogalactosyldiacylglycerol species 36:6, 36:5, and 36:4 after 1 day at 5 °C, and 10 days at 15 °C resulted in a perturbed content of 38:6 species. Changes were observed in the levels of phosphatidylethanolamine, and phosphatidylserine under white light supplemented with far-red light illumination at 15 °C, whereas robust changes were observed in the amount of several phosphatidylserine species at 5 °C. At 15 °C, the amount of some phosphatidylglycerol species increased as a result of white light supplemented with far-red light illumination after 1 day. The ceramide (42:2)-3 content increased regardless of the temperature. The double-bond index of phosphatidylglycerol, phosphatidylserine, phosphatidylcholine ceramide together with total double-bond index changed when the plant was grown at 15 °C as a function of white light supplemented with far-red light. white light supplemented with far-red light increased the monogalactosyldiacylglycerol/diacylglycerol ratio as well. The gene expression changes are well correlated with the alterations in the lipidome.
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Affiliation(s)
- Terézia Kovács
- Biological Research Centre, Institute of Plant Biology, H-6701 Szeged, Hungary;
- Department of Plant Biology, University of Szeged, 6720 Szeged, Hungary
- Correspondence:
| | - Mohamed Ahres
- Centre for Agricultural Research, Agricultural Institute, 2462 Martonvásár, Hungary; (M.A.); (T.P.); (G.G.)
- Festetics Doctoral School, Georgikon Campus, Szent István University, H-2100 Gödöllő, Hungary
| | - Tamás Pálmai
- Centre for Agricultural Research, Agricultural Institute, 2462 Martonvásár, Hungary; (M.A.); (T.P.); (G.G.)
| | - László Kovács
- Biological Research Centre, Institute of Plant Biology, H-6701 Szeged, Hungary;
| | - Matsuo Uemura
- Department of Plant-Bioscience, Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan;
| | - Cristina Crosatti
- CREA Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, 29017 San Protaso, Italy;
| | - Gabor Galiba
- Centre for Agricultural Research, Agricultural Institute, 2462 Martonvásár, Hungary; (M.A.); (T.P.); (G.G.)
- Festetics Doctoral School, Georgikon Campus, Szent István University, H-2100 Gödöllő, Hungary
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21
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Whitt L, Ricachenevsky FK, Ziegler GZ, Clemens S, Walker E, Maathuis FJM, Kear P, Baxter I. A curated list of genes that affect the plant ionome. PLANT DIRECT 2020; 4:e00272. [PMID: 33103043 PMCID: PMC7576880 DOI: 10.1002/pld3.272] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/26/2020] [Accepted: 08/28/2020] [Indexed: 05/07/2023]
Abstract
Understanding the mechanisms underlying plants' adaptation to their environment will require knowledge of the genes and alleles underlying elemental composition. Modern genetics is capable of quickly, and cheaply indicating which regions of DNA are associated with particular phenotypes in question, but most genes remain poorly annotated, hindering the identification of candidate genes. To help identify candidate genes underlying elemental accumulations, we have created the known ionome gene (KIG) list: a curated collection of genes experimentally shown to change uptake, accumulation, and distribution of elements. We have also created an automated computational pipeline to generate lists of KIG orthologs in other plant species using the PhytoMine database. The current version of KIG consists of 176 known genes covering 5 species, 23 elements, and their 1588 orthologs in 10 species. Analysis of the known genes demonstrated that most were identified in the model plant Arabidopsis thaliana, and that transporter coding genes and genes altering the accumulation of iron and zinc are overrepresented in the current list.
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Affiliation(s)
- Lauren Whitt
- Donald Danforth Plant Science CenterSaint LouisMOUSA
| | - Felipe Klein Ricachenevsky
- Departamento de Botânica Programa de Pós‐Graduação em Biologia Celular e MolecularUniversidade Federal do Rio Grande do SulPorto AlegreBrazil
| | | | | | | | | | | | - Ivan Baxter
- Donald Danforth Plant Science CenterSaint LouisMOUSA
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Iswanto ABB, Shon JC, Liu KH, Vu MH, Kumar R, Kim JY. Sphingolipids Modulate Secretion of Glycosylphosphatidylinositol-Anchored Plasmodesmata Proteins and Callose Deposition. PLANT PHYSIOLOGY 2020; 184:407-420. [PMID: 32636343 PMCID: PMC7479907 DOI: 10.1104/pp.20.00401] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 06/25/2020] [Indexed: 05/04/2023]
Abstract
Plasma membranes encapsulated in the symplasmic nanochannels of plasmodesmata (PD) contain abundant lipid rafts, which are enriched with sphingolipids (SLs) and sterols. Reduction of sterols has highlighted the role played by lipid raft integrity in the intercellular trafficking of glycosylphosphatidylinositol (GPI)-anchored PD proteins, particularly in affecting callose enhancement. The presence of callose at PD is strongly attributed to the regulation of callose accumulation and callose degradation by callose synthases and β-1,3-glucanases (BGs), respectively. SLs are implicated in signaling and membrane protein trafficking; however, the underlying processes linking SL composition to the control of symplasmic apertures remain unknown. The wide variety of SLs in plants prompted us to investigate which SL molecules are important for regulating symplasmic apertures in Arabidopsis (Arabidopsis thaliana). We introduced several potential SL pathway inhibitors and genetically modified SL contents using two independent SL pathway mutants. We were able to modulate callose deposition to control symplasmic connectivity through perturbations of SL metabolism. Alteration in glucosylhydroxyceramides or related SL composition particularly disturbed the secretory machinery for the GPI-anchored PdBG2 protein, resulting in an overaccumulation of callose. Moreover, our results revealed that SL-enriched lipid rafts link symplasmic channeling to PD callose homeostasis by controlling the targeting of GPI-anchored PdBG2. This study elevates our understanding of the molecular linkage underlying intracellular trafficking and precise targeting of GPI-anchored PD proteins incorporating glucosyl SLs.
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Affiliation(s)
- Arya Bagus Boedi Iswanto
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Jong Cheol Shon
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 702-701, Republic of Korea
- Environmental Chemistry Research Group, Korea Institute of Toxicology, Jinju 52834, Republic of Korea
| | - Kwang Hyeon Liu
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Minh Huy Vu
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Ritesh Kumar
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea
- Division of Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
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Fumonisin B1-Induced Changes in Cotton Fiber Elongation Revealed by Sphingolipidomics and Proteomics. Biomolecules 2020; 10:biom10091258. [PMID: 32878249 PMCID: PMC7564794 DOI: 10.3390/biom10091258] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 12/20/2022] Open
Abstract
Sphingolipids are essential biomolecules and membrane components, but their regulatory role in cotton fiber development is poorly understood. Here, we found that fumonisin B1 (FB1)—a sphingolipid synthesis inhibitor—could block fiber elongation severely. Using liquid chromatography tandem mass spectrometry (LC-MS/MS), we detected 95 sphingolipids that were altered by FB1 treatment; of these, 29 (mainly simple sphingolipids) were significantly increased, while 33 (mostly complex sphingolipids) were significantly decreased. A quantitative analysis of the global proteome, using an integrated quantitative approach with tandem mass tag (TMT) labeling and LC-MS/MS, indicated the upregulation of 633 and the downregulation of 672 proteins after FB1 treatment. Most differentially expressed proteins (DEPs) were involved in processes related to phenylpropanoid and flavonoid biosynthesis. In addition, up to 20 peroxidases (POD) were found to be upregulated, and POD activity was also increased by the inhibitor. To our knowledge, this is the first report on the effects of FB1 treatment on cotton fiber and ovule sphingolipidomics and proteomics. Our findings provide target metabolites and biological pathways for cotton fiber improvement.
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Gangurde SS, Wang H, Yaduru S, Pandey MK, Fountain JC, Chu Y, Isleib T, Holbrook CC, Xavier A, Culbreath AK, Ozias‐Akins P, Varshney RK, Guo B. Nested-association mapping (NAM)-based genetic dissection uncovers candidate genes for seed and pod weights in peanut (Arachis hypogaea). PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1457-1471. [PMID: 31808273 PMCID: PMC7206994 DOI: 10.1111/pbi.13311] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/13/2019] [Accepted: 11/15/2019] [Indexed: 05/05/2023]
Abstract
Multiparental genetic mapping populations such as nested-association mapping (NAM) have great potential for investigating quantitative traits and associated genomic regions leading to rapid discovery of candidate genes and markers. To demonstrate the utility and power of this approach, two NAM populations, NAM_Tifrunner and NAM_Florida-07, were used for dissecting genetic control of 100-pod weight (PW) and 100-seed weight (SW) in peanut. Two high-density SNP-based genetic maps were constructed with 3341 loci and 2668 loci for NAM_Tifrunner and NAM_Florida-07, respectively. The quantitative trait locus (QTL) analysis identified 12 and 8 major effect QTLs for PW and SW, respectively, in NAM_Tifrunner, and 13 and 11 major effect QTLs for PW and SW, respectively, in NAM_Florida-07. Most of the QTLs associated with PW and SW were mapped on the chromosomes A05, A06, B05 and B06. A genomewide association study (GWAS) analysis identified 19 and 28 highly significant SNP-trait associations (STAs) in NAM_Tifrunner and 11 and 17 STAs in NAM_Florida-07 for PW and SW, respectively. These significant STAs were co-localized, suggesting that PW and SW are co-regulated by several candidate genes identified on chromosomes A05, A06, B05, and B06. This study demonstrates the utility of NAM population for genetic dissection of complex traits and performing high-resolution trait mapping in peanut.
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Affiliation(s)
- Sunil S. Gangurde
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Hui Wang
- Crop Protection and Management Research UnitUSDA‐ARSTiftonGAUSA
- Department of Plant PathologyUniversity of GeorgiaTiftonGAUSA
| | - Shasidhar Yaduru
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- Crop Protection and Management Research UnitUSDA‐ARSTiftonGAUSA
- Department of Plant PathologyUniversity of GeorgiaTiftonGAUSA
| | - Manish K. Pandey
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Jake C. Fountain
- Crop Protection and Management Research UnitUSDA‐ARSTiftonGAUSA
- Department of Plant PathologyUniversity of GeorgiaTiftonGAUSA
| | - Ye Chu
- Horticulture DepartmentUniversity of GeorgiaTiftonGAUSA
| | - Thomas Isleib
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNCUSA
| | | | | | | | | | - Rajeev K. Varshney
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Baozhu Guo
- Department of Plant PathologyUniversity of GeorgiaTiftonGAUSA
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Lamers J, van der Meer T, Testerink C. How Plants Sense and Respond to Stressful Environments. PLANT PHYSIOLOGY 2020; 182:1624-1635. [PMID: 32132112 PMCID: PMC7140927 DOI: 10.1104/pp.19.01464] [Citation(s) in RCA: 196] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/26/2020] [Indexed: 05/18/2023]
Abstract
Plants are exposed to an ever-changing environment to which they have to adjust accordingly. Their response is tightly regulated by complex signaling pathways that all start with stimulus perception. Here, we give an overview of the latest developments in the perception of various abiotic stresses, including drought, salinity, flooding, and temperature stress. We discuss whether proposed perception mechanisms are true sensors, which is well established for some abiotic factors but not yet fully elucidated for others. In addition, we review the downstream cellular responses, many of which are shared by various stresses but result in stress-specific physiological and developmental output. New sensing mechanisms have been identified, including heat sensing by the photoreceptor phytochrome B, salt sensing by glycosylinositol phosphorylceramide sphingolipids, and drought sensing by the specific calcium influx channel OSCA1. The simultaneous occurrence of multiple stress conditions shows characteristic downstream signaling signatures that were previously considered general signaling responses. The integration of sensing of multiple stress conditions and subsequent signaling responses is a promising venue for future research to improve the understanding of plant abiotic stress perception.
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Affiliation(s)
- Jasper Lamers
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University and Research, 6708PB, Wageningen, The Netherlands
| | - Tom van der Meer
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University and Research, 6708PB, Wageningen, The Netherlands
| | - Christa Testerink
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University and Research, 6708PB, Wageningen, The Netherlands
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Wu S, Tan H, Hao X, Xie Z, Wang X, Li D, Tian L. Profiling miRNA expression in photo-thermo-sensitive male genic sterility line (PTGMS) PA64S under high and low temperature. PLANT SIGNALING & BEHAVIOR 2019; 14:1679015. [PMID: 31610741 PMCID: PMC6866692 DOI: 10.1080/15592324.2019.1679015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/29/2019] [Accepted: 10/07/2019] [Indexed: 06/10/2023]
Abstract
Peiai64S (PA64S) is a photo-thermo-sensitive genic male sterile line (PTGMS), with wide application in hybrid seed production in rice (Oryza sativa L.). Micro-RNAs are 21-24 nt, endogenously expressed small RNAs that have been characterized in various developmental stages of rice, but none have been studied with respect to the regulation of TGMS in rice. Here, we employed high-throughput sequencing to identify expression profiles of miRNAs in the anthers of PA64S at high (PA64S-H) and low temperature (PA64S-L). Two small RNA libraries from PA64S-H and PA64-L anthers were sequenced, and 263 known and 321 novel candidate miRNAs were identified. Based on the number of sequencing reads, a total of 133 known miRNAs were found to be differentially expressed between PA64S-H and PA64S-L. Target prediction showed that the target genes encode MYB and TCP transcription factors, and bHLH proteins. These target genes are related to pollen development and male sterility, suggesting that miRNA/targets may play roles in regulating TGMS in rice. Further, starch and sucrose metabolism pathways, sphingolipid metabolism, arginine and proline metabolism, and plant hormone signal transduction pathways were enriched by KEGG pathway annotation. These findings contribute to our understanding of the role of miRNAs during anther development and TGMS occurrence in rice.
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Affiliation(s)
- Sha Wu
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, P.R. China
| | - Hang Tan
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, P.R. China
| | - Xiaohua Hao
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, P.R. China
| | - Zijing Xie
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, P.R. China
| | - Xiaohui Wang
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, P.R. China
| | - Dongping Li
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, P.R. China
| | - Lianfu Tian
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, P.R. China
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27
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Membrane Lipid Remodeling in Response to Salinity. Int J Mol Sci 2019; 20:ijms20174264. [PMID: 31480391 PMCID: PMC6747501 DOI: 10.3390/ijms20174264] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 12/18/2022] Open
Abstract
Salinity is one of the most decisive environmental factors threatening the productivity of crop plants. Understanding the mechanisms of plant salt tolerance is critical to be able to maintain or improve crop yield under these adverse environmental conditions. Plant membranes act as biological barriers, protecting the contents of cells and organelles from biotic and abiotic stress, including salt stress. Alterations in membrane lipids in response to salinity have been observed in a number of plant species including both halophytes and glycophytes. Changes in membrane lipids can directly affect the properties of membrane proteins and activity of signaling molecules, adjusting the fluidity and permeability of membranes, and activating signal transduction pathways. In this review, we compile evidence on the salt stress responses of the major membrane lipids from different plant tissues, varieties, and species. The role of membrane lipids as signaling molecules in response to salinity is also discussed. Advances in mass spectrometry (MS)-based techniques have largely expanded our knowledge of salt-induced changes in lipids, however only a handful studies have investigated the underlying mechanisms of membrane lipidome regulation. This review provides a comprehensive overview of the recent works that have been carried out on lipid remodeling of plant membranes under salt treatment. Challenges and future perspectives in understanding the mechanisms of salt-induced changes to lipid metabolisms are proposed.
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28
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Shanmugarajah K, Linka N, Gräfe K, Smits SHJ, Weber APM, Zeier J, Schmitt L. ABCG1 contributes to suberin formation in Arabidopsis thaliana roots. Sci Rep 2019; 9:11381. [PMID: 31388073 DOI: 10.1007/978-94-007-7864-1_123-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/26/2019] [Indexed: 05/19/2023] Open
Abstract
Diffusion barriers enable plant survival under fluctuating environmental conditions. They control internal water potential and protect against biotic or abiotic stress factors. How these protective molecules are deposited to the extracellular environment is poorly understood. We here examined the role of the Arabidopsis ABC half-size transporter AtABCG1 in the formation of the extracellular root suberin layer. Quantitative analysis of extracellular long-chain fatty acids and aliphatic alcohols in the atabcg1 mutants demonstrated altered root suberin composition, specifically a reduction in longer chain dicarboxylic acids, fatty alcohols and acids. Accordingly, the ATP-hydrolyzing activity of heterologous expressed and purified AtABCG1 was strongly stimulated by fatty alcohols (C26-C30) and fatty acids (C24-C30) in a chain length dependent manner. These results are a first indication for the function of AtABCG1 in the transport of longer chain aliphatic monomers from the cytoplasm to the apoplastic space during root suberin formation.
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Affiliation(s)
- Kalpana Shanmugarajah
- Institute of Biochemistry, Heinrich-Heine University, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine University, Düsseldorf, Germany
| | - Nicole Linka
- Institute of Plant Biochemistry, Heinrich-Heine University, Düsseldorf, Germany
| | - Katharina Gräfe
- Institute of Biochemistry, Heinrich-Heine University, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine University, Düsseldorf, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich-Heine University, Düsseldorf, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Heinrich-Heine University, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine University, Düsseldorf, Germany
| | - Jürgen Zeier
- Institute for Molecular Ecophysiology of Plants, Heinrich-Heine University, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine University, Düsseldorf, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich-Heine University, Düsseldorf, Germany.
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine University, Düsseldorf, Germany.
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Fikas AA, Dilkes BP, Baxter I. Multivariate analysis reveals environmental and genetic determinants of element covariation in the maize grain ionome. PLANT DIRECT 2019; 3:e00139. [PMID: 31245778 PMCID: PMC6589523 DOI: 10.1002/pld3.139] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 02/25/2019] [Accepted: 04/02/2019] [Indexed: 05/06/2023]
Abstract
The integrated responses of biological systems to genetic and environmental variation result in substantial covariance in multiple phenotypes. The resultant pleiotropy, environmental effects, and genotype-by-environmental interactions (GxE) are foundational to our understanding of biology and genetics. Yet, the treatment of correlated characters, and the identification of the genes encoding functions that generate this covariance, has lagged. As a test case for analyzing the genetic basis underlying multiple correlated traits, we analyzed maize kernel ionomes from Intermated B73 x Mo17 (IBM) recombinant inbred populations grown in 10 environments. Plants obtain elements from the soil through genetic and biochemical pathways responsive to physiological state and environment. Most perturbations affect multiple elements which leads the ionome, the full complement of mineral nutrients in an organism, to vary as an integrated network rather than a set of distinct single elements. We compared quantitative trait loci (QTL) determining single-element variation to QTL that predict variation in principal components (PCs) of multiple-element covariance. Single-element and multivariate approaches detected partially overlapping sets of loci. QTL influencing trait covariation were detected at loci that were not found by mapping single-element traits. Moreover, this approach permitted testing environmental components of trait covariance, and identified multi-element traits that were determined by both genetic and environmental factors as well as genotype-by-environment interactions. Growth environment had a profound effect on the elemental profiles and multi-element phenotypes were significantly correlated with specific environmental variables.
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Affiliation(s)
- Alexandra Asaro Fikas
- Donald Danforth Plant Science CenterSt. LouisMissouri
- Washington University in St. LouisSt. LouisMissouri
| | - Brian P. Dilkes
- Department of BiochemistryPurdue UniversityWest LafayetteIndiana
| | - Ivan Baxter
- Donald Danforth Plant Science CenterSt. LouisMissouri
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Corbacho J, Inês C, Paredes MA, Labrador J, Cordeiro AM, Gallardo M, Gomez-Jimenez MC. Modulation of sphingolipid long-chain base composition and gene expression during early olive-fruit development, and putative role of brassinosteroid. JOURNAL OF PLANT PHYSIOLOGY 2018; 231:383-392. [PMID: 30390495 DOI: 10.1016/j.jplph.2018.10.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 10/04/2018] [Accepted: 10/18/2018] [Indexed: 05/21/2023]
Abstract
Sphingolipids are abundant membrane components and signalling molecules in various aspects of plant development. However, the role of sphingolipids in early fleshy-fruit growth has rarely been investigated. In this study, we first investigated the temporal changes in sphingolipid long-chain base (LCB) content, composition, and gene expression that occurred during flower opening and early fruit development in olive (Olea europaea L. cv Picual). Moreover, the interaction between sphingolipid and the plant hormone, brassinosteroid (BR), during the early fruit development was also explored. For this, BR levels were manipulated through the application of exogenous BRs (24-epibrassinolide, EBR) or a BR biosynthesis inhibitor (brassinazole, Brz) and their effects on early fruit development, sphingolipid LCB content, and gene expression were examined in olive fruit at 14 days post-anthesis (DPA). We here show that sphingolipid with C-4 hydroxylation and Δ8 desaturation with a preference for (E)-isomer formation are quantitatively the most important sphingolipids in olive reproductive organs. In this work, the total LCB amount significantly decreased at the anthesis stage, but olive sphingosine-1-phosphate lyase (OeSPL) gene was expressed exclusively in flower and upregulated during the anthesis, revealing an association with the d18:1(8E) accumulation. However, the LCB content increased in parallel with the upregulation of the expression of genes for key sphingolipid biosynthetic and LCB modification enzymes during early fruit development in olive. Likewise, we found that EBR exogenously applied to olive trees significantly stimulated the fruit growth rate whereas Brz inhibited fruit growth rate after 7 and 14 days of treatment. In addition, this inhibitory effect could be counteracted by the application of EBR. The promotion of early fruit growth was accompanied by the down-regulation of sphingolipid LCB content and gene expression in olive fruit, whereas Brz application raised levels of sphingolipid LCB content and gene expression in olive fruit after 7 and 14 days of treatment. Thus, our data indicate that endogenous sphingolipid LCB and gene-expression levels are intricately controlled during early fruit development and also suggest a possible link between BR, the sphingolipid content/gene expression, and early fruit development in olive.
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Affiliation(s)
- Jorge Corbacho
- Department of Plant Physiology, University of Extremadura, Avda de Elvas s/n, 06006 Badajoz, Spain
| | - Carla Inês
- Department of Plant Physiology, University of Extremadura, Avda de Elvas s/n, 06006 Badajoz, Spain
| | - Miguel A Paredes
- Department of Plant Physiology, University of Extremadura, Avda de Elvas s/n, 06006 Badajoz, Spain
| | - Juana Labrador
- Department of Plant Physiology, University of Extremadura, Avda de Elvas s/n, 06006 Badajoz, Spain
| | - Antonio M Cordeiro
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., UEIS Biotecnologia e Recursos Genéticos, Estrada de Gil Vaz, Apartado 6, 7351-901 Elvas, Portugal
| | - Mercedes Gallardo
- Department of Plant Physiology, University of Vigo, Campus Lagoas-Marcosende, s/n, 36310 Vigo, Spain
| | - Maria C Gomez-Jimenez
- Department of Plant Physiology, University of Extremadura, Avda de Elvas s/n, 06006 Badajoz, Spain.
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Schaefer RJ, Michno JM, Jeffers J, Hoekenga O, Dilkes B, Baxter I, Myers CL. Integrating Coexpression Networks with GWAS to Prioritize Causal Genes in Maize. THE PLANT CELL 2018; 30:2922-2942. [PMID: 30413654 PMCID: PMC6354270 DOI: 10.1105/tpc.18.00299] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 10/08/2018] [Accepted: 10/31/2018] [Indexed: 05/02/2023]
Abstract
Genome-wide association studies (GWAS) have identified loci linked to hundreds of traits in many different species. Yet, because linkage equilibrium implicates a broad region surrounding each identified locus, the causal genes often remain unknown. This problem is especially pronounced in nonhuman, nonmodel species, where functional annotations are sparse and there is frequently little information available for prioritizing candidate genes. We developed a computational approach, Camoco, that integrates loci identified by GWAS with functional information derived from gene coexpression networks. Using Camoco, we prioritized candidate genes from a large-scale GWAS examining the accumulation of 17 different elements in maize (Zea mays) seeds. Strikingly, we observed a strong dependence in the performance of our approach based on the type of coexpression network used: expression variation across genetically diverse individuals in a relevant tissue context (in our case, roots that are the primary elemental uptake and delivery system) outperformed other alternative networks. Two candidate genes identified by our approach were validated using mutants. Our study demonstrates that coexpression networks provide a powerful basis for prioritizing candidate causal genes from GWAS loci but suggests that the success of such strategies can highly depend on the gene expression data context. Both the software and the lessons on integrating GWAS data with coexpression networks generalize to species beyond maize.
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Affiliation(s)
- Robert J Schaefer
- Biomedical Informatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, Minnesota 55455
| | - Jean-Michel Michno
- Biomedical Informatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, Minnesota 55455
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Joseph Jeffers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Owen Hoekenga
- Cayuga Genetics Consulting Group LLC, Ithaca, New York 14850
| | - Brian Dilkes
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Ivan Baxter
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
- U.S. Department of Agriculture-Agricultural Research Service Plant Genetics Research Unit, St. Louis, Missouri 63132
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455
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32
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Misra BB, Reichman SM, Chen S. The guard cell ionome: Understanding the role of ions in guard cell functions. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 146:50-62. [PMID: 30458181 DOI: 10.1016/j.pbiomolbio.2018.11.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/01/2018] [Accepted: 11/16/2018] [Indexed: 12/20/2022]
Abstract
The ionome is critical for plant growth, productivity, defense, and it eventually affects human food quantity and quality. Located on the leaf surface, stomatal guard cells are critical gatekeepers for water, gas, and pathogens. Insights form ionomics (metallomics) is imperative as we enter an omics-driven systems biology era where an understanding of guard cell function and physiology is advanced through efforts in genomics, transcriptomics, proteomics, and metabolomics. While the roles of major cations (K, Ca) and anions (Cl) are well known in guard cell function, the related physiology, movement and regulation of trace elements, metal ions, and heavy metals are poorly understood. The majority of the information on the role of trace elements in guard cells emanates from classical feeding experiments, field or in vitro fortification, micropropagation, and microscopy studies, while novel insights are available from limited metal ion transporter and ion channel studies. Given the rejuvenated and recent interest in the constantly changing ionome in plant mineral balance and eventually in human nutrition and health, we looked into the far from established guard cell ionome in lieu of the modern omics era of high throughput research endeavors. Newer technologies and tools i.e., high resolution mass spectrometry, advanced imaging, and phenomics are now available to delve into the guard cell ionomes. In this review, research efforts on guard cell ionomes were collated and categorized, and we highlight the underlying role of the largely unknown ionome in guard cell function towards a systems physiology understanding of plant health and productivity.
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Affiliation(s)
- Biswapriya B Misra
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston Salem, 27157, NC, USA; Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, 32610, USA.
| | - Suzie M Reichman
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, 3001, Australia; Centre for Environmental Sustainability and Remediation, RMIT University, GPO Box 2476, Melbourne, 3001, Australia
| | - Sixue Chen
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, 32610, USA; Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, 32610, USA
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Ali U, Li H, Wang X, Guo L. Emerging Roles of Sphingolipid Signaling in Plant Response to Biotic and Abiotic Stresses. MOLECULAR PLANT 2018; 11:1328-1343. [PMID: 30336328 DOI: 10.1016/j.molp.2018.10.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/04/2018] [Accepted: 10/09/2018] [Indexed: 05/12/2023]
Abstract
Plant sphingolipids are not only structural components of the plasma membrane and other endomembrane systems but also act as signaling molecules during biotic and abiotic stresses. However, the roles of sphingolipids in plant signal transduction in response to environmental cues are yet to be investigated in detail. In this review, we discuss the signaling roles of sphingolipid metabolites with a focus on plant sphingolipids. We also mention some microbial sphingolipids that initiate signals during their interaction with plants, because of the limited literatures on their plant analogs. The equilibrium of nonphosphorylated and phosphorylated sphingolipid species determine the destiny of plant cells, whereas molecular connections among the enzymes responsible for this equilibrium in a coordinated signaling network are poorly understood. A mechanistic link between the phytohormone-sphingolipid interplay has also not yet been fully understood and many key participants involved in this complex interaction operating under stress conditions await to be identified. Future research is needed to fill these gaps and to better understand the signal pathways of plant sphingolipids and their interplay with other signals in response to environmental stresses.
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Affiliation(s)
- Usman Ali
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Hehuan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuemin Wang
- Department of Biology, University of Missouri, St. Louis, MO 63121, USA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
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Harrison PJ, Dunn T, Campopiano DJ. Sphingolipid biosynthesis in man and microbes. Nat Prod Rep 2018; 35:921-954. [PMID: 29863195 PMCID: PMC6148460 DOI: 10.1039/c8np00019k] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Indexed: 12/20/2022]
Abstract
A new review covering up to 2018 Sphingolipids are essential molecules that, despite their long history, are still stimulating interest today. The reasons for this are that, as well as playing structural roles within cell membranes, they have also been shown to perform a myriad of cell signalling functions vital to the correct function of eukaryotic and prokaryotic organisms. Indeed, sphingolipid disregulation that alters the tightly-controlled balance of these key lipids has been closely linked to a number of diseases such as diabetes, asthma and various neuropathologies. Sphingolipid biogenesis, metabolism and regulation is mediated by a large number of enzymes, proteins and second messengers. There appears to be a core pathway common to all sphingolipid-producing organisms but recent studies have begun to dissect out important, species-specific differences. Many of these have only recently been discovered and in most cases the molecular and biochemical details are only beginning to emerge. Where there is a direct link from classic biochemistry to clinical symptoms, a number a drug companies have undertaken a medicinal chemistry campaign to try to deliver a therapeutic intervention to alleviate a number of diseases. Where appropriate, we highlight targets where natural products have been exploited as useful tools. Taking all these aspects into account this review covers the structural, mechanistic and regulatory features of sphingolipid biosynthetic and metabolic enzymes.
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Affiliation(s)
- Peter J. Harrison
- School of Chemistry
, University of Edinburgh
,
David Brewster Road
, Edinburgh
, EH9 3FJ
, UK
.
| | - Teresa M. Dunn
- Department of Biochemistry and Molecular Biology
, Uniformed Services University
,
Bethesda
, Maryland
20814
, USA
| | - Dominic J. Campopiano
- School of Chemistry
, University of Edinburgh
,
David Brewster Road
, Edinburgh
, EH9 3FJ
, UK
.
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35
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Marquês JT, Marinho HS, de Almeida RF. Sphingolipid hydroxylation in mammals, yeast and plants – An integrated view. Prog Lipid Res 2018; 71:18-42. [DOI: 10.1016/j.plipres.2018.05.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/11/2018] [Accepted: 05/04/2018] [Indexed: 02/07/2023]
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Ziegler G, Nelson R, Granada S, Krishnan HB, Gillman JD, Baxter I. Genomewide association study of ionomic traits on diverse soybean populations from germplasm collections. PLANT DIRECT 2018; 2:e00033. [PMID: 31245681 PMCID: PMC6508489 DOI: 10.1002/pld3.33] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/06/2017] [Accepted: 11/14/2017] [Indexed: 05/17/2023]
Abstract
The elemental content of a soybean seed is a determined by both genetic and environmental factors and is an important component of its nutritional value. The elemental content is chemically stable, making the samples stored in germplasm repositories an intriguing source of experimental material. To test the efficacy of using samples from germplasm banks for gene discovery, we analyzed the elemental profile of seeds from 1,653 lines in the USDA Soybean Germplasm Collection. We observed large differences in the elemental profiles based on where the lines were grown, which lead us to break up the genetic analysis into multiple small experiments. Despite these challenges, we were able to identify candidate single nucleotide polymorphisms (SNPs) controlling elemental accumulation as well as lines with extreme elemental accumulation phenotypes. Our results suggest that elemental analysis of germplasm samples can identify SNPs in linkage disequilibrium to genes, which can be leveraged to assist in crop improvement efforts.
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Affiliation(s)
- Greg Ziegler
- USDA‐ARS Plant Genetics Research UnitSt. LouisMOUSA
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | - Randall Nelson
- Soybean/Maize Germplasm, Pathology and Genetics Research Unit and Department of Crop SciencesUSDA‐ARSUniversity of IllinoisUrbanaILUSA
| | | | - Hari B. Krishnan
- USDA‐ARS Plant Genetics Research UnitColumbiaMOUSA
- Plant Science DivisionUniversity of MissouriColumbiaMOUSA
| | - Jason D. Gillman
- USDA‐ARS Plant Genetics Research UnitColumbiaMOUSA
- Plant Science DivisionUniversity of MissouriColumbiaMOUSA
| | - Ivan Baxter
- USDA‐ARS Plant Genetics Research UnitSt. LouisMOUSA
- Donald Danforth Plant Science CenterSt. LouisMOUSA
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Tan S, Zhang P, Xiao W, Feng B, Chen LY, Li S, Li P, Zhao WZ, Qi XT, Yin LP. TMD1 domain and CRAC motif determine the association and disassociation of MxIRT1 with detergent-resistant membranes. Traffic 2017; 19:122-137. [PMID: 29112302 DOI: 10.1111/tra.12540] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 11/01/2017] [Accepted: 11/01/2017] [Indexed: 12/23/2022]
Abstract
Iron is essential for most living organisms. The iron-regulated transporter1 (IRT1) plays a major role in iron uptake in roots, and its trafficking from endoplasmic reticulum (ER) to plasma membrane (PM) is tightly coordinated with changes in iron environment. However, studies on the IRT1 response are limited. Here, we report that Malus xiaojinesis IRT1 (MxIRT1) associates with detergent-resistant membranes (DRMs, a biochemical counterpart of PM microdomains), whereas the PM microdomains are known platforms for signal transduction in the PM. Depending on the shift of MxIRT1 from microdomains to homogeneous regions in PM, MxIRT1-mediated iron absorption is activated by the cholesterol recognition/interaction amino acid consensus (CRAC) motif of MxIRT1. MxIRT1 initially associates with DRMs in ER via its transmembrane domain 1 (TMD1), and thus begins DRMs-dependent intracellular trafficking. Subsequently, MxIRT1 is sequestered in COPII vesicles via the ER export signal sequence in MxIRT1. These studies suggest that iron homeostasis is influenced by the CRAC motif and TMD1 domain due to their determination of MxIRT1-DRMs association.
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Affiliation(s)
- Song Tan
- College of Life Science, Capital Normal University, Beijing, China
| | - Peng Zhang
- College of Life Science, Capital Normal University, Beijing, China.,State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wei Xiao
- College of Life Science, Capital Normal University, Beijing, China.,Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Bing Feng
- College of Life Science, Capital Normal University, Beijing, China
| | - Lan-You Chen
- College of Life Science, Capital Normal University, Beijing, China
| | - Shuang Li
- College of Life Science, Capital Normal University, Beijing, China
| | - Peng Li
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Wei-Zhong Zhao
- School of Mathematical Sciences, Capital Normal University, Beijing, China
| | - Xiao-Ting Qi
- College of Life Science, Capital Normal University, Beijing, China
| | - Li-Ping Yin
- College of Life Science, Capital Normal University, Beijing, China
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Hindt MN, Akmakjian GZ, Pivarski KL, Punshon T, Baxter I, Salt DE, Guerinot ML. BRUTUS and its paralogs, BTS LIKE1 and BTS LIKE2, encode important negative regulators of the iron deficiency response in Arabidopsis thaliana. Metallomics 2017; 9:876-890. [PMID: 28620661 PMCID: PMC5558852 DOI: 10.1039/c7mt00152e] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Iron (Fe) is required for plant health, but it can also be toxic when present in excess. Therefore, Fe levels must be tightly controlled. The Arabidopsis thaliana E3 ligase BRUTUS (BTS) is involved in the negative regulation of the Fe deficiency response and we show here that the two A. thaliana BTS paralogs, BTS LIKE1 (BTSL1) and BTS LIKE2 (BTSL2) encode proteins that act redundantly as negative regulators of the Fe deficiency response. Loss of both of these E3 ligases enhances tolerance to Fe deficiency. We further generated a triple mutant with loss of both BTS paralogs and a partial loss of BTS expression that exhibits even greater tolerance to Fe-deficient conditions and increased Fe accumulation without any resulting Fe toxicity effects. Finally, we identified a mutant carrying a novel missense mutation of BTS that exhibits an Fe deficiency response in the root when grown under both Fe-deficient and Fe-sufficient conditions, leading to Fe toxicity when plants are grown under Fe-sufficient conditions.
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Affiliation(s)
- Maria N Hindt
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA.
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Yanagawa D, Ishikawa T, Imai H. Synthesis and degradation of long-chain base phosphates affect fumonisin B 1-induced cell death in Arabidopsis thaliana. JOURNAL OF PLANT RESEARCH 2017; 130:571-585. [PMID: 28303405 DOI: 10.1007/s10265-017-0923-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/07/2016] [Indexed: 05/12/2023]
Abstract
Fumonisin B1 (FB1), an inducer of cell death, disrupts sphingolipid metabolism; large accumulations of de novo synthesized free long-chain bases (LCBs) are observed. However, it remains unclear whether tolerance to FB1 toxicity in plants is connected with preventing the accumulation of free LCBs through their phosphorylation. Here a workflow for the extraction, detection and quantification of LCB phosphates (LCBPs) in Arabidopsis thaliana was developed. We studied the effect of expression of genes for three enzymes involved in the synthesis and degradation of LCBPs, LCB kinase (LCBK1), LCBP phosphatase (SPP1) and lyase (DPL1) on FB1-induced cell death. As expected, large accumulations of saturated free LCBs, dihydrosphingosine and phytosphingosine, were observed in the FB1-treated leaves. On the other hand, a high level of sphingenine phosphate was found in the FB1-treated leaves even though free sphingenine was found in low amounts in these leaves. In comparison of WT and spp1 plants, the LCBP/LCB ratio is likely to be correlated with the degree of FB1-induced cell death determined by trypan blue staining. The FB1-treated leaves in dpl1 plants showed severe cell death and the elevation of free LCBs and LCBPs. LCBK1-OX and -KD plants showed resistance and sensitivity to FB1, respectively, whereas free LCB and LCBP levels in FB1-treated LCBK1-OX and -KD plants were moderately different to those in FB1-treated WT plants. Overall, the findings described here suggest that LCBP/LCB homeostasis is an important topic that participates in the tolerance of plant cells to FB1.
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Affiliation(s)
- Daiki Yanagawa
- Department of Biology, Graduate School of Natural Science, Konan University, Kobe, 658-8501, Japan
- The Institute for Integrative Neurobiology, Konan University, Kobe, 658-8501, Japan
| | - Toshiki Ishikawa
- Graduate School of Science and Engineering, Saitama University, Saitama, 338-8570, Japan
| | - Hiroyuki Imai
- Department of Biology, Graduate School of Natural Science, Konan University, Kobe, 658-8501, Japan.
- The Institute for Integrative Neurobiology, Konan University, Kobe, 658-8501, Japan.
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Lin Z, Zhang X, Wang Z, Jiang Y, Liu Z, Alexander D, Li G, Wang S, Ding Y. Metabolomic analysis of pathways related to rice grain chalkiness by a notched-belly mutant with high occurrence of white-belly grains. BMC PLANT BIOLOGY 2017; 17:39. [PMID: 28166731 PMCID: PMC5294873 DOI: 10.1186/s12870-017-0985-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 01/25/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Grain chalkiness is a highly undesirable trait deleterious to rice appearance and milling quality. The physiological and molecular foundation of chalkiness formation is still partially understood, because of the complex interactions between multiple genes and growing environments. RESULTS We report the untargeted metabolomic analysis of grains from a notched-belly mutant (DY1102) with high percentage of white-belly, which predominantly occurs in the bottom part proximal to the embryo. Metabolites in developing grains were profiled on the composite platforms of UPLC/MS/MS and GC/MS. Sampling times were 5, 10, 15, and 20 days after anthesis, the critical time points for chalkiness formation. A total of 214 metabolites were identified, covering most of the central metabolic pathways and partial secondary pathways including amino acids, carbohydrates, lipids, cofactors, peptides, nucleotides, phytohormones, and secondary metabolites. A comparison of the bottom chalky part and the upper translucent part of developing grains of DY1102 resulted in 180 metabolites related to chalkiness formation. CONCLUSIONS Generally, in comparison to the translucent upper part, the chalky endosperm had lower levels of metabolites regarding carbon and nitrogen metabolism for synthesis of storage starch and protein, which was accompanied by perturbation of pathways participating in scavenging of reactive oxygen species, osmorugulation, cell wall synthesis, and mineral ion homeostasis. Based on these results, metabolic mechanism of chalkiness formation is discussed, with the role of embryo highlighted.
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Affiliation(s)
- Zhaomiao Lin
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350013 People’s Republic of China
| | - Xincheng Zhang
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
| | - Zunxin Wang
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
| | - Yutong Jiang
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
| | - Zhenghui Liu
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095 People’s Republic of China
| | | | - Ganghua Li
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
| | - Shaohua Wang
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
| | - Yanfeng Ding
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
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Tartaglio V, Rennie EA, Cahoon R, Wang G, Baidoo E, Mortimer JC, Cahoon EB, Scheller HV. Glycosylation of inositol phosphorylceramide sphingolipids is required for normal growth and reproduction in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:278-290. [PMID: 27643972 DOI: 10.1111/tpj.13382] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/10/2016] [Accepted: 09/12/2016] [Indexed: 05/05/2023]
Abstract
Sphingolipids are a major component of plant plasma membranes and endomembranes, and mediate a diverse range of biological processes. Study of the highly glycosylated glycosyl inositol phosphorylceramide (GIPC) sphingolipids has been slow as a result of challenges associated with the extractability of GIPCs, and their functions in the plant remain poorly characterized. We recently discovered an Arabidopsis GIPC glucuronosyltransferase, INOSITOL PHOSPHORYLCERAMIDE GLUCURONOSYLTRANSFERASE 1 (IPUT1), which is the first enzyme in the GIPC glycosylation pathway. Plants homozygous for the iput1 loss-of-function mutation were unobtainable, and so the developmental effects of reduced GIPC glucuronosylation could not be analyzed in planta. Using a pollen-specific rescue construct, we have here isolated homozygous iput1 mutants. The iput1 mutants show severe dwarfism, compromised pollen tube guidance, and constitutive activation of salicyclic acid-mediated defense pathways. The mutants also possess reduced GIPCs, increased ceramides, and an increased incorporation of short-chain fatty acids and dihydroxylated bases into inositol phosphorylceramides and GIPCs. The assignment of a direct role for GIPC glycan head groups in the impaired processes in iput1 mutants is complicated by the vast compensatory changes in the sphingolipidome; however, our results reveal that the glycosylation steps of GIPC biosynthesis are important regulated components of sphingolipid metabolism. This study corroborates previously suggested roles for GIPC glycans in plant growth and defense, suggests important roles for them in reproduction and demonstrates that the entire sphingolipidome is sensitive to their status.
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Affiliation(s)
- Virginia Tartaglio
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Emilie A Rennie
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Rebecca Cahoon
- Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - George Wang
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Edward Baidoo
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jennifer C Mortimer
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Edgar B Cahoon
- Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Henrik V Scheller
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
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Begum MA, Shi XX, Tan Y, Zhou WW, Hannun Y, Obeid L, Mao C, Zhu ZR. Molecular Characterization of Rice OsLCB2a1 Gene and Functional Analysis of its Role in Insect Resistance. FRONTIERS IN PLANT SCIENCE 2016; 7:1789. [PMID: 27990147 PMCID: PMC5130998 DOI: 10.3389/fpls.2016.01789] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/14/2016] [Indexed: 05/22/2023]
Abstract
In plants, sphingolipids, such as long-chain bases (LCBs), act as bioactive molecules in stress responses. Until now, it is still not clear if these lipids are involved in biotic stress responses to herbivore. Herein we report that a rice LCB gene, OsLCB2a1 encoding a subunit of serine palmitoyltransferase (SPT), a key enzyme responsible for the de novo biosynthesis of sphingolipids, plays a critical role in plant defense response to the brown planthopper (BPH) attack and that its up-regulation protects plants from herbivore infestation. Transcripts of OsLCB2a1 gene in rice seedlings were increased at 4 h, but decreased at 8-24 h after BPH attack. Sphingolipid measurement profiling revealed that overexpression of OsLCB2a1 in Arabidopsis thaliana increased trihydroxylated LCB phytosphingosine (t18:0) and phytoceramide by 1.7 and 1.3-fold, respectively, compared with that of wild type (WT) plants. Transgenic Arabidopsis plants also showed higher callose and wax deposition in leaves than that of WT. Overexpression of OsLCB2a1 gene in A. thaliana reduced the population size of green peach aphid (Myzus persicae). Moreover, the electrical penetration graph (EPG) results indicated that the aphids encounter resistance factors while reaching for the phloem on the transgenic plants. The defense response genes related to salicylic acid signaling pathway, remained uplgulated in the OsLCB2a1-overexpressing transgenic plants. Our data highlight the key functions of OsLCB2a1 in biotic stress response in plants.
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Affiliation(s)
- Mahfuj A. Begum
- State Key Laboratory of Rice Biology, Key Laboratory of Agricultural Entomology, Ministry of Agriculture and Institute of Insect Sciences, Zhejiang UniversityHangzhou, China
| | - Xiao-Xiao Shi
- State Key Laboratory of Rice Biology, Key Laboratory of Agricultural Entomology, Ministry of Agriculture and Institute of Insect Sciences, Zhejiang UniversityHangzhou, China
| | - Ye Tan
- State Key Laboratory of Rice Biology, Key Laboratory of Agricultural Entomology, Ministry of Agriculture and Institute of Insect Sciences, Zhejiang UniversityHangzhou, China
| | - Wen-Wu Zhou
- State Key Laboratory of Rice Biology, Key Laboratory of Agricultural Entomology, Ministry of Agriculture and Institute of Insect Sciences, Zhejiang UniversityHangzhou, China
| | - Yusuf Hannun
- Stony Brook Cancer Center, Department of Medicine, The State University of New York at Stony BrookNew York, NY, USA
| | - Lina Obeid
- Stony Brook Cancer Center, Department of Medicine, The State University of New York at Stony BrookNew York, NY, USA
| | - Cungui Mao
- Stony Brook Cancer Center, Department of Medicine, The State University of New York at Stony BrookNew York, NY, USA
| | - Zeng-Rong Zhu
- State Key Laboratory of Rice Biology, Key Laboratory of Agricultural Entomology, Ministry of Agriculture and Institute of Insect Sciences, Zhejiang UniversityHangzhou, China
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Thomas CL, Alcock TD, Graham NS, Hayden R, Matterson S, Wilson L, Young SD, Dupuy LX, White PJ, Hammond JP, Danku JMC, Salt DE, Sweeney A, Bancroft I, Broadley MR. Root morphology and seed and leaf ionomic traits in a Brassica napus L. diversity panel show wide phenotypic variation and are characteristic of crop habit. BMC PLANT BIOLOGY 2016; 16:214. [PMID: 27716103 PMCID: PMC5050600 DOI: 10.1186/s12870-016-0902-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 09/25/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Mineral nutrient uptake and utilisation by plants are controlled by many traits relating to root morphology, ion transport, sequestration and translocation. The aims of this study were to determine the phenotypic diversity in root morphology and leaf and seed mineral composition of a polyploid crop species, Brassica napus L., and how these traits relate to crop habit. Traits were quantified in a diversity panel of up to 387 genotypes: 163 winter, 127 spring, and seven semiwinter oilseed rape (OSR) habits, 35 swede, 15 winter fodder, and 40 exotic/unspecified habits. Root traits of 14 d old seedlings were measured in a 'pouch and wick' system (n = ~24 replicates per genotype). The mineral composition of 3-6 rosette-stage leaves, and mature seeds, was determined on compost-grown plants from a designed experiment (n = 5) by inductively coupled plasma-mass spectrometry (ICP-MS). RESULTS Seed size explained a large proportion of the variation in root length. Winter OSR and fodder habits had longer primary and lateral roots than spring OSR habits, with generally lower mineral concentrations. A comparison of the ratios of elements in leaf and seed parts revealed differences in translocation processes between crop habits, including those likely to be associated with crop-selection for OSR seeds with lower sulphur-containing glucosinolates. Combining root, leaf and seed traits in a discriminant analysis provided the most accurate characterisation of crop habit, illustrating the interdependence of plant tissues. CONCLUSIONS High-throughput morphological and composition phenotyping reveals complex interrelationships between mineral acquisition and accumulation linked to genetic control within and between crop types (habits) in B. napus. Despite its recent genetic ancestry (<10 ky), root morphology, and leaf and seed composition traits could potentially be used in crop improvement, if suitable markers can be identified and if these correspond with suitable agronomy and quality traits.
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Affiliation(s)
- C. L. Thomas
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
| | - T. D. Alcock
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - N. S. Graham
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - R. Hayden
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - S. Matterson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - L. Wilson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - S. D. Young
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - L. X. Dupuy
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
| | - P. J. White
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
- Distinguished Scientist Fellowship Program, King Saud University, Riyadh, 11451 Kingdom of Saudi Arabia
| | - J. P. Hammond
- School of Agriculture, Policy and Development and the Centre for Food Security, University of Reading, Whiteknights, PO Box 237, Reading, RG6 6AR UK
| | - J. M. C. Danku
- University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UU UK
| | - D. E. Salt
- University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UU UK
| | - A. Sweeney
- Department of Biology, University of York, Heslington, York, YO10 5DD UK
| | - I. Bancroft
- Department of Biology, University of York, Heslington, York, YO10 5DD UK
| | - M. R. Broadley
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
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44
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Huang XY, Chao DY, Koprivova A, Danku J, Wirtz M, Müller S, Sandoval FJ, Bauwe H, Roje S, Dilkes B, Hell R, Kopriva S, Salt DE. Nuclear Localised MORE SULPHUR ACCUMULATION1 Epigenetically Regulates Sulphur Homeostasis in Arabidopsis thaliana. PLoS Genet 2016; 12:e1006298. [PMID: 27622452 PMCID: PMC5021336 DOI: 10.1371/journal.pgen.1006298] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 08/12/2016] [Indexed: 12/25/2022] Open
Abstract
Sulphur (S) is an essential element for all living organisms. The uptake, assimilation and metabolism of S in plants are well studied. However, the regulation of S homeostasis remains largely unknown. Here, we report on the identification and characterisation of the more sulphur accumulation1 (msa1-1) mutant. The MSA1 protein is localized to the nucleus and is required for both S-adenosylmethionine (SAM) production and DNA methylation. Loss of function of the nuclear localised MSA1 leads to a reduction in SAM in roots and a strong S-deficiency response even at ample S supply, causing an over-accumulation of sulphate, sulphite, cysteine and glutathione. Supplementation with SAM suppresses this high S phenotype. Furthermore, mutation of MSA1 affects genome-wide DNA methylation, including the methylation of S-deficiency responsive genes. Elevated S accumulation in msa1-1 requires the increased expression of the sulphate transporter genes SULTR1;1 and SULTR1;2 which are also differentially methylated in msa1-1. Our results suggest a novel function for MSA1 in the nucleus in regulating SAM biosynthesis and maintaining S homeostasis epigenetically via DNA methylation. Sulphur is an essential element for all living organisms including plants. Plants take up sulphur from the soil mainly in the form of inorganic sulphate. The uptake of sulphate and assimilation of sulphur have been well studied. However, the regulation of sulphur accumulation in plants remains largely unknown. In this study, we characterize the high leaf sulphur mutant more sulphur accumulation1 (msa1-1) and demonstrate the function of MSA1 in controlling sulphur accumulation in Arabidopsis thaliana. The MSA1 protein is localized to the nucleus and is required for the biosynthesis of S-adenosylmethionine (SAM) which is a universal methyl donor for many methylation reactions, including DNA methylation. Loss of function of MSA1 reduces the SAM level in roots and affects genome-wide DNA methylation, including the methylation of sulphate transporter genes. We show that the high sulphur phenotype of msa1-1 requires elevated expression of the sulphate transporter genes which are differentially methylated in msa1-1. Our results suggest a connection between sulphur homeostasis and DNA methylation that is mediated by MSA1.
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Affiliation(s)
- Xin-Yuan Huang
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Dai-Yin Chao
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Anna Koprivova
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - John Danku
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Markus Wirtz
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Steffen Müller
- Department of Plant Physiology, University of Rostock, Rostock, Germany
| | - Francisco J. Sandoval
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, United States of America
| | - Hermann Bauwe
- Department of Plant Physiology, University of Rostock, Rostock, Germany
| | - Sanja Roje
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, United States of America
| | - Brian Dilkes
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, United States of America
| | - Rüdiger Hell
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Stanislav Kopriva
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - David E Salt
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
- * E-mail:
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45
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Watanabe T, Maejima E, Yoshimura T, Urayama M, Yamauchi A, Owadano M, Okada R, Osaki M, Kanayama Y, Shinano T. The Ionomic Study of Vegetable Crops. PLoS One 2016; 11:e0160273. [PMID: 27478901 PMCID: PMC4968822 DOI: 10.1371/journal.pone.0160273] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 07/15/2016] [Indexed: 02/03/2023] Open
Abstract
Soil contains various essential and nonessential elements, all of which can be absorbed by plants. Plant ionomics is the study of the accumulation of these elements (the ionome) in plants. The ionomic profile of a plant is affected by various factors, including species, variety, organ, and environment. In this study, we cultivated various vegetable crop species and cultivars under the same field conditions and analyzed the level of accumulation of each element in the edible and nonedible parts using ionomic techniques. The concentration of each element in the edible parts differed between species, which could be partly explained by differences in the types of edible organs (root, leaf, seed, and fruit). For example, the calcium concentration was lower in seeds and fruit than in other organs because of the higher dependency of calcium accumulation on xylem transfer. The concentration of several essential microelements and nonessential elements in the edible parts also varied greatly between cultivars of the same species, knowledge of which will help in the breeding of vegetables that are biofortified or contain lower concentrations of toxic elements. Comparison of the ionomes of the fruit and leaves of tomato (Solanum lycopersicum) and eggplant (S. melongena) indicated that cadmium and boron had higher levels of accumulation in eggplant fruit, likely because of their effective transport in the phloem. We also found that homologous elements that have been reported to share the same uptake/transport system often showed significant correlation only in a few families and that the slopes of these relationships differed between families. Therefore, these differences in the characteristics of mineral accumulation are likely to affect the ionomic profiles of different families.
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Affiliation(s)
- Toshihiro Watanabe
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kitaku, Sapporo, 0608589, Japan
- * E-mail:
| | - Eriko Maejima
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kitaku, Sapporo, 0608589, Japan
| | - Tomoko Yoshimura
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kitaku, Sapporo, 0608589, Japan
| | - Masaru Urayama
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kitaku, Sapporo, 0608589, Japan
| | - Aiko Yamauchi
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kitaku, Sapporo, 0608589, Japan
| | - Masako Owadano
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kitaku, Sapporo, 0608589, Japan
| | - Ryosuke Okada
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kitaku, Sapporo, 0608589, Japan
| | - Mitsuru Osaki
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kitaku, Sapporo, 0608589, Japan
| | - Yoshinori Kanayama
- Graduate School of Agricultural Science, Tohoku University, Sendai, 9818555, Japan
| | - Takuro Shinano
- Agricultural Radiation Research Center, NARO Tohoku Agricultural Research Center, 50 Aza Harajyukuminami, Arai, Fukushima, 9602156, Japan
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46
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Huang XY, Salt DE. Plant Ionomics: From Elemental Profiling to Environmental Adaptation. MOLECULAR PLANT 2016; 9:787-97. [PMID: 27212388 DOI: 10.1016/j.molp.2016.05.003] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 05/12/2016] [Accepted: 05/16/2016] [Indexed: 05/03/2023]
Abstract
Ionomics is a high-throughput elemental profiling approach to study the molecular mechanistic basis underlying mineral nutrient and trace element composition (also known as the ionome) of living organisms. Since the concept of ionomics was first introduced more than 10 years ago, significant progress has been made in the identification of genes and gene networks that control the ionome. In this update, we summarize the progress made in using the ionomics approach over the last decade, including the identification of genes by forward genetics and the study of natural ionomic variation. We further discuss the potential application of ionomics to the investigation of the ecological functions of ionomic alleles in adaptation to the environment.
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Affiliation(s)
- Xin-Yuan Huang
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen AB24 3UU, UK
| | - David E Salt
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen AB24 3UU, UK.
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47
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Ziv C, Malitsky S, Othman A, Ben-Dor S, Wei Y, Zheng S, Aharoni A, Hornemann T, Vardi A. Viral serine palmitoyltransferase induces metabolic switch in sphingolipid biosynthesis and is required for infection of a marine alga. Proc Natl Acad Sci U S A 2016; 113:E1907-16. [PMID: 26984500 PMCID: PMC4822627 DOI: 10.1073/pnas.1523168113] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Marine viruses are the most abundant biological entities in the oceans shaping community structure and nutrient cycling. The interaction between the bloom-forming alga Emiliania huxleyi and its specific large dsDNA virus (EhV) is a major factor determining the fate of carbon in the ocean, thus serving as a key host-pathogen model system. The EhV genome encodes for a set of genes involved in the de novo sphingolipid biosynthesis, not reported in any viral genome to date. We combined detailed lipidomic and biochemical analyses to characterize the functional role of this virus-encoded pathway during lytic viral infection. We identified a major metabolic shift, mediated by differential substrate specificity of virus-encoded serine palmitoyltransferase, a key enzyme of sphingolipid biosynthesis. Consequently, unique viral glycosphingolipids, composed of unusual hydroxylated C17 sphingoid bases (t17:0) were highly enriched in the infected cells, and their synthesis was found to be essential for viral assembly. These findings uncover the biochemical bases of the virus-induced metabolic rewiring of the host sphingolipid biosynthesis during the chemical "arms race" in the ocean.
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Affiliation(s)
- Carmit Ziv
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sergey Malitsky
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alaa Othman
- Institute for Clinical Chemistry, University Hospital Zurich, 8091 Zurich, Switzerland; Institute of Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, 23562 Lübeck, Germany
| | - Shifra Ben-Dor
- Biological Services Unit, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yu Wei
- Institute for Clinical Chemistry, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Shuning Zheng
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Thorsten Hornemann
- Institute for Clinical Chemistry, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel;
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48
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Plett D, Baumann U, Schreiber AW, Holtham L, Kalashyan E, Toubia J, Nau J, Beatty M, Rafalski A, Dhugga KS, Tester M, Garnett T, Kaiser BN. Maize maintains growth in response to decreased nitrate supply through a highly dynamic and developmental stage-specific transcriptional response. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:342-53. [PMID: 26038196 DOI: 10.1111/pbi.12388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 03/18/2015] [Accepted: 03/24/2015] [Indexed: 05/10/2023]
Abstract
Elucidation of the gene networks underlying the response to N supply and demand will facilitate the improvement of the N uptake efficiency of plants. We undertook a transcriptomic analysis of maize to identify genes responding to both a non-growth-limiting decrease in NO3- provision and to development-based N demand changes at seven representative points across the life cycle. Gene co-expression networks were derived by cluster analysis of the transcript profiles. The majority of NO3--responsive transcription occurred at 11 (D11), 18 (D18) and 29 (D29) days after emergence, with differential expression predominating in the root at D11 and D29 and in the leaf at D18. A cluster of 98 probe sets was identified, the expression pattern of which is similar to that of the high-affinity NO3- transporter (NRT2) genes across the life cycle. The cluster is enriched with genes encoding enzymes and proteins of lipid metabolism and transport, respectively. These are candidate genes for the response of maize to N supply and demand. Only a few patterns of differential gene expression were observed over the entire life cycle; however, the composition of the classes of the genes differentially regulated at individual time points was unique, suggesting tightly controlled regulation of NO3--responsive gene expression.
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Affiliation(s)
- Darren Plett
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Ute Baumann
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Andreas W Schreiber
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Luke Holtham
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Elena Kalashyan
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - John Toubia
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - John Nau
- DuPont Pioneer, Johnston, IA, USA
| | | | | | | | - Mark Tester
- Division of Biological and Environmental Sciences and Engineering, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Trevor Garnett
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Brent N Kaiser
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
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49
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Abstract
Sphingolipids, a once overlooked class of lipids in plants, are now recognized as abundant and essential components of plasma membrane and other endomembranes of plant cells. In addition to providing structural integrity to plant membranes, sphingolipids contribute to Golgi trafficking and protein organizational domains in the plasma membrane. Sphingolipid metabolites have also been linked to the regulation of cellular processes, including programmed cell death. Advances in mass spectrometry-based sphingolipid profiling and analyses of Arabidopsis mutants have enabled fundamental discoveries in sphingolipid structural diversity, metabolism, and function that are reviewed here. These discoveries are laying the groundwork for the tailoring of sphingolipid biosynthesis and catabolism for improved tolerance of plants to biotic and abiotic stresses.
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Affiliation(s)
- Kyle D Luttgeharm
- Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska-Lincoln, E318 Beadle Center, 1901 Vine Street, Lincoln, NE, 68588, USA
| | - Athen N Kimberlin
- Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska-Lincoln, E318 Beadle Center, 1901 Vine Street, Lincoln, NE, 68588, USA
| | - Edgar B Cahoon
- Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska-Lincoln, E318 Beadle Center, 1901 Vine Street, Lincoln, NE, 68588, USA.
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50
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Watanabe T, Urayama M, Shinano T, Okada R, Osaki M. Application of ionomics to plant and soil in fields under long-term fertilizer trials. SPRINGERPLUS 2015; 4:781. [PMID: 26702370 PMCID: PMC4684559 DOI: 10.1186/s40064-015-1562-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/25/2015] [Indexed: 11/23/2022]
Abstract
Ionomics is the study of elemental accumulation in living organisms using high-throughput elemental profiling. In the present study, we examined the ionomic responses to nutrient deficiency in maize grown in the field in long-term fertilizer trials. Furthermore, the available elements in the field soils were analyzed to investigate their changes under long-term fertilizer treatment and the ionomic relationships between plant and soil. Maize was cultivated in a field with the following five long-term fertilizer treatments: complete fertilization, fertilization without nitrogen, without phosphorus, without potassium, and no fertilization. Concentrations of 22 elements in leaves at an early flowering stage and in soils after harvest were determined. The fertilizer treatments changed the availabilities of many elements in soils. For example, available cesium was decreased by 39 % and increased by 126 % by fertilizations without nitrogen and potassium, respectively. Effects of treatments on the ionome in leaves were evaluated using the translocation ratio (the concentration in leaves relative to the available concentration in soils) for each element. Nitrogen deficiency specifically increased the uptake ability of molybdenum, which
might induce the enhancement of nitrogen assimilation and/or endophytic nitrogen fixation in plant. Potassium deficiency drastically enhanced the uptake ability of various cationic elements. These elements might act as alternatives to K in osmoregulation and counterion of organic/inorganic anions. Two major groups of elements were detected by multivariate analyses of plant ionome. Elements in the same group may be linked more or less in uptake and/or translocation systems. No significant correlation between plant and soil was found in concentrations of many elements, even though various soil extraction methods were applied, implying that the interactions between the target and other elements in soil must be considered when analyzing mineral dynamics between plant and soil.
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Affiliation(s)
- Toshihiro Watanabe
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kitaku, Sapporo, 0608589 Japan
| | - Masaru Urayama
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kitaku, Sapporo, 0608589 Japan
| | - Takuro Shinano
- Agricultural Radiation Research Center, NARO Tohoku Agricultural Research Center, 50 Aza Harajyukuminami, Arai, Fukushima, 9602156 Japan
| | - Ryosuke Okada
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kitaku, Sapporo, 0608589 Japan
| | - Mitsuru Osaki
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kitaku, Sapporo, 0608589 Japan
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